ss2v110: build/scripts-3.6/SeqSero2

author	cstrittmatter
date	Mon, 27 Apr 2020 01:11:53 -0400
parents
children

rev	line source
2 d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	1 #!/gal2001/Seqserotest/env/bin/python
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	2
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	3 import sys
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	4 import time
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	5 import random
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	6 import os
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	7 import subprocess
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	8 import gzip
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	9 import io
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	10 import pickle
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	11 import argparse
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	12 import itertools
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	13 from distutils.version import LooseVersion
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	14 from distutils.spawn import find_executable
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	15 sys.path.insert(1,sys.path[0]+'/..')
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	16
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	17 try:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	18 from .version import SeqSero2_version
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	19 except Exception: #ImportError
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	20 from version import SeqSero2_version
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	21
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	22 ### SeqSero Kmer
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	23 def parse_args():
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	24 "Parse the input arguments, use '-h' for help."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	25 parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.0')#add "-m <data_type>" in future
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	26 parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data.
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	27 parser.add_argument("-t",choices=['1','2','3','4','5','6'],help="<int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	28 parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	29 parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	30 parser.add_argument("-m",choices=['k','a'],default="a",help="<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	31 parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	32 parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	33 parser.add_argument("-c",action="store_true",help="<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	34 parser.add_argument("-s",action="store_true",help="<flag>: if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	35 parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	36 parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	37 return parser.parse_args()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	38
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	39 ### check paths of dependencies
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	40 check_dependencies = parse_args().check
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	41 dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py']
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	42 if check_dependencies:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	43 for item in dependencies:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	44 ext_path = find_executable(item)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	45 if ext_path is not None:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	46 print ("Using "+item+" - "+ext_path)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	47 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	48 print ("ERROR: can not find "+item+" in PATH")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	49 sys.exit()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	50 ### end of --check
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	51
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	52 def reverse_complement(sequence):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	53 complement = {
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	54 'A': 'T',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	55 'C': 'G',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	56 'G': 'C',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	57 'T': 'A',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	58 'N': 'N',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	59 'M': 'K',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	60 'R': 'Y',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	61 'W': 'W',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	62 'S': 'S',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	63 'Y': 'R',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	64 'K': 'M',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	65 'V': 'B',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	66 'H': 'D',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	67 'D': 'H',
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	68 'B': 'V'
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	69 }
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	70 return "".join(complement[base] for base in reversed(sequence))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	71
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	72
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	73 def createKmerDict_reads(list_of_strings, kmer):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	74 kmer_table = {}
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	75 for string in list_of_strings:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	76 sequence = string.strip('\n')
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	77 for i in range(len(sequence) - kmer + 1):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	78 new_mer = sequence[i:i + kmer].upper()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	79 new_mer_rc = reverse_complement(new_mer)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	80 if new_mer in kmer_table:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	81 kmer_table[new_mer.upper()] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	82 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	83 kmer_table[new_mer.upper()] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	84 if new_mer_rc in kmer_table:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	85 kmer_table[new_mer_rc.upper()] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	86 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	87 kmer_table[new_mer_rc.upper()] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	88 return kmer_table
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	89
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	90
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	91 def multifasta_dict(multifasta):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	92 multifasta_list = [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	93 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	94 ]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	95 headers = [i for i in multifasta_list if i[0] == '>']
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	96 multifasta_dict = {}
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	97 for h in headers:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	98 start = multifasta_list.index(h)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	99 for element in multifasta_list[start + 1:]:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	100 if element[0] == '>':
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	101 break
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	102 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	103 if h[1:] in multifasta_dict:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	104 multifasta_dict[h[1:]] += element
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	105 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	106 multifasta_dict[h[1:]] = element
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	107 return multifasta_dict
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	108
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	109
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	110 def multifasta_single_string(multifasta):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	111 multifasta_list = [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	112 line.strip() for line in open(multifasta, 'r')
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	113 if (len(line.strip()) > 0) and (line.strip()[0] != '>')
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	114 ]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	115 return ''.join(multifasta_list)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	116
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	117
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	118 def chunk_a_long_sequence(long_sequence, chunk_size=60):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	119 chunk_list = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	120 steps = len(long_sequence) // 60 #how many chunks
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	121 for i in range(steps):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	122 chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	123 chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	124 return chunk_list
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	125
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	126
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	127 def target_multifasta_kmerizer(multifasta, k, kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	128 forward_length = 300 #if find the target, put forward 300 bases
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	129 reverse_length = 2200 #if find the target, put backward 2200 bases
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	130 chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	131 target_mers = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	132 long_single_string = multifasta_single_string(multifasta)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	133 multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	134 unit_length = len(multifasta_list[0])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	135 forward_lines = int(forward_length / unit_length) + 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	136 reverse_lines = int(forward_length / unit_length) + 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	137 start_num = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	138 end_num = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	139 for i in range(len(multifasta_list)):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	140 if i not in range(start_num, end_num): #avoid computational repetition
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	141 line = multifasta_list[i]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	142 start = int((len(line) - k) // 2)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	143 s1 = line[start:k + start]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	144 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	145 if i - forward_lines >= 0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	146 start_num = i - forward_lines
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	147 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	148 start_num = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	149 if i + reverse_lines <= len(multifasta_list) - 1:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	150 end_num = i + reverse_lines
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	151 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	152 end_num = len(multifasta_list) - 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	153 target_list = [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	154 x.strip() for x in multifasta_list[start_num:end_num]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	155 ]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	156 target_line = "".join(target_list)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	157 target_mers += [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	158 k1 for k1 in createKmerDict_reads([str(target_line)], k)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	159 ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	160 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	161 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	162 return set(target_mers)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	163
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	164
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	165 def target_read_kmerizer(file, k, kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	166 i = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	167 n_reads = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	168 total_coverage = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	169 target_mers = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	170 if file.endswith(".gz"):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	171 file_content = io.BufferedReader(gzip.open(file))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	172 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	173 file_content = open(file, "r").readlines()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	174 for line in file_content:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	175 start = int((len(line) - k) // 2)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	176 if i % 4 == 2:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	177 if file.endswith(".gz"):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	178 s1 = line[start:k + start].decode()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	179 line = line.decode()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	180 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	181 s1 = line[start:k + start]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	182 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	183 n_reads += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	184 total_coverage += len(line)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	185 target_mers += [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	186 k1 for k1 in createKmerDict_reads([str(line)], k)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	187 ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	188 i += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	189 if total_coverage >= 4000000:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	190 break
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	191 return set(target_mers)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	192
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	193
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	194 def minion_fasta_kmerizer(file, k, kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	195 i = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	196 n_reads = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	197 total_coverage = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	198 target_mers = {}
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	199 for line in open(file):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	200 if i % 2 == 0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	201 for kmer, rc_kmer in kmers(line.strip().upper(), k):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	202 if (kmer in kmerDict) or (rc_kmer in kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	203 if kmer in target_mers:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	204 target_mers[kmer] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	205 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	206 target_mers[kmer] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	207 if rc_kmer in target_mers:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	208 target_mers[rc_kmer] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	209 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	210 target_mers[rc_kmer] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	211 i += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	212 return set([h for h in target_mers])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	213
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	214
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	215 def minion_fastq_kmerizer(file, k, kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	216 i = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	217 n_reads = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	218 total_coverage = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	219 target_mers = {}
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	220 for line in open(file):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	221 if i % 4 == 2:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	222 for kmer, rc_kmer in kmers(line.strip().upper(), k):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	223 if (kmer in kmerDict) or (rc_kmer in kmerDict):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	224 if kmer in target_mers:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	225 target_mers[kmer] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	226 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	227 target_mers[kmer] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	228 if rc_kmer in target_mers:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	229 target_mers[rc_kmer] += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	230 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	231 target_mers[rc_kmer] = 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	232 i += 1
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	233 return set([h for h in target_mers])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	234
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	235
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	236 def multifasta_single_string2(multifasta):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	237 single_string = ''
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	238 with open(multifasta, 'r') as f:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	239 for line in f:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	240 if line.strip()[0] == '>':
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	241 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	242 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	243 single_string += line.strip()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	244 return single_string
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	245
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	246
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	247 def kmers(seq, k):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	248 rev_comp = reverse_complement(seq)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	249 for start in range(1, len(seq) - k + 1):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	250 yield seq[start:start + k], rev_comp[-(start + k):-start]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	251
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	252
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	253 def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	254 multi_seq_dict = multifasta_dict(multifasta)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	255 lib_dict = {}
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	256 for h in multi_seq_dict:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	257 lib_dict[h] = set(
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	258 [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	259 return lib_dict
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	260
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	261
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	262 def Combine(b, c):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	263 fliC_combinations = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	264 fliC_combinations.append(",".join(c))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	265 temp_combinations = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	266 for i in range(len(b)):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	267 for x in itertools.combinations(b, i + 1):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	268 temp_combinations.append(",".join(x))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	269 for x in temp_combinations:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	270 temp = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	271 for y in c:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	272 temp.append(y)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	273 temp.append(x)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	274 temp = ",".join(temp)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	275 temp = temp.split(",")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	276 temp.sort()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	277 temp = ",".join(temp)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	278 fliC_combinations.append(temp)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	279 return fliC_combinations
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	280
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	281
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	282 def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	283 #like test_output_06012017.txt
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	284 #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	285 from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	286 rename_dict_not_anymore=[rename_dict[x] for x in rename_dict]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	287 rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	288 seronames = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	289 seronames_none_subspecies=[]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	290 for i in range(len(phase1)):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	291 fliC_combine = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	292 fljB_combine = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	293 if phaseO[i] == Otype: # no VII in KW, but it's there
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	294 ### for fliC, detect every possible combinations to avoid the effect of "["
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	295 if phase1[i].count("[") == 0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	296 fliC_combine.append(phase1[i])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	297 elif phase1[i].count("[") >= 1:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	298 c = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	299 b = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	300 if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count(
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	301 "[") == 1:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	302 content = phase1[i].replace("[", "").replace("]", "")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	303 fliC_combine.append(content)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	304 fliC_combine.append("-")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	305 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	306 for x in phase1[i].split(","):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	307 if "[" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	308 b.append(x.replace("[", "").replace("]", ""))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	309 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	310 c.append(x)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	311 fliC_combine = Combine(
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	312 b, c
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	313 ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	314 ### end of fliC "[" detect
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	315 ### for fljB, detect every possible combinations to avoid the effect of "["
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	316 if phase2[i].count("[") == 0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	317 fljB_combine.append(phase2[i])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	318 elif phase2[i].count("[") >= 1:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	319 d = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	320 e = []
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	321 if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count(
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	322 "[") == 1:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	323 content = phase2[i].replace("[", "").replace("]", "")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	324 fljB_combine.append(content)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	325 fljB_combine.append("-")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	326 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	327 for x in phase2[i].split(","):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	328 if "[" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	329 d.append(x.replace("[", "").replace("]", ""))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	330 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	331 e.append(x)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	332 fljB_combine = Combine(d, e)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	333 ### end of fljB "[" detect
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	334 new_fliC = fliC.split(
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	335 ","
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	336 ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	337 new_fliC.sort()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	338 new_fliC = ",".join(new_fliC)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	339 new_fljB = fljB.split(",")
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	340 new_fljB.sort()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	341 new_fljB = ",".join(new_fljB)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	342 if (new_fliC in fliC_combine
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	343 or fliC in fliC_combine) and (new_fljB in fljB_combine
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	344 or fljB in fljB_combine):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	345 ######start, remove_list,rename_dict, added on 11/11/2018
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	346 if sero[i] not in remove_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	347 temp_sero=sero[i]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	348 if temp_sero in rename_dict:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	349 temp_sero=rename_dict[temp_sero] #rename if in the rename list
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	350 if temp_sero not in seronames:#the new sero may already included, if yes, then not consider
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	351 if subs[i] == subspecies:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	352 seronames.append(temp_sero)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	353 seronames_none_subspecies.append(temp_sero)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	354 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	355 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	356 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	357 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	358 ######end, added on 11/11/2018
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	359 #analyze seronames
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	360 subspecies_pointer=""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	361 if len(seronames) == 0 and len(seronames_none_subspecies)!=0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	362 # ed_SL_12182019: modified to fix the subspecies output problem
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	363 #seronames=seronames_none_subspecies
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	364 seronames=["N/A"]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	365 #subspecies_pointer="1"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	366 subspecies_pointer="0"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	367 if len(seronames) == 0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	368 seronames = [
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	369 "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	370 ]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	371 star = ""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	372 star_line = ""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	373 if len(seronames) > 1: #there are two possible predictions for serotypes
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	374 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	375 #changed 04072019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	376 #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	377 if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	378 star="*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	379 star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	380 #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	381 if Otype=="":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	382 Otype="-"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	383 predict_form = Otype + ":" + fliC + ":" + fljB
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	384 predict_sero = (" or ").join(seronames)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	385 ###special test for Enteritidis
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	386 if predict_form == "9:g,m:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	387 sdf = "-"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	388 for x in special_gene_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	389 if x.startswith("sdf"):
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	390 sdf = "+"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	391 #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	392 star_line="sdf gene detected. "
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	393 #predict_form = predict_form + " Sdf prediction:" + sdf
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	394 predict_form = predict_form #changed 04072019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	395 if sdf == "-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	396 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	397 #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	398 star_line="sdf gene not detected. "
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	399 #changed in 04072019, for new output
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	400 #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	401 #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	402 predict_sero = "Gallinarum or Enteritidis"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	403 ###end of special test for Enteritidis
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	404 elif predict_form == "4:i:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	405 predict_sero = "I 4,[5],12:i:-" # change serotype name
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	406 elif predict_form == "4:r:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	407 predict_sero = "N/A (4:r:-)"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	408 elif predict_form == "4:b:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	409 predict_sero = "N/A (4:b:-)"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	410 #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	411 #predict_sero = "Newport"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	412 #star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	413 #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	414 claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	415 if "N/A" in predict_sero:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	416 claim = ""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	417 #special test for Typhimurium
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	418 if "Typhimurium" in predict_sero or predict_form == "4:i:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	419 normal = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	420 mutation = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	421 for x in special_gene_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	422 if "oafA-O-4_full" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	423 normal = float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	424 elif "oafA-O-4_5-" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	425 mutation = float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	426 if normal > mutation:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	427 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	428 elif normal < mutation:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	429 #predict_sero = predict_sero.strip() + "(O5-)"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	430 predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	431 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	432 #star_line = "Detected the deletion of O5-."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	433 star_line = "Detected a deletion that causes O5- variant of Typhimurium. "
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	434 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	435 pass
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	436 #special test for Paratyphi B
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	437 if "Paratyphi B" in predict_sero or predict_form == "4:b:-":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	438 normal = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	439 mutation = 0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	440 for x in special_gene_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	441 if "gntR-family-regulatory-protein_dt-positive" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	442 normal = float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	443 elif "gntR-family-regulatory-protein_dt-negative" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	444 mutation = float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	445 #print(normal,mutation)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	446 if normal > mutation:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	447 #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	448 predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	449 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	450 #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	451 star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. "
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	452 elif normal < mutation:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	453 #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	454 predict_sero = predict_sero.strip()
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	455 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	456 #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	457 star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. "
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	458 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	459 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	460 #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	461 star_line = " " ## ed_SL_05152019: do not report this situation.
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	462 #special test for O13,22 and O13,23
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	463 if Otype=="13":
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	464 #ex_dir = os.path.dirname(os.path.realpath(__file__))
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	465 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	466 f = open(ex_dir + '/special.pickle', 'rb')
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	467 special = pickle.load(f)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	468 O22_O23=special['O22_O23']
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	469 if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	470 O22_score=0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	471 O23_score=0
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	472 for x in special_gene_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	473 if "O:22" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	474 O22_score = O22_score+float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	475 elif "O:23" in x:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	476 O23_score = O23_score+float(special_gene_list[x])
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	477 #print(O22_score,O23_score)
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	478 for z in O22_O23[0]:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	479 if predict_sero.split(" or ")[0] in z:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	480 if O22_score > O23_score:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	481 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	482 #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	483 predict_sero = z[0]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	484 elif O22_score < O23_score:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	485 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	486 #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	487 predict_sero = z[1]
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	488 else:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	489 star = "*"
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	490 #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	491 if " or " in predict_sero:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	492 star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "."
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	493 #special test for O6,8
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	494 #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	495 #for x in merge_O68_list:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	496 # if x in predict_sero:
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	497 # predict_sero=x
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	498 # star=""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	499 # star_line=""
d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: diff changeset	500 #special test for Montevideo; most of them are monophasic

2

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1 #!/gal2001/Seqserotest/env/bin/python

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

2

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

3 import sys

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

4 import time

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

5 import random

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

6 import os

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

7 import subprocess

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

8 import gzip

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

9 import io

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

10 import pickle

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

11 import argparse

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

12 import itertools

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

13 from distutils.version import LooseVersion

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

14 from distutils.spawn import find_executable

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

15 sys.path.insert(1,sys.path[0]+'/..')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

16

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

17 try:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

18 from .version import SeqSero2_version

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

19 except Exception: #ImportError

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

20 from version import SeqSero2_version

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

21

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

22 ### SeqSero Kmer

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

23 def parse_args():

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

24 "Parse the input arguments, use '-h' for help."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

25 parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.0')#add "-m <data_type>" in future

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

26 parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data.

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

27 parser.add_argument("-t",choices=['1','2','3','4','5','6'],help="<int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

28 parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

29 parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

30 parser.add_argument("-m",choices=['k','a'],default="a",help="<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

31 parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

32 parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

33 parser.add_argument("-c",action="store_true",help="<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

34 parser.add_argument("-s",action="store_true",help="<flag>: if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

35 parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

36 parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

37 return parser.parse_args()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

38

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

39 ### check paths of dependencies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

40 check_dependencies = parse_args().check

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

41 dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py']

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

42 if check_dependencies:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

43 for item in dependencies:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

44 ext_path = find_executable(item)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

45 if ext_path is not None:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

46 print ("Using "+item+" - "+ext_path)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

47 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

48 print ("ERROR: can not find "+item+" in PATH")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

49 sys.exit()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

50 ### end of --check

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

51

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

52 def reverse_complement(sequence):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

53 complement = {

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

54 'A': 'T',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

55 'C': 'G',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

56 'G': 'C',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

57 'T': 'A',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

58 'N': 'N',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

59 'M': 'K',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

60 'R': 'Y',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

61 'W': 'W',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

62 'S': 'S',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

63 'Y': 'R',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

64 'K': 'M',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

65 'V': 'B',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

66 'H': 'D',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

67 'D': 'H',

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

68 'B': 'V'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

69 }

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

70 return "".join(complement[base] for base in reversed(sequence))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

71

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

72

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

73 def createKmerDict_reads(list_of_strings, kmer):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

74 kmer_table = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

75 for string in list_of_strings:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

76 sequence = string.strip('\n')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

77 for i in range(len(sequence) - kmer + 1):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

78 new_mer = sequence[i:i + kmer].upper()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

79 new_mer_rc = reverse_complement(new_mer)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

80 if new_mer in kmer_table:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

81 kmer_table[new_mer.upper()] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

82 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

83 kmer_table[new_mer.upper()] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

84 if new_mer_rc in kmer_table:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

85 kmer_table[new_mer_rc.upper()] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

86 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

87 kmer_table[new_mer_rc.upper()] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

88 return kmer_table

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

89

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

90

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

91 def multifasta_dict(multifasta):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

92 multifasta_list = [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

93 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

94 ]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

95 headers = [i for i in multifasta_list if i[0] == '>']

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

96 multifasta_dict = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

97 for h in headers:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

98 start = multifasta_list.index(h)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

99 for element in multifasta_list[start + 1:]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

100 if element[0] == '>':

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

101 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

102 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

103 if h[1:] in multifasta_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

104 multifasta_dict[h[1:]] += element

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

105 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

106 multifasta_dict[h[1:]] = element

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

107 return multifasta_dict

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

108

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

109

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

110 def multifasta_single_string(multifasta):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

111 multifasta_list = [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

112 line.strip() for line in open(multifasta, 'r')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

113 if (len(line.strip()) > 0) and (line.strip()[0] != '>')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

114 ]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

115 return ''.join(multifasta_list)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

116

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

117

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

118 def chunk_a_long_sequence(long_sequence, chunk_size=60):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

119 chunk_list = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

120 steps = len(long_sequence) // 60 #how many chunks

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

121 for i in range(steps):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

122 chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

123 chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

124 return chunk_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

125

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

126

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

127 def target_multifasta_kmerizer(multifasta, k, kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

128 forward_length = 300 #if find the target, put forward 300 bases

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

129 reverse_length = 2200 #if find the target, put backward 2200 bases

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

130 chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

131 target_mers = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

132 long_single_string = multifasta_single_string(multifasta)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

133 multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

134 unit_length = len(multifasta_list[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

135 forward_lines = int(forward_length / unit_length) + 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

136 reverse_lines = int(forward_length / unit_length) + 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

137 start_num = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

138 end_num = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

139 for i in range(len(multifasta_list)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

140 if i not in range(start_num, end_num): #avoid computational repetition

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

141 line = multifasta_list[i]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

142 start = int((len(line) - k) // 2)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

143 s1 = line[start:k + start]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

144 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

145 if i - forward_lines >= 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

146 start_num = i - forward_lines

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

147 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

148 start_num = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

149 if i + reverse_lines <= len(multifasta_list) - 1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

150 end_num = i + reverse_lines

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

151 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

152 end_num = len(multifasta_list) - 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

153 target_list = [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

154 x.strip() for x in multifasta_list[start_num:end_num]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

155 ]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

156 target_line = "".join(target_list)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

157 target_mers += [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

158 k1 for k1 in createKmerDict_reads([str(target_line)], k)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

159 ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

160 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

161 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

162 return set(target_mers)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

163

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

164

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

165 def target_read_kmerizer(file, k, kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

166 i = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

167 n_reads = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

168 total_coverage = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

169 target_mers = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

170 if file.endswith(".gz"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

171 file_content = io.BufferedReader(gzip.open(file))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

172 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

173 file_content = open(file, "r").readlines()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

174 for line in file_content:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

175 start = int((len(line) - k) // 2)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

176 if i % 4 == 2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

177 if file.endswith(".gz"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

178 s1 = line[start:k + start].decode()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

179 line = line.decode()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

180 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

181 s1 = line[start:k + start]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

182 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

183 n_reads += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

184 total_coverage += len(line)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

185 target_mers += [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

186 k1 for k1 in createKmerDict_reads([str(line)], k)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

187 ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

188 i += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

189 if total_coverage >= 4000000:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

190 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

191 return set(target_mers)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

192

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

193

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

194 def minion_fasta_kmerizer(file, k, kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

195 i = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

196 n_reads = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

197 total_coverage = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

198 target_mers = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

199 for line in open(file):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

200 if i % 2 == 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

201 for kmer, rc_kmer in kmers(line.strip().upper(), k):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

202 if (kmer in kmerDict) or (rc_kmer in kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

203 if kmer in target_mers:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

204 target_mers[kmer] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

205 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

206 target_mers[kmer] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

207 if rc_kmer in target_mers:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

208 target_mers[rc_kmer] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

209 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

210 target_mers[rc_kmer] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

211 i += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

212 return set([h for h in target_mers])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

213

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

214

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

215 def minion_fastq_kmerizer(file, k, kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

216 i = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

217 n_reads = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

218 total_coverage = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

219 target_mers = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

220 for line in open(file):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

221 if i % 4 == 2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

222 for kmer, rc_kmer in kmers(line.strip().upper(), k):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

223 if (kmer in kmerDict) or (rc_kmer in kmerDict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

224 if kmer in target_mers:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

225 target_mers[kmer] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

226 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

227 target_mers[kmer] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

228 if rc_kmer in target_mers:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

229 target_mers[rc_kmer] += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

230 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

231 target_mers[rc_kmer] = 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

232 i += 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

233 return set([h for h in target_mers])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

234

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

235

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

236 def multifasta_single_string2(multifasta):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

237 single_string = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

238 with open(multifasta, 'r') as f:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

239 for line in f:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

240 if line.strip()[0] == '>':

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

241 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

242 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

243 single_string += line.strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

244 return single_string

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

245

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

246

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

247 def kmers(seq, k):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

248 rev_comp = reverse_complement(seq)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

249 for start in range(1, len(seq) - k + 1):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

250 yield seq[start:start + k], rev_comp[-(start + k):-start]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

251

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

252

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

253 def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

254 multi_seq_dict = multifasta_dict(multifasta)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

255 lib_dict = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

256 for h in multi_seq_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

257 lib_dict[h] = set(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

258 [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

259 return lib_dict

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

260

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

261

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

262 def Combine(b, c):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

263 fliC_combinations = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

264 fliC_combinations.append(",".join(c))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

265 temp_combinations = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

266 for i in range(len(b)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

267 for x in itertools.combinations(b, i + 1):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

268 temp_combinations.append(",".join(x))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

269 for x in temp_combinations:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

270 temp = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

271 for y in c:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

272 temp.append(y)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

273 temp.append(x)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

274 temp = ",".join(temp)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

275 temp = temp.split(",")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

276 temp.sort()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

277 temp = ",".join(temp)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

278 fliC_combinations.append(temp)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

279 return fliC_combinations

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

280

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

281

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

282 def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

283 #like test_output_06012017.txt

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

284 #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

285 from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

286 rename_dict_not_anymore=[rename_dict[x] for x in rename_dict]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

287 rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

288 seronames = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

289 seronames_none_subspecies=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

290 for i in range(len(phase1)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

291 fliC_combine = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

292 fljB_combine = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

293 if phaseO[i] == Otype: # no VII in KW, but it's there

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

294 ### for fliC, detect every possible combinations to avoid the effect of "["

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

295 if phase1[i].count("[") == 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

296 fliC_combine.append(phase1[i])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

297 elif phase1[i].count("[") >= 1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

298 c = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

299 b = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

300 if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

301 "[") == 1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

302 content = phase1[i].replace("[", "").replace("]", "")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

303 fliC_combine.append(content)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

304 fliC_combine.append("-")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

305 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

306 for x in phase1[i].split(","):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

307 if "[" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

308 b.append(x.replace("[", "").replace("]", ""))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

309 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

310 c.append(x)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

311 fliC_combine = Combine(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

312 b, c

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

313 ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

314 ### end of fliC "[" detect

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

315 ### for fljB, detect every possible combinations to avoid the effect of "["

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

316 if phase2[i].count("[") == 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

317 fljB_combine.append(phase2[i])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

318 elif phase2[i].count("[") >= 1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

319 d = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

320 e = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

321 if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

322 "[") == 1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

323 content = phase2[i].replace("[", "").replace("]", "")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

324 fljB_combine.append(content)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

325 fljB_combine.append("-")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

326 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

327 for x in phase2[i].split(","):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

328 if "[" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

329 d.append(x.replace("[", "").replace("]", ""))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

330 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

331 e.append(x)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

332 fljB_combine = Combine(d, e)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

333 ### end of fljB "[" detect

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

334 new_fliC = fliC.split(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

335 ","

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

336 ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

337 new_fliC.sort()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

338 new_fliC = ",".join(new_fliC)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

339 new_fljB = fljB.split(",")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

340 new_fljB.sort()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

341 new_fljB = ",".join(new_fljB)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

342 if (new_fliC in fliC_combine

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

343 or fliC in fliC_combine) and (new_fljB in fljB_combine

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

344 or fljB in fljB_combine):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

345 ######start, remove_list,rename_dict, added on 11/11/2018

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

346 if sero[i] not in remove_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

347 temp_sero=sero[i]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

348 if temp_sero in rename_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

349 temp_sero=rename_dict[temp_sero] #rename if in the rename list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

350 if temp_sero not in seronames:#the new sero may already included, if yes, then not consider

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

351 if subs[i] == subspecies:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

352 seronames.append(temp_sero)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

353 seronames_none_subspecies.append(temp_sero)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

354 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

355 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

356 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

357 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

358 ######end, added on 11/11/2018

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

359 #analyze seronames

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

360 subspecies_pointer=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

361 if len(seronames) == 0 and len(seronames_none_subspecies)!=0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

362 # ed_SL_12182019: modified to fix the subspecies output problem

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

363 #seronames=seronames_none_subspecies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

364 seronames=["N/A"]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

365 #subspecies_pointer="1"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

366 subspecies_pointer="0"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

367 if len(seronames) == 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

368 seronames = [

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

369 "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

370 ]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

371 star = ""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

372 star_line = ""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

373 if len(seronames) > 1: #there are two possible predictions for serotypes

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

374 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

375 #changed 04072019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

376 #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

377 if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

378 star="*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

379 star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

380 #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

381 if Otype=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

382 Otype="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

383 predict_form = Otype + ":" + fliC + ":" + fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

384 predict_sero = (" or ").join(seronames)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

385 ###special test for Enteritidis

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

386 if predict_form == "9:g,m:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

387 sdf = "-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

388 for x in special_gene_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

389 if x.startswith("sdf"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

390 sdf = "+"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

391 #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

392 star_line="sdf gene detected. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

393 #predict_form = predict_form + " Sdf prediction:" + sdf

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

394 predict_form = predict_form #changed 04072019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

395 if sdf == "-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

396 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

397 #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

398 star_line="sdf gene not detected. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

399 #changed in 04072019, for new output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

400 #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

401 #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

402 predict_sero = "Gallinarum or Enteritidis"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

403 ###end of special test for Enteritidis

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

404 elif predict_form == "4:i:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

405 predict_sero = "I 4,[5],12:i:-" # change serotype name

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

406 elif predict_form == "4:r:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

407 predict_sero = "N/A (4:r:-)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

408 elif predict_form == "4:b:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

409 predict_sero = "N/A (4:b:-)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

410 #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

411 #predict_sero = "Newport"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

412 #star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

413 #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

414 claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

415 if "N/A" in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

416 claim = ""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

417 #special test for Typhimurium

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

418 if "Typhimurium" in predict_sero or predict_form == "4:i:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

419 normal = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

420 mutation = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

421 for x in special_gene_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

422 if "oafA-O-4_full" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

423 normal = float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

424 elif "oafA-O-4_5-" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

425 mutation = float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

426 if normal > mutation:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

427 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

428 elif normal < mutation:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

429 #predict_sero = predict_sero.strip() + "(O5-)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

430 predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

431 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

432 #star_line = "Detected the deletion of O5-."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

433 star_line = "Detected a deletion that causes O5- variant of Typhimurium. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

434 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

435 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

436 #special test for Paratyphi B

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

437 if "Paratyphi B" in predict_sero or predict_form == "4:b:-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

438 normal = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

439 mutation = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

440 for x in special_gene_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

441 if "gntR-family-regulatory-protein_dt-positive" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

442 normal = float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

443 elif "gntR-family-regulatory-protein_dt-negative" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

444 mutation = float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

445 #print(normal,mutation)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

446 if normal > mutation:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

447 #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

448 predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

449 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

450 #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

451 star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

452 elif normal < mutation:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

453 #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

454 predict_sero = predict_sero.strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

455 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

456 #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

457 star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

458 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

459 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

460 #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

461 star_line = " " ## ed_SL_05152019: do not report this situation.

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

462 #special test for O13,22 and O13,23

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

463 if Otype=="13":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

464 #ex_dir = os.path.dirname(os.path.realpath(__file__))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

465 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

466 f = open(ex_dir + '/special.pickle', 'rb')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

467 special = pickle.load(f)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

468 O22_O23=special['O22_O23']

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

469 if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

470 O22_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

471 O23_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

472 for x in special_gene_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

473 if "O:22" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

474 O22_score = O22_score+float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

475 elif "O:23" in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

476 O23_score = O23_score+float(special_gene_list[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

477 #print(O22_score,O23_score)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

478 for z in O22_O23[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

479 if predict_sero.split(" or ")[0] in z:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

480 if O22_score > O23_score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

481 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

482 #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

483 predict_sero = z[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

484 elif O22_score < O23_score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

485 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

486 #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

487 predict_sero = z[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

488 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

489 star = "*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

490 #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

491 if " or " in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

492 star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

493 #special test for O6,8

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

494 #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

495 #for x in merge_O68_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

496 # if x in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

497 # predict_sero=x

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

498 # star=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

499 # star_line=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

500 #special test for Montevideo; most of them are monophasic

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

501 #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

502 #star="*"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

503 #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

504 return predict_form, predict_sero, star, star_line, claim

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

505 ### End of SeqSero Kmer part

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

506

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

507 ### Begin of SeqSero2 allele prediction and output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

508 def xml_parse_score_comparision_seqsero(xmlfile):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

509 #used to do seqsero xml analysis

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

510 from Bio.Blast import NCBIXML

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

511 handle=open(xmlfile)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

512 handle=NCBIXML.parse(handle)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

513 handle=list(handle)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

514 List=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

515 List_score=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

516 List_ids=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

517 List_query_region=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

518 for i in range(len(handle)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

519 if len(handle[i].alignments)>0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

520 for j in range(len(handle[i].alignments)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

521 score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

522 ids=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

523 cover_region=set() #fixed problem that repeated calculation leading percentage > 1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

524 List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

525 for z in range(len(handle[i].alignments[j].hsps)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

526 hsp=handle[i].alignments[j].hsps[z]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

527 temp=set(range(hsp.query_start,hsp.query_end))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

528 if len(cover_region)==0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

529 cover_region=cover_region|temp

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

530 fraction=1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

531 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

532 fraction=1-len(cover_region&temp)/float(len(temp))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

533 cover_region=cover_region|temp

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

534 if "last" in handle[i].query or "first" in handle[i].query:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

535 score+=hsp.bits*fraction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

536 ids+=float(hsp.identities)/handle[i].query_length*fraction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

537 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

538 score+=hsp.bits*fraction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

539 ids+=float(hsp.identities)/handle[i].query_length*fraction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

540 List_score.append(score)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

541 List_ids.append(ids)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

542 List_query_region.append(cover_region)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

543 temp=zip(List,List_score,List_ids,List_query_region)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

544 Final_list=sorted(temp, key=lambda d:d[1], reverse = True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

545 return Final_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

546

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

547

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

548 def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

549 Old=L

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

550 L.sort()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

551 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

552 count=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

553 for j in range(len(L)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

554 y=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

555 for x in Old:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

556 if L[j]==x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

557 y+=1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

558 count.append(y)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

559 if sort_on_fre!="none":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

560 d=zip(*sorted(zip(count, L)))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

561 L=d[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

562 count=d[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

563 return (L,count)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

564

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

565 def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

566 #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

567 #this is mainly used for

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

568 a=nodes_vs_score_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

569 fliC_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

570 fljB_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

571 for z in a:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

572 if "fliC" in z[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

573 fliC_score+=z[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

574 elif "fljB" in z[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

575 fljB_score+=z[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

576 if fliC_score>=fljB_score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

577 role="fliC"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

578 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

579 role="fljB"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

580 return (role,abs(fliC_score-fljB_score))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

581

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

582 def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

583 #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

584 #also used when no head or tail got blasted score for the contig

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

585 role=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

586 for z in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

587 if node_name in z[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

588 role=z[0].split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

589 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

590 return role

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

591

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

592 def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

593 #nodes_list is the c created by c,d=Uniq(nodes) in below function

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

594 first_target=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

595 role_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

596 for x in nodes_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

597 a=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

598 role=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

599 for y in tail_head_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

600 if x in y[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

601 a.append(y)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

602 if len(a)==4:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

603 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

604 if diff<20:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

605 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

606 elif len(a)==3:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

607 ###however, if the one with highest score is the fewer one, compare their accumulation score

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

608 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

609 if diff<20:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

610 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

611 ###end of above score comparison

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

612 elif len(a)==2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

613 #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

614 temp=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

615 for z in a:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

616 temp.append(z[0].split("_")[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

617 m,n=Uniq(temp)#should only have one choice, but weird situation might occur too

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

618 if len(m)==1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

619 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

620 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

621 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

622 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

623 if diff<20:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

624 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

625 ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

626 elif len(a)==1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

627 #that one

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

628 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

629 if diff<20:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

630 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

631 #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

632 else:#a==0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

633 #use Final_list_passed best match

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

634 for z in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

635 if x in z[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

636 role=z[0].split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

637 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

638 #print x,role,len(a)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

639 role_list.append((role,x))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

640 if len(role_list)==2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

641 if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

642 #just use score to do a final test

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

643 role_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

644 for x in nodes_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

645 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

646 role_list.append((role,x))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

647 return role_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

648

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

649 def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

650 #used to decide which contig is FliC and which one is fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

651 contigs=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

652 nodes=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

653 for x in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

654 if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

655 nodes.append(x[0].split("___")[1].strip())

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

656 c,d=Uniq(nodes)#c is node_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

657 #print c

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

658 tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

659 roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

660 return roles

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

661

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

662 def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

663 #decide O based on Final_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

664 O_choice="?"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

665 O_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

666 special_genes={}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

667 nodes=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

668 for x in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

669 if x[0].startswith("O-"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

670 nodes.append(x[0].split("___")[1].strip())

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

671 elif not x[0].startswith("fl"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

672 special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

673 #print "special_genes:",special_genes

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

674 c,d=Uniq(nodes)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

675 #print "potential O antigen contig",c

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

676 final_O=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

677 O_nodes_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

678 for x in c:#c is the list for contigs

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

679 temp=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

680 for y in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

681 if x in y[0] and y[0].startswith("O-"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

682 final_O.append(y)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

683 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

684 ### O contig has the problem of two genes on same contig, so do additional test

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

685 potenial_new_gene=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

686 for x in final_O:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

687 pointer=0 #for genes merged or not

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

688 #not consider O-1,3,19_not_in_3,10, too short compared with others

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

689 if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

690 pointer=x[0].split("___")[1].strip()#store the contig name

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

691 print(pointer)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

692 if pointer!=0:#it has potential merge event

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

693 for y in Final_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

694 if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

695 potenial_new_gene=y

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

696 #print(potenial_new_gene)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

697 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

698 if potenial_new_gene!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

699 print("two differnt genes in same contig, fix it for O antigen")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

700 print(potenial_new_gene[:3])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

701 pointer=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

702 for y in final_O:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

703 if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

704 pointer=1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

705 if pointer!=0: #changed to consider two genes in same contig

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

706 final_O.append(potenial_new_gene)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

707 ### end of the two genes on same contig test

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

708 final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

709 if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

710 #print "$$$No Otype, due to no hit"#may need to be changed

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

711 O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

712 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

713 highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

714 O_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

715 O_list_less_contamination=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

716 for x in final_O:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

717 if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

718 O_list.append(x[0].split("__")[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

719 O_nodes_list.append(x[0].split("___")[1])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

720 if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

721 O_list_less_contamination.append(x[0].split("__")[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

722 ### special test for O9,46 and O3,10 family

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

723 if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

724 if "O-9,46_wzy" in O_list or "O-9,46_wzy_partial" in O_list:#and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

725 O_choice="O-9,46"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

726 #print "$$$Most possilble Otype: O-9,46"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

727 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

728 O_choice="O-9,46,27"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

729 #print "$$$Most possilble Otype: O-9,46,27"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

730 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

731 O_choice="O-9"#next, detect O9 vs O2?

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

732 O2=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

733 O9=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

734 for z in special_genes:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

735 if "tyr-O-9" in z:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

736 O9=special_genes[z]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

737 elif "tyr-O-2" in z:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

738 O2=special_genes[z]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

739 if O2>O9:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

740 O_choice="O-2"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

741 elif O2<O9:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

742 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

743 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

744 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

745 #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

746 elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

747 if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

748 O_choice="O-3,10"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

749 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

750 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

751 O_choice="O-1,3,19"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

752 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

753 ### end of special test for O9,46 and O3,10 family

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

754 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

755 try:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

756 max_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

757 for x in final_O:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

758 if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

759 max_score=x[2]#change from x[-1] to x[2],08172018

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

760 O_choice=x[0].split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

761 if O_choice=="O-1,3,19":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

762 O_choice=final_O[1][0].split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

763 #print "$$$Most possilble Otype: ",O_choice

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

764 except:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

765 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

766 #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

767 if O_choice=="O-9,46,27" and len(O_list)==2 and "O-4_wzx" in O_list: #special for very low chance sitatuion between O4 and O9,27,46, this is for serotypes like Bredeney and Schwarzengrund (normallly O-4 will have higher score, but sometimes sequencing quality may affect the prediction)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

768 O_choice="O-4"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

769 #print "O:",O_choice,O_nodes_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

770 Otypes=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

771 for x in O_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

772 if x!="O-1,3,19_not_in_3,10":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

773 if "O-9,46_" not in x:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

774 Otypes.append(x.split("_")[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

775 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

776 Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

777 #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

778 Otypes_uniq,Otypes_fre=Uniq(Otypes)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

779 contamination_O=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

780 if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

781 if len(Otypes_uniq)>2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

782 contamination_O="potential contamination from O antigen signals"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

783 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

784 if len(Otypes_uniq)>1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

785 if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

786 contamination_O=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

787 elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

788 contamination_O=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

789 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

790 contamination_O="potential contamination from O antigen signals"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

791 return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

792 ### End of SeqSero2 allele prediction and output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

793

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

794 def get_input_files(make_dir,input_file,data_type,dirpath):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

795 #tell input files from datatype

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

796 #"<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

797 for_fq=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

798 rev_fq=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

799 os.chdir(make_dir)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

800 if data_type=="1":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

801 input_file=input_file[0].split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

802 if input_file.endswith(".sra"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

803 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

804 for_fq=input_file.replace(".sra","_1.fastq")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

805 rev_fq=input_file.replace(".sra","_2.fastq")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

806 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

807 core_id=input_file.split(".fastq")[0].split(".fq")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

808 for_fq=core_id+"_1.fastq"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

809 rev_fq=core_id+"_2.fastq"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

810 if input_file.endswith(".gz"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

811 subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

812 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

813 subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

814 elif data_type=="2":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

815 for_fq=input_file[0].split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

816 rev_fq=input_file[1].split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

817 elif data_type=="3":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

818 input_file=input_file[0].split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

819 if input_file.endswith(".sra"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

820 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

821 for_fq=input_file.replace(".sra","_1.fastq")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

822 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

823 for_fq=input_file

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

824 elif data_type in ["4","5","6"]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

825 for_fq=input_file[0].split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

826 os.chdir("..")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

827 return for_fq,rev_fq

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

828

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

829 def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

830 #get O and H types from Final_list from blast parsing; allele mode

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

831 from Bio import SeqIO

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

832 fliC_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

833 fljB_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

834 fliC_contig="NA"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

835 fljB_contig="NA"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

836 fliC_region=set([0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

837 fljB_region=set([0,])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

838 fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

839 fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

840 O_choice="-"#no need to decide O contig for now, should be only one

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

841 O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

842 O_choice=O_choice.split("-")[-1].strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

843 if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

844 O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

845 H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

846 #add alignment locations, used for further selection, 03312019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

847 for i in range(len(H_contig_roles)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

848 x=H_contig_roles[i]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

849 for y in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

850 if x[1] in y[0] and y[0].startswith(x[0]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

851 H_contig_roles[i]+=H_contig_roles[i]+(y[-1],)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

852 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

853 log_file=open("SeqSero_log.txt","a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

854 extract_file=open("Extracted_antigen_alleles.fasta","a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

855 handle_fasta=list(SeqIO.parse(new_fasta,"fasta"))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

856

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

857 #print("O_contigs:")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

858 log_file.write("O_contigs:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

859 extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

860 extract_file.write("#O_contigs:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

861 for x in O_nodes_roles:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

862 if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

863 #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1])))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

864 log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

865 title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

866 seqs=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

867 for z in handle_fasta:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

868 if x[0].split("___")[-1]==z.description:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

869 seqs=str(z.seq)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

870 extract_file.write(title+seqs+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

871 if len(H_contig_roles)!=0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

872 highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

873 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

874 highest_H_coverage=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

875 for x in H_contig_roles:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

876 #if multiple choices, temporately select the one with longest length for now, will revise in further change

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

877 if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

878 fliC_contig=x[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

879 fliC_length=len(x[-1])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

880 elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

881 fljB_contig=x[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

882 fljB_length=len(x[-1])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

883 for x in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

884 if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

885 fliC_choice=x[0].split("_")[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

886 elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

887 fljB_choice=x[0].split("_")[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

888 elif fliC_choice!="-" and fljB_choice!="-":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

889 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

890 #now remove contigs not in middle core part

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

891 first_allele="NA"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

892 first_allele_percentage=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

893 for x in Final_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

894 if x[0].startswith("fliC") or x[0].startswith("fljB"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

895 first_allele=x[0].split("__")[0] #used to filter those un-middle contigs

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

896 first_allele_percentage=x[2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

897 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

898 additional_contigs=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

899 for x in Final_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

900 if first_allele in x[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

901 if (fliC_contig == x[0].split("___")[-1]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

902 fliC_region=x[3]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

903 elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

904 fljB_region=x[3]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

905 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

906 if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

907 additional_contigs.append(x)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

908 #else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

909 #print x[:3]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

910 #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

911 if first_allele_percentage>0.9:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

912 if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

913 target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region))))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

914 elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

915 target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region))))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

916 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

917 target_region=set()#doesn't do anything

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

918 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

919 target_region=set()#doesn't do anything

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

920 #print(target_region)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

921 #print(additional_contigs)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

922 target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

923 target_region=target_region2|target_region

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

924 for x in additional_contigs:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

925 removal=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

926 contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

927 if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5<len(x[3])<contig_length*1.5: #consider length and alignment length for now, but very loose,0.5 and 1.5 as cut-off

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

928 removal=1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

929 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

930 if first_allele_percentage > 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

931 removal=1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

932 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

933 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

934 if removal==1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

935 for y in H_contig_roles:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

936 if y[1] in x[0]:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

937 H_contig_roles.remove(y)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

938 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

939 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

940 #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

941 #end of removing none-middle contigs

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

942 #print("H_contigs:")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

943 log_file.write("H_contigs:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

944 extract_file.write("#H_contigs:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

945 H_contig_stat=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

946 H1_cont_stat={}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

947 H2_cont_stat={}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

948 for i in range(len(H_contig_roles)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

949 x=H_contig_roles[i]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

950 a=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

951 for y in Final_list_passed:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

952 if x[1] in y[0] and y[0].startswith(x[0]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

953 if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

954 for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

955 if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

956 #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1])))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

957 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

958 H_contig_roles[i]="can't decide fliC or fljB, may be third phase"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

959 title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

960 seqs=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

961 for z in handle_fasta:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

962 if x[1]==z.description:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

963 seqs=str(z.seq)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

964 extract_file.write(title+seqs+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

965 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

966 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

967 #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1])))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

968 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

969 title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

970 seqs=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

971 for z in handle_fasta:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

972 if x[1]==z.description:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

973 seqs=str(z.seq)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

974 extract_file.write(title+seqs+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

975 if x[0]=="fliC":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

976 if y[0].split("_")[1] not in H1_cont_stat:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

977 H1_cont_stat[y[0].split("_")[1]]=y[2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

978 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

979 H1_cont_stat[y[0].split("_")[1]]+=y[2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

980 if x[0]=="fljB":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

981 if y[0].split("_")[1] not in H2_cont_stat:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

982 H2_cont_stat[y[0].split("_")[1]]=y[2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

983 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

984 H2_cont_stat[y[0].split("_")[1]]+=y[2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

985 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

986 #detect contaminations

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

987 #print(H1_cont_stat)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

988 #print(H2_cont_stat)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

989 H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

990 H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

991 contamination_H=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

992 if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

993 contamination_H="potential contamination from H antigen signals"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

994 elif len(H2_cont_stat_list)==1 and fljB_contig=="NA":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

995 contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

996 #get additional antigens

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

997 """

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

998 if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

999 if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1000 O_choice="O-9,46"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1001 #print "$$$Most possilble Otype: O-9,46"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1002 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1003 O_choice="O-9,46,27"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1004 #print "$$$Most possilble Otype: O-9,46,27"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1005 elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1006 if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1007 O_choice="O-3,10"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1008 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1009 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1010 O_choice="O-1,3,19"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1011 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1012 ### end of special test for O9,46 and O3,10 family

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1013

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1014 if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1015 if len(Otypes_uniq)>2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1016 contamination_O="potential contamination from O antigen signals"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1017 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1018 if len(Otypes_uniq)>1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1019 if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1020 contamination_O=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1021 elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1022 contamination_O=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1023 """

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1024 additonal_antigents=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1025 #print(contamination_O)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1026 #print(contamination_H)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1027 log_file.write(contamination_O+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1028 log_file.write(contamination_H+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1029 log_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1030 return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1031

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1032 def get_input_K(input_file,lib_dict,data_type,k_size):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1033 #kmer mode; get input_Ks from dict and data_type

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1034 kmers = []

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1035 for h in lib_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1036 kmers += lib_dict[h]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1037 if data_type == '4':

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1038 input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1039 elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1040 input_Ks = target_read_kmerizer(input_file, k_size, set(kmers))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1041 elif data_type == '5':#minion_2d_fasta

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1042 input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1043 if data_type == '6':#minion_2d_fastq

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1044 input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1045 return input_Ks

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1046

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1047 def get_kmer_dict(lib_dict,input_Ks):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1048 #kmer mode; get predicted types

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1049 O_dict = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1050 H_dict = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1051 Special_dict = {}

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1052 for h in lib_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1053 score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1054 if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1055 if h.startswith('O-') and score > 25:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1056 O_dict[h] = score

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1057 if h.startswith('fl') and score > 40:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1058 H_dict[h] = score

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1059 if (h[:2] != 'fl') and (h[:2] != 'O-'):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1060 Special_dict[h] = score

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1061 return O_dict,H_dict,Special_dict

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1062

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1063 def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1064 log_file=open("SeqSero_log.txt","a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1065 log_file.write("O_scores:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1066 #call O:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1067 highest_O = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1068 if len(O_dict) == 0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1069 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1070 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1071 for x in O_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1072 log_file.write(x+"\t"+str(O_dict[x])+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1073 if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1074 #if 'O-9,46_wzy__1191' in O_dict or "O-9,46_wzy_partial__216" in O_dict: # and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1075 #modified to fix miscall of O-9,46

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1076 if ('O-9,46_wzy__1191' in O_dict and O_dict['O-9,46_wzy__1191']>40) or ("O-9,46_wzy_partial__216" in O_dict and O_dict["O-9,46_wzy_partial__216"]>40): # and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1077 highest_O = "O-9,46"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1078 elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1079 highest_O = "O-9,46,27"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1080 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1081 highest_O = "O-9" # next, detect O9 vs O2?

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1082 O2 = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1083 O9 = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1084 for z in Special_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1085 if "tyr-O-9" in z:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1086 O9 = float(Special_dict[z])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1087 if "tyr-O-2" in z:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1088 O2 = float(Special_dict[z])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1089 if O2 > O9:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1090 highest_O = "O-2"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1091 elif ("O-3,10_wzx__1539" in O_dict) and (

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1092 "O-9,46_wzy__1191" in O_dict

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1093 ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1094 if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1095 highest_O = "O-3,10"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1096 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1097 highest_O = "O-1,3,19"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1098 ### end of special test for O9,46 and O3,10 family

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1099 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1100 try:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1101 max_score = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1102 for x in O_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1103 if float(O_dict[x]) >= max_score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1104 max_score = float(O_dict[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1105 #highest_O = x.split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1106 # ed_SL_12182019: modified to fix the O-9,46 error example1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1107 if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1108 highest_O = "O-9"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1109 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1110 highest_O = x.split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1111 if highest_O == "O-1,3,19":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1112 highest_O = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1113 max_score = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1114 for x in O_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1115 if x == 'O-1,3,19_not_in_3,10__130':

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1116 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1117 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1118 if float(O_dict[x]) >= max_score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1119 max_score = float(O_dict[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1120 #highest_O = x.split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1121 # ed_SL_12182019: modified to fix the O-9,46 error example1

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1122 if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1123 highest_O = "O-9"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1124 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1125 highest_O = x.split("_")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1126 except:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1127 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1128 #call_fliC:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1129 if len(H_dict)!=0:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1130 highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1131 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1132 highest_H_score_both_BC=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1133 highest_fliC = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1134 highest_fliC_raw = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1135 highest_Score = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1136 log_file.write("\nH_scores:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1137 for s in H_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1138 log_file.write(s+"\t"+str(H_dict[s])+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1139 if s.startswith('fliC'):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1140 if float(H_dict[s]) > highest_Score:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1141 highest_fliC = s.split('_')[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1142 highest_fliC_raw = s

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1143 highest_Score = float(H_dict[s])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1144 #call_fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1145 highest_fljB = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1146 highest_fljB_raw = '-'

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1147 highest_Score = 0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1148 for s in H_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1149 if s.startswith('fljB'):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1150 if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1151 #highest_fljB = s.split('_')[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1152 #highest_fljB_raw = s

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1153 #highest_Score = float(H_dict[s])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1154 if s.split('_')[1]!=highest_fliC:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1155 highest_fljB = s.split('_')[1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1156 highest_fljB_raw = s

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1157 highest_Score = float(H_dict[s])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1158 log_file.write("\nSpecial_scores:\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1159 for s in Special_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1160 log_file.write(s+"\t"+str(Special_dict[s])+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1161 log_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1162 return highest_O,highest_fliC,highest_fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1163

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1164 def get_temp_file_names(for_fq,rev_fq):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1165 #seqsero2 -a; get temp file names

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1166 sam=for_fq+".sam"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1167 bam=for_fq+".bam"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1168 sorted_bam=for_fq+"_sorted.bam"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1169 mapped_fq1=for_fq+"_mapped.fq"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1170 mapped_fq2=rev_fq+"_mapped.fq"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1171 combined_fq=for_fq+"_combined.fq"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1172 for_sai=for_fq+".sai"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1173 rev_sai=rev_fq+".sai"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1174 return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1175

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1176 def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1177 #seqsero2 -a; do mapping and sort

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1178 print("building database...")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1179 subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1180 print("mapping...")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1181 if mapping_mode=="mem":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1182 subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1183 elif mapping_mode=="sam":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1184 if fnameB!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1185 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1186 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1187 subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1188 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1189 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1190 subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1191 subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1192 ### check the version of samtools then use differnt commands

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1193 samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1194 out, err = samtools_version.communicate()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1195 version = str(err).split("ersion:")[1].strip().split(" ")[0].strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1196 print("check samtools version:",version)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1197 ### end of samtools version check and its analysis

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1198 if LooseVersion(version)<=LooseVersion("1.2"):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1199 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1200 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1201 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1202

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1203 def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1204 #seqsero2 -a; extract, assembly and blast

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1205 subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1206 #print("fnameA:",fnameA)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1207 #print("fnameB:",fnameB)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1208 if fnameB!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1209 subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1210 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1211 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1212 outdir=current_time+"_temp"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1213 print("assembling...")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1214 if int(threads)>4:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1215 t="4"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1216 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1217 t=threads

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1218 if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1219 if fnameB!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1220 subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1221 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1222 subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1223 new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1224 #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1225 subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1226 #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1227 subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1228 print("blasting...","\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1229 xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1230 subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1231 subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1232 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1233 xmlfile="NA"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1234 return xmlfile,new_fasta

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1235

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1236 def judge_subspecies(fnameA):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1237 #seqsero2 -a; judge subspecies on just forward raw reads fastq

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1238 salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1239 out, err = salmID_output.communicate()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1240 out=out.decode("utf-8")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1241 file=open("data_log.txt","a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1242 file.write(out)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1243 file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1244 salm_species_scores=out.split("\n")[1].split("\t")[6:]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1245 salm_species_results=out.split("\n")[0].split("\t")[6:]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1246 max_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1247 max_score_index=1 #default is 1, means "I"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1248 for i in range(len(salm_species_scores)):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1249 if max_score<float(salm_species_scores[i]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1250 max_score=float(salm_species_scores[i])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1251 max_score_index=i

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1252 prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1253 #if float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1254 if float(out.split("\n")[1].split("\t")[4]) > 10 and float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): ## ed_SL_0318: change SalmID_ssp_threshold

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1255 prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1256 #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1257 if max_score<60:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1258 prediction="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1259 return prediction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1260

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1261 def judge_subspecies_Kmer(Special_dict):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1262 #seqsero2 -k;

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1263 max_score=0

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1264 prediction="-" #default should be I

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1265 for x in Special_dict:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1266 #if "mer" in x: ## ed_SL_0318: change ssp_threshold

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1267 if "mer" in x and float(Special_dict[x]) > 60:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1268 if max_score<float(Special_dict[x]):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1269 max_score=float(Special_dict[x])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1270 prediction=x.split("_")[-1].strip()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1271 if x.split("_")[-1].strip()=="bongori" and float(Special_dict[x])>95:#if bongori already, then no need to test enterica

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1272 prediction="bongori"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1273 break

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1274 return prediction

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1275

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1276 ## ed_SL_11232019: add notes for missing antigen

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1277 def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1278 antigen_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1279 if ssp != '-':

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1280 if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:-

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1281 antigen_note = 'H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1282 NA_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1283 elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1284 antigen_note = 'fliC was not detected. This is an atypical result that should be further investigated. Most Salmonella strains have fliC, encoding the Phase 1 H antigen, even if it is not expressed. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1285 NA_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1286 elif O_antigen == '-' and H1_antigen != '-': # -:H1:X

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1287 antigen_note = 'O antigen was not detected. This result may be due to a rough strain that has deleted the rfb region. For raw reads input, the k-mer workflow is sometimes more sensitive than the microassembly workflow in detecting O antigen. Caution should be used with this approach because the k-mer result may be due to low levels of contamination. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1288 NA_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1289 elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:-

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1290 antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1291 NA_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1292 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1293 antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1294 NA_note = ''

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1295 # if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1296 # antigen_note = 'No subspecies marker was detected and less than 2 serotype antigens were detected; further, this genome was not identified as Salmonella. This is an atypical result that should be further investigated. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1297 # else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1298 # antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. '

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1299 return (antigen_note,NA_note)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1300

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1301 def main():

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1302 #combine SeqSeroK and SeqSero2, also with SalmID

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1303 args = parse_args()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1304 input_file = args.i

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1305 data_type = args.t

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1306 analysis_mode = args.m

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1307 mapping_mode=args.b

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1308 threads=args.p

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1309 make_dir=args.d

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1310 clean_mode=args.c

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1311 sample_name=args.n

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1312 ingore_header=args.s

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1313 k_size=27 #will change for bug fixing

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1314 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1315 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1316 seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1317 database="H_and_O_and_specific_genes.fasta"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1318 note="Note: "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1319 NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1320 if len(sys.argv)==1:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1321 subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1322 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1323 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1324 request_id += str(random.randint(1, 10000000))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1325 if make_dir is None:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1326 make_dir="SeqSero_result_"+request_id

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1327 if os.path.isdir(make_dir):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1328 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1329 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1330 subprocess.check_call(["mkdir",make_dir])

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1331 #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1332 #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1333 subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1334 #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument).

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1335 ############################begin the real analysis

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1336 if analysis_mode=="a":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1337 if data_type in ["1","2","3"]:#use allele mode

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1338 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1339 os.chdir(make_dir)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1340 ###add a function to tell input files

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1341 fnameA=for_fq.split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1342 fnameB=rev_fq.split("/")[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1343 current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime())

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1344 sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1345 map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1346 ### avoid error out when micro assembly fails. ed_SL_03172020

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1347 try:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1348 xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1349 except (UnboundLocalError, subprocess.CalledProcessError):

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1350 xmlfile="NA"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1351 H1_cont_stat_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1352 H2_cont_stat_list=[]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1353 ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1354 if xmlfile=="NA":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1355 O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1356 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1357 Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1358 file=open("data_log.txt","a")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1359 for x in Final_list:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1360 file.write("\t".join(str(y) for y in x)+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1361 file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1362 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1363 O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1364 subspecies=judge_subspecies(fnameA) #predict subspecies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1365 ###output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1366 predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1367 claim="" #04132019, disable claim for new report requirement

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1368 contamination_report=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1369 H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1370 if contamination_O!="" and contamination_H=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1371 contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1372 elif contamination_O=="" and contamination_H!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1373 contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1374 elif contamination_O!="" and contamination_H!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1375 contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"."

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1376 if contamination_report!="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1377 #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1378 contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. "

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1379 #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1380 #if contamination_report+star_line+claim=="": #0413, new output style

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1381 # note=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1382 #else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1383 # note="Note:"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1384

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1385 ### ed_SL_11232019: add notes for missing antigen

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1386 if O_choice=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1387 O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1388 antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1389 if sample_name:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1390 print ("Sample name:\t"+sample_name)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1391 ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1392

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1393 if clean_mode:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1394 subprocess.check_call("rm -rf ../"+make_dir,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1395 make_dir="none-output-directory due to '-c' flag"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1396 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1397 new_file=open("SeqSero_result.txt","w")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1398 ### ed_SL_01152020: add new output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1399 conta_note="yes" if "inter-serotype contamination" in contamination_report else "no"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1400 tsv_file=open("SeqSero_result.tsv","w")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1401 if ingore_header:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1402 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1403 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1404 tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tPotential inter-serotype contamination\tNote\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1405 if sample_name:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1406 new_file.write("Sample name:\t"+sample_name+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1407 tsv_file.write(sample_name+'\t')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1408 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1409 tsv_file.write(input_file[0].split('/')[-1]+'\t')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1410 ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1411 if "N/A" not in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1412 new_file.write("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1413 "Input files:\t"+"\t".join(input_file)+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1414 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1415 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1416 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1417 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1418 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1419 "Predicted serotype:\t"+predict_sero+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1420 note+contamination_report+star_line+claim+antigen_note+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1421 tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+conta_note+"\t"+contamination_report+star_line+claim+antigen_note+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1422 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1423 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1424 star_line="" #04132019, for new output requirement, diable star_line if "NA" in output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1425 new_file.write("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1426 "Input files:\t"+"\t".join(input_file)+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1427 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1428 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1429 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1430 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1431 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1432 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1433 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1434 tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+conta_note+"\t"+NA_note+contamination_report+star_line+claim+antigen_note+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1435 new_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1436 tsv_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1437 #subprocess.check_call("cat Seqsero_result.txt",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1438 #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1439 subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1440 if "N/A" not in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1441 #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1442 print("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1443 "Input files:\t"+"\t".join(input_file)+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1444 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1445 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1446 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1447 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1448 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1449 "Predicted serotype:\t"+predict_sero+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1450 note+contamination_report+star_line+claim+antigen_note+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1451 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1452 print("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1453 "Input files:\t"+"\t".join(input_file)+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1454 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1455 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1456 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1457 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1458 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1459 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1460 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1461 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1462 print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1463 elif analysis_mode=="k":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1464 #ex_dir = os.path.dirname(os.path.realpath(__file__))

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1465 ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1466 #output_mode = args.mode

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1467 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1468 input_file = for_fq #-k will just use forward because not all reads were used

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1469 os.chdir(make_dir)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1470 f = open(ex_dir + '/antigens.pickle', 'rb')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1471 lib_dict = pickle.load(f)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1472 f.close

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1473 input_Ks=get_input_K(input_file,lib_dict,data_type,k_size)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1474 O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1475 highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1476 subspecies=judge_subspecies_Kmer(Special_dict)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1477 if subspecies=="IIb" or subspecies=="IIa":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1478 subspecies="II"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1479 predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes(

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1480 highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1481 claim="" #no claim any more based on new output requirement

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1482 #if star_line+claim=="": #0413, new output style

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1483 # note=""

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1484 #else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1485 # note="Note:"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1486

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1487 ### ed_SL_11232019: add notes for missing antigen

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1488 if highest_O.split('-')[-1]=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1489 O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1490 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1491 O_choice=highest_O.split('-')[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1492 antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1493 if sample_name:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1494 print ("Sample name:\t"+sample_name)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1495 ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1496

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1497 if clean_mode:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1498 subprocess.check_call("rm -rf ../"+make_dir,shell=True)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1499 make_dir="none-output-directory due to '-c' flag"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1500 # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1501 # if highest_O.split('-')[-1]=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1502 # O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1503 # else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1504 # O_choice=highest_O.split('-')[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1505 # ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1506 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1507 # if highest_O.split('-')[-1]=="":

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1508 # O_choice="-"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1509 # else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1510 # O_choice=highest_O.split('-')[-1]

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1511 #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero)

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1512 new_file=open("SeqSero_result.txt","w")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1513 #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1514 ### ed_SL_01152020: add new output

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1515 tsv_file=open("SeqSero_result.tsv","w")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1516 if ingore_header:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1517 pass

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1518 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1519 tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tNote\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1520 if sample_name:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1521 new_file.write("Sample name:\t"+sample_name+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1522 tsv_file.write(sample_name+'\t')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1523 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1524 tsv_file.write(input_file.split('/')[-1]+'\t')

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1525 ###

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1526 if "N/A" not in predict_sero:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1527 new_file.write("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1528 "Input files:\t"+input_file+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1529 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1530 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1531 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1532 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1533 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1534 "Predicted serotype:\t"+predict_sero+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1535 note+star_line+claim+antigen_note+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1536 tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+star_line+claim+antigen_note+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1537 else:

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1538 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1539 star_line = "" #changed for new output requirement, 04132019

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1540 new_file.write("Output directory:\t"+make_dir+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1541 "Input files:\t"+input_file+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1542 "O antigen prediction:\t"+O_choice+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1543 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1544 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1545 "Predicted subspecies:\t"+subspecies+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1546 "Predicted antigenic profile:\t"+predict_form+"\n"+

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1547 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1548 note+NA_note+star_line+claim+antigen_note+"\n")#+##

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1549 tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+NA_note+star_line+claim+antigen_note+"\n")

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1550 new_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter

parents:

diff changeset

1551 tsv_file.close()

d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324

cstrittmatter