ss2v110: build/scripts-3.6/SeqSero2

annotate build/scripts-3.6/SeqSero2_package.py @ 14:047956dacae4 draft default tip

planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty

author	cstrittmatter
date	Thu, 21 May 2020 22:01:02 -0400
parents	e6437d423693
children

rev	line source
10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1 #!/Users/charles.strittmatter/miniconda3/bin/python
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	2
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	3 import sys
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	4 import time
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	5 import random
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	6 import os
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	7 import subprocess
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	8 import gzip
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	9 import io
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	10 import pickle
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	11 import argparse
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	12 import itertools
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	13 from distutils.version import LooseVersion
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	14 from distutils.spawn import find_executable
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	15 sys.path.insert(1,sys.path[0]+'/..')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	16
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	17 try:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	18 from .version import SeqSero2_version
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	19 except Exception: #ImportError
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	20 from version import SeqSero2_version
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	21
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	22 ### SeqSero Kmer
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	23 def parse_args():
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	24 "Parse the input arguments, use '-h' for help."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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: v1.1.1')#add "-m <data_type>" in future
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	31 parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	35 parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	36 parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	37 return parser.parse_args()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	38
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	39 ### check paths of dependencies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	40 check_dependencies = parse_args().check
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	41 dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py']
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	42 if check_dependencies:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	43 for item in dependencies:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	44 ext_path = find_executable(item)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	45 if ext_path is not None:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	46 print ("Using "+item+" - "+ext_path)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	47 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	48 print ("ERROR: can not find "+item+" in PATH")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	49 sys.exit()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	50 ### end of --check
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	51
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	52 def reverse_complement(sequence):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	53 complement = {
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	54 'A': 'T',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	55 'C': 'G',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	56 'G': 'C',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	57 'T': 'A',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	58 'N': 'N',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	59 'M': 'K',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	60 'R': 'Y',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	61 'W': 'W',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	62 'S': 'S',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	63 'Y': 'R',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	64 'K': 'M',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	65 'V': 'B',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	66 'H': 'D',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	67 'D': 'H',
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	68 'B': 'V'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	69 }
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	70 return "".join(complement[base] for base in reversed(sequence))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	71
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	72
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	73 def createKmerDict_reads(list_of_strings, kmer):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	74 kmer_table = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	75 for string in list_of_strings:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	76 sequence = string.strip('\n')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	77 for i in range(len(sequence) - kmer + 1):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	78 new_mer = sequence[i:i + kmer].upper()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	79 new_mer_rc = reverse_complement(new_mer)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	80 if new_mer in kmer_table:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	81 kmer_table[new_mer.upper()] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	82 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	83 kmer_table[new_mer.upper()] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	84 if new_mer_rc in kmer_table:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	85 kmer_table[new_mer_rc.upper()] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	86 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	87 kmer_table[new_mer_rc.upper()] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	88 return kmer_table
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	89
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	90
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	91 def multifasta_dict(multifasta):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	92 multifasta_list = [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	93 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	94 ]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	95 headers = [i for i in multifasta_list if i[0] == '>']
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	96 multifasta_dict = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	97 for h in headers:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	98 start = multifasta_list.index(h)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	99 for element in multifasta_list[start + 1:]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	100 if element[0] == '>':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	101 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	102 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	103 if h[1:] in multifasta_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	104 multifasta_dict[h[1:]] += element
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	105 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	106 multifasta_dict[h[1:]] = element
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	107 return multifasta_dict
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	108
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	109
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	110 def multifasta_single_string(multifasta):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	111 multifasta_list = [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	112 line.strip() for line in open(multifasta, 'r')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	113 if (len(line.strip()) > 0) and (line.strip()[0] != '>')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	114 ]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	115 return ''.join(multifasta_list)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	116
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	117
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	118 def chunk_a_long_sequence(long_sequence, chunk_size=60):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	119 chunk_list = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	120 steps = len(long_sequence) // 60 #how many chunks
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	121 for i in range(steps):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	122 chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	123 chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	124 return chunk_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	125
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	126
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	127 def target_multifasta_kmerizer(multifasta, k, kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	128 forward_length = 300 #if find the target, put forward 300 bases
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	129 reverse_length = 2200 #if find the target, put backward 2200 bases
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	131 target_mers = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	132 long_single_string = multifasta_single_string(multifasta)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	133 multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	134 unit_length = len(multifasta_list[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	135 forward_lines = int(forward_length / unit_length) + 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	136 reverse_lines = int(forward_length / unit_length) + 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	137 start_num = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	138 end_num = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	139 for i in range(len(multifasta_list)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	140 if i not in range(start_num, end_num): #avoid computational repetition
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	141 line = multifasta_list[i]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	142 start = int((len(line) - k) // 2)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	143 s1 = line[start:k + start]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	144 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	145 if i - forward_lines >= 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	146 start_num = i - forward_lines
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	147 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	148 start_num = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	149 if i + reverse_lines <= len(multifasta_list) - 1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	150 end_num = i + reverse_lines
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	151 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	152 end_num = len(multifasta_list) - 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	153 target_list = [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	154 x.strip() for x in multifasta_list[start_num:end_num]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	155 ]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	156 target_line = "".join(target_list)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	157 target_mers += [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	158 k1 for k1 in createKmerDict_reads([str(target_line)], k)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	160 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	161 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	162 return set(target_mers)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	163
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	164
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	165 def target_read_kmerizer(file, k, kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	166 i = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	167 n_reads = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	168 total_coverage = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	169 target_mers = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	170 if file.endswith(".gz"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	171 file_content = io.BufferedReader(gzip.open(file))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	172 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	173 file_content = open(file, "r").readlines()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	174 for line in file_content:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	175 start = int((len(line) - k) // 2)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	176 if i % 4 == 2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	177 if file.endswith(".gz"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	178 s1 = line[start:k + start].decode()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	179 line = line.decode()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	180 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	181 s1 = line[start:k + start]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	182 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	183 n_reads += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	184 total_coverage += len(line)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	185 target_mers += [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	186 k1 for k1 in createKmerDict_reads([str(line)], k)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	188 i += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	189 if total_coverage >= 4000000:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	190 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	191 return set(target_mers)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	192
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	193
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	194 def minion_fasta_kmerizer(file, k, kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	195 i = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	196 n_reads = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	197 total_coverage = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	198 target_mers = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	199 for line in open(file):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	200 if i % 2 == 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	201 for kmer, rc_kmer in kmers(line.strip().upper(), k):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	202 if (kmer in kmerDict) or (rc_kmer in kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	203 if kmer in target_mers:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	204 target_mers[kmer] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	205 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	206 target_mers[kmer] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	207 if rc_kmer in target_mers:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	208 target_mers[rc_kmer] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	209 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	210 target_mers[rc_kmer] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	211 i += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	212 return set([h for h in target_mers])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	213
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	214
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	215 def minion_fastq_kmerizer(file, k, kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	216 i = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	217 n_reads = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	218 total_coverage = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	219 target_mers = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	220 for line in open(file):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	221 if i % 4 == 2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	222 for kmer, rc_kmer in kmers(line.strip().upper(), k):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	223 if (kmer in kmerDict) or (rc_kmer in kmerDict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	224 if kmer in target_mers:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	225 target_mers[kmer] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	226 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	227 target_mers[kmer] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	228 if rc_kmer in target_mers:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	229 target_mers[rc_kmer] += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	230 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	231 target_mers[rc_kmer] = 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	232 i += 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	233 return set([h for h in target_mers])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	234
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	235
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	236 def multifasta_single_string2(multifasta):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	237 single_string = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	238 with open(multifasta, 'r') as f:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	239 for line in f:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	240 if line.strip()[0] == '>':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	241 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	242 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	243 single_string += line.strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	244 return single_string
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	245
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	246
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	247 def kmers(seq, k):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	248 rev_comp = reverse_complement(seq)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	249 for start in range(1, len(seq) - k + 1):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	250 yield seq[start:start + k], rev_comp[-(start + k):-start]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	251
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	252
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	253 def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	254 multi_seq_dict = multifasta_dict(multifasta)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	255 lib_dict = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	256 for h in multi_seq_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	257 lib_dict[h] = set(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	258 [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	259 return lib_dict
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	260
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	261
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	262 def Combine(b, c):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	263 fliC_combinations = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	264 fliC_combinations.append(",".join(c))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	265 temp_combinations = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	266 for i in range(len(b)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	267 for x in itertools.combinations(b, i + 1):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	268 temp_combinations.append(",".join(x))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	269 for x in temp_combinations:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	270 temp = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	271 for y in c:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	272 temp.append(y)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	273 temp.append(x)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	274 temp = ",".join(temp)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	275 temp = temp.split(",")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	276 temp.sort()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	277 temp = ",".join(temp)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	278 fliC_combinations.append(temp)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	279 return fliC_combinations
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	280
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	281
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	282 def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	283 #like test_output_06012017.txt
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	285 from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	286 rename_dict_not_anymore=[rename_dict[x] for x in rename_dict]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	287 rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	288 seronames = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	289 seronames_none_subspecies=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	290 for i in range(len(phase1)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	291 fliC_combine = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	292 fljB_combine = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	293 if phaseO[i] == Otype: # no VII in KW, but it's there
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	294 ### for fliC, detect every possible combinations to avoid the effect of "["
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	295 if phase1[i].count("[") == 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	296 fliC_combine.append(phase1[i])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	297 elif phase1[i].count("[") >= 1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	298 c = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	299 b = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	300 if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	301 "[") == 1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	302 content = phase1[i].replace("[", "").replace("]", "")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	303 fliC_combine.append(content)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	304 fliC_combine.append("-")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	305 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	306 for x in phase1[i].split(","):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	307 if "[" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	308 b.append(x.replace("[", "").replace("]", ""))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	309 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	310 c.append(x)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	311 fliC_combine = Combine(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	312 b, c
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	313 ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	314 ### end of fliC "[" detect
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	315 ### for fljB, detect every possible combinations to avoid the effect of "["
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	316 if phase2[i].count("[") == 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	317 fljB_combine.append(phase2[i])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	318 elif phase2[i].count("[") >= 1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	319 d = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	320 e = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	321 if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	322 "[") == 1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	323 content = phase2[i].replace("[", "").replace("]", "")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	324 fljB_combine.append(content)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	325 fljB_combine.append("-")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	326 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	327 for x in phase2[i].split(","):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	328 if "[" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	329 d.append(x.replace("[", "").replace("]", ""))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	330 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	331 e.append(x)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	332 fljB_combine = Combine(d, e)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	333 ### end of fljB "[" detect
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	334 new_fliC = fliC.split(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	335 ","
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	337 new_fliC.sort()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	338 new_fliC = ",".join(new_fliC)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	339 new_fljB = fljB.split(",")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	340 new_fljB.sort()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	341 new_fljB = ",".join(new_fljB)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	342 if (new_fliC in fliC_combine
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	343 or fliC in fliC_combine) and (new_fljB in fljB_combine
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	344 or fljB in fljB_combine):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	345 ######start, remove_list,rename_dict, added on 11/11/2018
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	346 if sero[i] not in remove_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	347 temp_sero=sero[i]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	348 if temp_sero in rename_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	349 temp_sero=rename_dict[temp_sero] #rename if in the rename list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	350 if temp_sero not in seronames:#the new sero may already included, if yes, then not consider
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	351 if subs[i] == subspecies:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	352 seronames.append(temp_sero)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	353 seronames_none_subspecies.append(temp_sero)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	354 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	355 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	356 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	357 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	358 ######end, added on 11/11/2018
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	359 #analyze seronames
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	360 subspecies_pointer=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	361 if len(seronames) == 0 and len(seronames_none_subspecies)!=0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	362 # ed_SL_12182019: modified to fix the subspecies output problem
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	363 #seronames=seronames_none_subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	364 seronames=["N/A"]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	365 #subspecies_pointer="1"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	366 subspecies_pointer="0"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	367 if len(seronames) == 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	368 seronames = [
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	369 "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	370 ]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	371 star = ""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	372 star_line = ""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	373 if len(seronames) > 1: #there are two possible predictions for serotypes
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	374 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	375 #changed 04072019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	376 #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	377 if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	378 star="*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	381 if Otype=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	382 Otype="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	383 predict_form = Otype + ":" + fliC + ":" + fljB
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	384 predict_sero = (" or ").join(seronames)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	385 ###special test for Enteritidis
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	386 if predict_form == "9:g,m:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	387 sdf = "-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	388 for x in special_gene_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	389 if x.startswith("sdf"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	390 sdf = "+"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	391 #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	392 star_line="sdf gene detected. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	393 #predict_form = predict_form + " Sdf prediction:" + sdf
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	394 predict_form = predict_form #changed 04072019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	395 if sdf == "-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	396 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	397 #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	398 star_line="sdf gene not detected. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	399 #changed in 04072019, for new output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	401 #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	402 predict_sero = "Gallinarum or Enteritidis"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	403 ###end of special test for Enteritidis
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	404 elif predict_form == "4:i:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	405 predict_sero = "I 4,[5],12:i:-" # change serotype name
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	406 elif predict_form == "4:r:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	407 predict_sero = "N/A (4:r:-)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	408 elif predict_form == "4:b:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	409 predict_sero = "N/A (4:b:-)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	410 #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	411 #predict_sero = "Newport"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	412 #star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	413 #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	415 if "N/A" in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	416 claim = ""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	417 #special test for Typhimurium
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	418 if "Typhimurium" in predict_sero or predict_form == "4:i:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	419 normal = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	420 mutation = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	421 for x in special_gene_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	422 if "oafA-O-4_full" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	423 normal = float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	424 elif "oafA-O-4_5-" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	425 mutation = float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	426 if normal > mutation:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	427 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	428 elif normal < mutation:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	429 #predict_sero = predict_sero.strip() + "(O5-)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	430 predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	431 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	432 #star_line = "Detected the deletion of O5-."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	433 star_line = "Detected a deletion that causes O5- variant of Typhimurium. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	434 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	435 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	436 #special test for Paratyphi B
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	437 if "Paratyphi B" in predict_sero or predict_form == "4:b:-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	438 normal = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	439 mutation = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	440 for x in special_gene_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	441 if "gntR-family-regulatory-protein_dt-positive" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	442 normal = float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	443 elif "gntR-family-regulatory-protein_dt-negative" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	444 mutation = float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	445 #print(normal,mutation)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	446 if normal > mutation:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	447 #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	448 predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	449 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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(+)."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	451 star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	452 elif normal < mutation:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	453 #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	454 predict_sero = predict_sero.strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	455 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	456 #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	457 star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	458 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	459 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	461 star_line = " " ## ed_SL_05152019: do not report this situation.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	462 #special test for O13,22 and O13,23
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	463 if Otype=="13":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	464 #ex_dir = os.path.dirname(os.path.realpath(__file__))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	466 f = open(ex_dir + '/special.pickle', 'rb')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	467 special = pickle.load(f)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	468 O22_O23=special['O22_O23']
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	470 O22_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	471 O23_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	472 for x in special_gene_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	473 if "O:22" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	474 O22_score = O22_score+float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	475 elif "O:23" in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	476 O23_score = O23_score+float(special_gene_list[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	477 #print(O22_score,O23_score)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	478 for z in O22_O23[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	479 if predict_sero.split(" or ")[0] in z:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	480 if O22_score > O23_score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	481 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	482 #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	483 predict_sero = z[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	484 elif O22_score < O23_score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	485 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	486 #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	487 predict_sero = z[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	488 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	489 star = "*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	490 #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	491 if " or " in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	492 star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	493 #special test for O6,8
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	494 #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	495 #for x in merge_O68_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	496 # if x in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	497 # predict_sero=x
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	498 # star=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	499 # star_line=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	500 #special test for Montevideo; most of them are monophasic
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	502 #star="*"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	504 return predict_form, predict_sero, star, star_line, claim
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	505 ### End of SeqSero Kmer part
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	506
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	507 ### Begin of SeqSero2 allele prediction and output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	508 def xml_parse_score_comparision_seqsero(xmlfile):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	509 #used to do seqsero xml analysis
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	510 from Bio.Blast import NCBIXML
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	511 handle=open(xmlfile)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	512 handle=NCBIXML.parse(handle)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	513 handle=list(handle)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	514 List=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	515 List_score=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	516 List_ids=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	517 List_query_region=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	518 for i in range(len(handle)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	519 if len(handle[i].alignments)>0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	520 for j in range(len(handle[i].alignments)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	521 score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	522 ids=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	523 cover_region=set() #fixed problem that repeated calculation leading percentage > 1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	524 List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	525 for z in range(len(handle[i].alignments[j].hsps)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	526 hsp=handle[i].alignments[j].hsps[z]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	527 temp=set(range(hsp.query_start,hsp.query_end))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	528 if len(cover_region)==0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	529 cover_region=cover_region\|temp
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	530 fraction=1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	531 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	532 fraction=1-len(cover_region&temp)/float(len(temp))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	533 cover_region=cover_region\|temp
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	534 if "last" in handle[i].query or "first" in handle[i].query:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	535 score+=hsp.bits*fraction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	536 ids+=float(hsp.identities)/handle[i].query_length*fraction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	537 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	538 score+=hsp.bits*fraction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	539 ids+=float(hsp.identities)/handle[i].query_length*fraction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	540 List_score.append(score)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	541 List_ids.append(ids)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	542 List_query_region.append(cover_region)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	543 temp=zip(List,List_score,List_ids,List_query_region)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	544 Final_list=sorted(temp, key=lambda d:d[1], reverse = True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	545 return Final_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	546
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	547
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	548 def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	549 Old=L
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	550 L.sort()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	551 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	552 count=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	553 for j in range(len(L)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	554 y=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	555 for x in Old:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	556 if L[j]==x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	557 y+=1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	558 count.append(y)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	559 if sort_on_fre!="none":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	560 d=zip(*sorted(zip(count, L)))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	561 L=d[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	562 count=d[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	563 return (L,count)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	564
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	565 def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	567 #this is mainly used for
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	568 a=nodes_vs_score_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	569 fliC_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	570 fljB_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	571 for z in a:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	572 if "fliC" in z[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	573 fliC_score+=z[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	574 elif "fljB" in z[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	575 fljB_score+=z[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	576 if fliC_score>=fljB_score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	577 role="fliC"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	578 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	579 role="fljB"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	580 return (role,abs(fliC_score-fljB_score))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	581
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	582 def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	584 #also used when no head or tail got blasted score for the contig
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	585 role=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	586 for z in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	587 if node_name in z[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	588 role=z[0].split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	589 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	590 return role
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	591
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	592 def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	593 #nodes_list is the c created by c,d=Uniq(nodes) in below function
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	594 first_target=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	595 role_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	596 for x in nodes_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	597 a=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	598 role=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	599 for y in tail_head_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	600 if x in y[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	601 a.append(y)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	602 if len(a)==4:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	603 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	604 if diff<20:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	605 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	606 elif len(a)==3:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	607 ###however, if the one with highest score is the fewer one, compare their accumulation score
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	608 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	609 if diff<20:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	610 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	611 ###end of above score comparison
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	612 elif len(a)==2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	614 temp=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	615 for z in a:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	616 temp.append(z[0].split("_")[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	617 m,n=Uniq(temp)#should only have one choice, but weird situation might occur too
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	618 if len(m)==1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	619 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	620 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	621 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	622 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	623 if diff<20:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	624 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	625 ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	626 elif len(a)==1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	627 #that one
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	628 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	629 if diff<20:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	630 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	632 else:#a==0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	633 #use Final_list_passed best match
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	634 for z in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	635 if x in z[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	636 role=z[0].split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	637 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	638 #print x,role,len(a)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	639 role_list.append((role,x))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	640 if len(role_list)==2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	642 #just use score to do a final test
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	643 role_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	644 for x in nodes_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	645 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	646 role_list.append((role,x))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	647 return role_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	648
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	649 def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	650 #used to decide which contig is FliC and which one is fljB
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	651 contigs=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	652 nodes=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	653 for x in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	654 if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	655 nodes.append(x[0].split("___")[1].strip())
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	656 c,d=Uniq(nodes)#c is node_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	657 #print c
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	658 tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	659 roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	660 return roles
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	661
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	662 def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	663 #decide O based on Final_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	664 O_choice="?"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	665 O_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	666 special_genes={}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	667 nodes=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	668 for x in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	669 if x[0].startswith("O-"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	670 nodes.append(x[0].split("___")[1].strip())
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	671 elif not x[0].startswith("fl"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	672 special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	673 #print "special_genes:",special_genes
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	674 c,d=Uniq(nodes)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	675 #print "potential O antigen contig",c
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	676 final_O=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	677 O_nodes_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	678 for x in c:#c is the list for contigs
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	679 temp=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	680 for y in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	681 if x in y[0] and y[0].startswith("O-"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	682 final_O.append(y)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	683 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	684 ### O contig has the problem of two genes on same contig, so do additional test
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	685 potenial_new_gene=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	686 for x in final_O:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	687 pointer=0 #for genes merged or not
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	688 #not consider O-1,3,19_not_in_3,10, too short compared with others
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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 3002 (for secureity can use 400*2) as flank region
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	690 pointer=x[0].split("___")[1].strip()#store the contig name
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	691 print(pointer)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	692 if pointer!=0:#it has potential merge event
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	693 for y in Final_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	695 potenial_new_gene=y
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	696 #print(potenial_new_gene)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	697 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	698 if potenial_new_gene!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	699 print("two differnt genes in same contig, fix it for O antigen")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	700 print(potenial_new_gene[:3])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	701 pointer=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	702 for y in final_O:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	703 if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	704 pointer=1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	705 if pointer!=0: #changed to consider two genes in same contig
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	706 final_O.append(potenial_new_gene)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	707 ### end of the two genes on same contig test
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	708 final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	710 #print "$$$No Otype, due to no hit"#may need to be changed
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	711 O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	712 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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]])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	714 O_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	715 O_list_less_contamination=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	716 for x in final_O:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	718 O_list.append(x[0].split("__")[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	719 O_nodes_list.append(x[0].split("___")[1])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	720 if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	721 O_list_less_contamination.append(x[0].split("__")[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	722 ### special test for O9,46 and O3,10 family
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	725 O_choice="O-9,46"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	726 #print "$$$Most possilble Otype: O-9,46"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	727 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	728 O_choice="O-9,46,27"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	729 #print "$$$Most possilble Otype: O-9,46,27"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	730 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	731 O_choice="O-9"#next, detect O9 vs O2?
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	732 O2=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	733 O9=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	734 for z in special_genes:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	735 if "tyr-O-9" in z:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	736 O9=special_genes[z]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	737 elif "tyr-O-2" in z:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	738 O2=special_genes[z]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	739 if O2>O9:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	740 O_choice="O-2"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	741 elif O2<O9:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	742 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	743 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	744 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	748 O_choice="O-3,10"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	749 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	750 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	751 O_choice="O-1,3,19"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	752 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	753 ### end of special test for O9,46 and O3,10 family
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	754 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	755 try:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	756 max_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	757 for x in final_O:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	758 if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage0.15:#use x[2],08172018, the "coverage identity = cover_length identity"; also meet coverage threshold
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	759 max_score=x[2]#change from x[-1] to x[2],08172018
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	760 O_choice=x[0].split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	761 if O_choice=="O-1,3,19":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	762 O_choice=final_O[1][0].split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	763 #print "$$$Most possilble Otype: ",O_choice
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	764 except:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	765 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	766 #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	768 O_choice="O-4"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	769 #print "O:",O_choice,O_nodes_list
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	770 Otypes=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	771 for x in O_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	772 if x!="O-1,3,19_not_in_3,10":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	773 if "O-9,46_" not in x:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	774 Otypes.append(x.split("_")[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	775 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	776 Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	777 #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	778 Otypes_uniq,Otypes_fre=Uniq(Otypes)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	779 contamination_O=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	781 if len(Otypes_uniq)>2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	782 contamination_O="potential contamination from O antigen signals"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	783 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	784 if len(Otypes_uniq)>1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	786 contamination_O=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	788 contamination_O=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	789 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	790 contamination_O="potential contamination from O antigen signals"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	791 return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	792 ### End of SeqSero2 allele prediction and output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	793
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	794 def get_input_files(make_dir,input_file,data_type,dirpath):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	795 #tell input files from datatype
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	797 for_fq=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	798 rev_fq=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	799 os.chdir(make_dir)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	800 if data_type=="1":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	801 input_file=input_file[0].split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	802 if input_file.endswith(".sra"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	803 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	804 for_fq=input_file.replace(".sra","_1.fastq")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	805 rev_fq=input_file.replace(".sra","_2.fastq")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	806 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	807 core_id=input_file.split(".fastq")[0].split(".fq")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	808 for_fq=core_id+"_1.fastq"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	809 rev_fq=core_id+"_2.fastq"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	810 if input_file.endswith(".gz"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	811 subprocess.check_call("gzip -dc "+input_file+" \| "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	812 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	813 subprocess.check_call("cat "+input_file+" \| "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	814 elif data_type=="2":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	815 for_fq=input_file[0].split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	816 rev_fq=input_file[1].split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	817 elif data_type=="3":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	818 input_file=input_file[0].split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	819 if input_file.endswith(".sra"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	820 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	821 for_fq=input_file.replace(".sra","_1.fastq")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	822 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	823 for_fq=input_file
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	824 elif data_type in ["4","5","6"]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	825 for_fq=input_file[0].split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	826 os.chdir("..")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	827 return for_fq,rev_fq
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	828
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	829 def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	830 #get O and H types from Final_list from blast parsing; allele mode
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	831 from Bio import SeqIO
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	832 fliC_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	833 fljB_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	834 fliC_contig="NA"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	835 fljB_contig="NA"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	836 fliC_region=set([0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	837 fljB_region=set([0,])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	838 fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	839 fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	840 O_choice="-"#no need to decide O contig for now, should be only one
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	842 O_choice=O_choice.split("-")[-1].strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	844 O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	846 #add alignment locations, used for further selection, 03312019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	847 for i in range(len(H_contig_roles)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	848 x=H_contig_roles[i]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	849 for y in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	850 if x[1] in y[0] and y[0].startswith(x[0]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	851 H_contig_roles[i]+=H_contig_roles[i]+(y[-1],)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	852 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	853 log_file=open("SeqSero_log.txt","a")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	854 extract_file=open("Extracted_antigen_alleles.fasta","a")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	855 handle_fasta=list(SeqIO.parse(new_fasta,"fasta"))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	856
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	857 #print("O_contigs:")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	858 log_file.write("O_contigs:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	860 extract_file.write("#O_contigs:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	861 for x in O_nodes_roles:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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])))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	866 seqs=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	867 for z in handle_fasta:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	868 if x[0].split("___")[-1]==z.description:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	869 seqs=str(z.seq)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	870 extract_file.write(title+seqs+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	871 if len(H_contig_roles)!=0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	873 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	874 highest_H_coverage=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	875 for x in H_contig_roles:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	876 #if multiple choices, temporately select the one with longest length for now, will revise in further change
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	878 fliC_contig=x[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	879 fliC_length=len(x[-1])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	881 fljB_contig=x[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	882 fljB_length=len(x[-1])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	883 for x in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	884 if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	885 fliC_choice=x[0].split("_")[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	886 elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	887 fljB_choice=x[0].split("_")[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	888 elif fliC_choice!="-" and fljB_choice!="-":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	889 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	890 #now remove contigs not in middle core part
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	891 first_allele="NA"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	892 first_allele_percentage=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	893 for x in Final_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	894 if x[0].startswith("fliC") or x[0].startswith("fljB"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	895 first_allele=x[0].split("__")[0] #used to filter those un-middle contigs
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	896 first_allele_percentage=x[2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	897 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	898 additional_contigs=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	899 for x in Final_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	900 if first_allele in x[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	901 if (fliC_contig == x[0].split("___")[-1]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	902 fliC_region=x[3]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	903 elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	904 fljB_region=x[3]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	905 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	906 if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	907 additional_contigs.append(x)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	908 #else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	909 #print x[:3]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	911 if first_allele_percentage>0.9:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	912 if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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))))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	914 elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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))))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	916 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	917 target_region=set()#doesn't do anything
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	918 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	919 target_region=set()#doesn't do anything
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	920 #print(target_region)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	921 #print(additional_contigs)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	923 target_region=target_region2\|target_region
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	924 for x in additional_contigs:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	925 removal=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	926 contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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_length0.5<len(x[3])<contig_length1.5: #consider length and alignment length for now, but very loose,0.5 and 1.5 as cut-off
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	928 removal=1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	929 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	931 removal=1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	932 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	933 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	934 if removal==1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	935 for y in H_contig_roles:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	936 if y[1] in x[0]:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	937 H_contig_roles.remove(y)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	938 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	939 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	940 #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length0.5,len(x[3]),contig_length1.5)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	941 #end of removing none-middle contigs
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	942 #print("H_contigs:")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	943 log_file.write("H_contigs:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	944 extract_file.write("#H_contigs:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	945 H_contig_stat=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	946 H1_cont_stat={}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	947 H2_cont_stat={}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	948 for i in range(len(H_contig_roles)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	949 x=H_contig_roles[i]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	950 a=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	951 for y in Final_list_passed:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	952 if x[1] in y[0] and y[0].startswith(x[0]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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])))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	958 H_contig_roles[i]="can't decide fliC or fljB, may be third phase"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	960 seqs=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	961 for z in handle_fasta:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	962 if x[1]==z.description:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	963 seqs=str(z.seq)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	964 extract_file.write(title+seqs+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	965 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	966 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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])))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	970 seqs=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	971 for z in handle_fasta:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	972 if x[1]==z.description:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	973 seqs=str(z.seq)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	974 extract_file.write(title+seqs+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	975 if x[0]=="fliC":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	976 if y[0].split("_")[1] not in H1_cont_stat:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	977 H1_cont_stat[y[0].split("_")[1]]=y[2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	978 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	979 H1_cont_stat[y[0].split("_")[1]]+=y[2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	980 if x[0]=="fljB":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	981 if y[0].split("_")[1] not in H2_cont_stat:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	982 H2_cont_stat[y[0].split("_")[1]]=y[2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	983 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	984 H2_cont_stat[y[0].split("_")[1]]+=y[2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	985 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	986 #detect contaminations
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	987 #print(H1_cont_stat)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	988 #print(H2_cont_stat)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	989 H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	990 H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	991 contamination_H=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	992 if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	993 contamination_H="potential contamination from H antigen signals"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	994 elif len(H2_cont_stat_list)==1 and fljB_contig=="NA":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	995 contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	996 #get additional antigens
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	997 """
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	999 if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1000 O_choice="O-9,46"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1001 #print "$$$Most possilble Otype: O-9,46"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1002 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1003 O_choice="O-9,46,27"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1004 #print "$$$Most possilble Otype: O-9,46,27"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1007 O_choice="O-3,10"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1008 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1009 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1010 O_choice="O-1,3,19"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1011 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1012 ### end of special test for O9,46 and O3,10 family
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1013
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1015 if len(Otypes_uniq)>2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1016 contamination_O="potential contamination from O antigen signals"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1017 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1018 if len(Otypes_uniq)>1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1020 contamination_O=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1022 contamination_O=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1023 """
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1024 additonal_antigents=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1025 #print(contamination_O)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1026 #print(contamination_H)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1027 log_file.write(contamination_O+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1028 log_file.write(contamination_H+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1029 log_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1031
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1032 def get_input_K(input_file,lib_dict,data_type,k_size):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1033 #kmer mode; get input_Ks from dict and data_type
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1034 kmers = []
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1035 for h in lib_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1036 kmers += lib_dict[h]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1037 if data_type == '4':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1038 input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1039 elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1040 input_Ks = target_read_kmerizer(input_file, k_size, set(kmers))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1041 elif data_type == '5':#minion_2d_fasta
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1042 input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1043 if data_type == '6':#minion_2d_fastq
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1044 input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1045 return input_Ks
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1046
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1047 def get_kmer_dict(lib_dict,input_Ks):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1048 #kmer mode; get predicted types
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1049 O_dict = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1050 H_dict = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1051 Special_dict = {}
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1052 for h in lib_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1053 score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1055 if h.startswith('O-') and score > 25:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1056 O_dict[h] = score
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1057 if h.startswith('fl') and score > 40:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1058 H_dict[h] = score
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1059 if (h[:2] != 'fl') and (h[:2] != 'O-'):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1060 Special_dict[h] = score
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1061 return O_dict,H_dict,Special_dict
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1062
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1063 def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1064 log_file=open("SeqSero_log.txt","a")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1065 log_file.write("O_scores:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1066 #call O:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1067 highest_O = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1068 if len(O_dict) == 0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1069 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1070 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1071 for x in O_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1072 log_file.write(x+"\t"+str(O_dict[x])+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1075 #modified to fix miscall of O-9,46
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1077 highest_O = "O-9,46"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1078 elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1079 highest_O = "O-9,46,27"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1080 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1081 highest_O = "O-9" # next, detect O9 vs O2?
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1082 O2 = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1083 O9 = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1084 for z in Special_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1085 if "tyr-O-9" in z:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1086 O9 = float(Special_dict[z])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1087 if "tyr-O-2" in z:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1088 O2 = float(Special_dict[z])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1089 if O2 > O9:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1090 highest_O = "O-2"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1091 elif ("O-3,10_wzx__1539" in O_dict) and (
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1092 "O-9,46_wzy__1191" in O_dict
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1093 ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1095 highest_O = "O-3,10"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1096 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1097 highest_O = "O-1,3,19"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1098 ### end of special test for O9,46 and O3,10 family
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1099 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1100 try:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1101 max_score = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1102 for x in O_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1103 if float(O_dict[x]) >= max_score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1104 max_score = float(O_dict[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1105 #highest_O = x.split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1106 # ed_SL_12182019: modified to fix the O-9,46 error example1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1108 highest_O = "O-9"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1109 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1110 highest_O = x.split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1111 if highest_O == "O-1,3,19":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1112 highest_O = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1113 max_score = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1114 for x in O_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1115 if x == 'O-1,3,19_not_in_3,10__130':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1116 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1117 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1118 if float(O_dict[x]) >= max_score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1119 max_score = float(O_dict[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1120 #highest_O = x.split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1121 # ed_SL_12182019: modified to fix the O-9,46 error example1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1123 highest_O = "O-9"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1124 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1125 highest_O = x.split("_")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1126 except:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1127 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1128 #call_fliC:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1129 if len(H_dict)!=0:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1131 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1132 highest_H_score_both_BC=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1133 highest_fliC = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1134 highest_fliC_raw = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1135 highest_Score = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1136 log_file.write("\nH_scores:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1137 for s in H_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1138 log_file.write(s+"\t"+str(H_dict[s])+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1139 if s.startswith('fliC'):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1140 if float(H_dict[s]) > highest_Score:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1141 highest_fliC = s.split('_')[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1142 highest_fliC_raw = s
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1143 highest_Score = float(H_dict[s])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1144 #call_fljB
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1145 highest_fljB = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1146 highest_fljB_raw = '-'
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1147 highest_Score = 0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1148 for s in H_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1149 if s.startswith('fljB'):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1151 #highest_fljB = s.split('_')[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1152 #highest_fljB_raw = s
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1153 #highest_Score = float(H_dict[s])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1154 if s.split('_')[1]!=highest_fliC:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1155 highest_fljB = s.split('_')[1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1156 highest_fljB_raw = s
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1157 highest_Score = float(H_dict[s])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1158 log_file.write("\nSpecial_scores:\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1159 for s in Special_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1160 log_file.write(s+"\t"+str(Special_dict[s])+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1161 log_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1162 return highest_O,highest_fliC,highest_fljB
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1163
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1164 def get_temp_file_names(for_fq,rev_fq):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1165 #seqsero2 -a; get temp file names
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1166 sam=for_fq+".sam"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1167 bam=for_fq+".bam"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1168 sorted_bam=for_fq+"_sorted.bam"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1169 mapped_fq1=for_fq+"_mapped.fq"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1170 mapped_fq2=rev_fq+"_mapped.fq"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1171 combined_fq=for_fq+"_combined.fq"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1172 for_sai=for_fq+".sai"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1173 rev_sai=rev_fq+".sai"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1174 return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1175
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1176 def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1177 #seqsero2 -a; do mapping and sort
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1178 print("building database...")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1179 subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1180 print("mapping...")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1181 if mapping_mode=="mem":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1182 subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1183 elif mapping_mode=="sam":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1184 if fnameB!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1185 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1186 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1187 subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1188 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1189 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1190 subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1191 subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1192 ### check the version of samtools then use differnt commands
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1193 samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1194 out, err = samtools_version.communicate()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1195 version = str(err).split("ersion:")[1].strip().split(" ")[0].strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1196 print("check samtools version:",version)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1197 ### end of samtools version check and its analysis
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1198 if LooseVersion(version)<=LooseVersion("1.2"):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1199 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1200 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1201 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1202
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1204 #seqsero2 -a; extract, assembly and blast
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1205 subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1206 #print("fnameA:",fnameA)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1207 #print("fnameB:",fnameB)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1208 if fnameB!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1210 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1211 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1212 outdir=current_time+"_temp"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1213 print("assembling...")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1214 if int(threads)>4:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1215 t="4"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1216 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1217 t=threads
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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 "-:-:-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1219 if fnameB!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1221 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1223 new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1224 #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1225 subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1226 #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1227 subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1228 print("blasting...","\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1229 xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1232 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1233 xmlfile="NA"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1234 return xmlfile,new_fasta
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1235
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1236 def judge_subspecies(fnameA):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1237 #seqsero2 -a; judge subspecies on just forward raw reads fastq
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1238 salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1239 out, err = salmID_output.communicate()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1240 out=out.decode("utf-8")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1241 file=open("data_log.txt","a")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1242 file.write(out)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1243 file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1244 salm_species_scores=out.split("\n")[1].split("\t")[6:]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1245 salm_species_results=out.split("\n")[0].split("\t")[6:]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1246 max_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1247 max_score_index=1 #default is 1, means "I"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1248 for i in range(len(salm_species_scores)):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1249 if max_score<float(salm_species_scores[i]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1250 max_score=float(salm_species_scores[i])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1251 max_score_index=i
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1252 prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1255 prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1256 #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1257 if max_score<60:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1258 prediction="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1259 return prediction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1260
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1261 def judge_subspecies_Kmer(Special_dict):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1262 #seqsero2 -k;
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1263 max_score=0
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1264 prediction="-" #default should be I
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1265 for x in Special_dict:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1266 #if "mer" in x: ## ed_SL_0318: change ssp_threshold
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1267 if "mer" in x and float(Special_dict[x]) > 60:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1268 if max_score<float(Special_dict[x]):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1269 max_score=float(Special_dict[x])
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1270 prediction=x.split("_")[-1].strip()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1272 prediction="bongori"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1273 break
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1274 return prediction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1275
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1276 ## ed_SL_11232019: add notes for missing antigen
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1277 def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1278 antigen_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1279 if ssp != '-':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1280 if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:-
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1282 NA_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1283 elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1285 NA_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1286 elif O_antigen == '-' and H1_antigen != '-': # -:H1:X
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1288 NA_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1289 elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:-
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1290 antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1291 NA_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1292 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1294 NA_note = ''
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1295 # if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1297 # else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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. '
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1299 return (antigen_note,NA_note)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1300
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1301 def main():
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1302 #combine SeqSeroK and SeqSero2, also with SalmID
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1303 args = parse_args()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1304 input_file = args.i
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1305 data_type = args.t
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1306 analysis_mode = args.m
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1307 mapping_mode=args.b
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1308 threads=args.p
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1309 make_dir=args.d
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1310 clean_mode=args.c
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1311 sample_name=args.n
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1312 ingore_header=args.s
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1313 k_size=27 #will change for bug fixing
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1314 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1317 database="H_and_O_and_specific_genes.fasta"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1318 note="Note: "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1320 if len(sys.argv)==1:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1321 subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1322 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1323 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1324 request_id += str(random.randint(1, 10000000))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1325 if make_dir is None:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1326 make_dir="SeqSero_result_"+request_id
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1327 make_dir=os.path.abspath(make_dir)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1328 if os.path.isdir(make_dir):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1329 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1330 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1331 subprocess.check_call("mkdir -p "+make_dir,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1332 #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1333 #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1334 subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1335 #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).
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1336 ############################begin the real analysis
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1337 if analysis_mode=="a":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1338 if data_type in ["1","2","3"]:#use allele mode
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1339 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1340 os.chdir(make_dir)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1341 ###add a function to tell input files
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1342 fnameA=for_fq.split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1343 fnameB=rev_fq.split("/")[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1344 current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime())
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1345 sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1346 map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1347 ### avoid error out when micro assembly fails. ed_SL_03172020
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1348 try:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1349 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1350 except (UnboundLocalError, subprocess.CalledProcessError):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1351 xmlfile="NA"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1352 H1_cont_stat_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1353 H2_cont_stat_list=[]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1354 ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1355 if xmlfile=="NA":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1356 O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1357 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1358 Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1359 file=open("data_log.txt","a")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1360 for x in Final_list:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1361 file.write("\t".join(str(y) for y in x)+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1362 file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1363 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)]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1364 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1365 subspecies=judge_subspecies(fnameA) #predict subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1366 ###output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1367 predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1368 claim="" #04132019, disable claim for new report requirement
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1369 contamination_report=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1370 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]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1371 if contamination_O!="" and contamination_H=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1372 contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1373 elif contamination_O=="" and contamination_H!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1374 contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1375 elif contamination_O!="" and contamination_H!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1376 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)+"."
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1377 if contamination_report!="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1378 #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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1379 contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. "
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1380 #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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1381 #if contamination_report+star_line+claim=="": #0413, new output style
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1382 # note=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1383 #else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1384 # note="Note:"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1385
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1386 ### ed_SL_11232019: add notes for missing antigen
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1387 if O_choice=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1388 O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1389 antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1390 if sample_name:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1391 print ("Sample name:\t"+sample_name)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1392 ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1393
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1394 if clean_mode:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1395 subprocess.check_call("rm -rf ../"+make_dir,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1396 make_dir="none-output-directory due to '-c' flag"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1397 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1398 new_file=open("SeqSero_result.txt","w")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1399 ### ed_SL_01152020: add new output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1400 conta_note="yes" if "inter-serotype contamination" in contamination_report else "no"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1401 tsv_file=open("SeqSero_result.tsv","w")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1402 if ingore_header:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1403 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1404 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1405 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1406 if sample_name:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1407 new_file.write("Sample name:\t"+sample_name+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1408 tsv_file.write(sample_name+'\t')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1409 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1410 tsv_file.write(input_file[0].split('/')[-1]+'\t')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1411 ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1412 if "N/A" not in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1413 new_file.write("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1414 "Input files:\t"+"\t".join(input_file)+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1415 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1416 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1417 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1418 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1419 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1420 "Predicted serotype:\t"+predict_sero+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1421 note+contamination_report+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1422 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1423 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1424 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1425 star_line="" #04132019, for new output requirement, diable star_line if "NA" in output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1426 new_file.write("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1427 "Input files:\t"+"\t".join(input_file)+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1428 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1429 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1430 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1431 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1432 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1433 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1434 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1435 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1436 new_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1437 tsv_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1438 #subprocess.check_call("cat Seqsero_result.txt",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1439 #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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1440 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)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1441 if "N/A" not in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1442 #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")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1443 print("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1444 "Input files:\t"+"\t".join(input_file)+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1445 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1446 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1447 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1448 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1449 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1450 "Predicted serotype:\t"+predict_sero+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1451 note+contamination_report+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1452 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1453 print("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1454 "Input files:\t"+"\t".join(input_file)+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1455 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1456 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1457 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1458 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1459 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1460 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1461 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1462 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1463 print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1464 elif analysis_mode=="k":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1465 #ex_dir = os.path.dirname(os.path.realpath(__file__))
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1466 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
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1467 #output_mode = args.mode
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1468 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1469 input_file = for_fq #-k will just use forward because not all reads were used
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1470 os.chdir(make_dir)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1471 f = open(ex_dir + '/antigens.pickle', 'rb')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1472 lib_dict = pickle.load(f)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1473 f.close
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1474 input_Ks=get_input_K(input_file,lib_dict,data_type,k_size)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1475 O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1476 highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1477 subspecies=judge_subspecies_Kmer(Special_dict)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1478 if subspecies=="IIb" or subspecies=="IIa":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1479 subspecies="II"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1480 predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes(
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1481 highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1482 claim="" #no claim any more based on new output requirement
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1483 #if star_line+claim=="": #0413, new output style
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1484 # note=""
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1485 #else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1486 # note="Note:"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1487
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1488 ### ed_SL_11232019: add notes for missing antigen
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1489 if highest_O.split('-')[-1]=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1490 O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1491 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1492 O_choice=highest_O.split('-')[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1493 antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1494 if sample_name:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1495 print ("Sample name:\t"+sample_name)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1496 ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1497
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1498 if clean_mode:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1499 subprocess.check_call("rm -rf ../"+make_dir,shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1500 make_dir="none-output-directory due to '-c' flag"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1501 # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1502 # if highest_O.split('-')[-1]=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1503 # O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1504 # else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1505 # O_choice=highest_O.split('-')[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1506 # ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1507 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1508 # if highest_O.split('-')[-1]=="":
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1509 # O_choice="-"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1510 # else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1511 # O_choice=highest_O.split('-')[-1]
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1512 #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1513 new_file=open("SeqSero_result.txt","w")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1514 #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")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1515 ### ed_SL_01152020: add new output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1516 tsv_file=open("SeqSero_result.tsv","w")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1517 if ingore_header:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1518 pass
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1519 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1520 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1521 if sample_name:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1522 new_file.write("Sample name:\t"+sample_name+"\n")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1523 tsv_file.write(sample_name+'\t')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1524 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1525 tsv_file.write(input_file.split('/')[-1]+'\t')
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1526 ###
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1527 if "N/A" not in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1528 new_file.write("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1529 "Input files:\t"+input_file+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1530 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1531 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1532 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1533 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1534 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1535 "Predicted serotype:\t"+predict_sero+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1536 note+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1537 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1538 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1539 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1540 star_line = "" #changed for new output requirement, 04132019
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1541 new_file.write("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1542 "Input files:\t"+input_file+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1543 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1544 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1545 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1546 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1547 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1548 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1549 note+NA_note+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1550 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")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1551 new_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1552 tsv_file.close()
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1553 subprocess.call("rm .fasta .fastq .gz .fq temp.txt .sra 2> /dev/null",shell=True)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1554 if "N/A" not in predict_sero:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1555 print("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1556 "Input files:\t"+input_file+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1557 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1558 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1559 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1560 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1561 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1562 "Predicted serotype:\t"+predict_sero+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1563 note+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1564 else:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1565 print("Output directory:\t"+make_dir+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1566 "Input files:\t"+input_file+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1567 "O antigen prediction:\t"+O_choice+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1568 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1569 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1570 "Predicted subspecies:\t"+subspecies+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1571 "Predicted antigenic profile:\t"+predict_form+"\n"+
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1572 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1573 note+NA_note+star_line+claim+antigen_note+"\n")#+##
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1574
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1575 if __name__ == '__main__':
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: diff changeset	1576 main()

Mercurial > repos > cstrittmatter > ss2v110

annotate build/scripts-3.6/SeqSero2_package.py @ 14:047956dacae4 draft default tip