ss2v110: bin/SeqSero2_package.py annotate

annotate bin/SeqSero2_package.py @ 8:357e38526e2a draft

planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty

author	cstrittmatter
date	Thu, 30 Apr 2020 21:16:45 -0400
parents	aa54a94b9aeb
children	e6437d423693

rev	line source
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1 #!/usr/bin/env python3
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	2
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	3 import sys
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	4 import time
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	5 import random
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	6 import os
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	7 import subprocess
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	8 import gzip
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	9 import io
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	10 import pickle
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	11 import argparse
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	12 import itertools
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	13 from distutils.version import LooseVersion
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	14 from distutils.spawn import find_executable
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	15 sys.path.insert(1,sys.path[0]+'/..')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	16
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	17 try:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	18 from .version import SeqSero2_version
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	19 except Exception: #ImportError
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	20 from version import SeqSero2_version
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	21
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	22 ### SeqSero Kmer
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	23 def parse_args():
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	24 "Parse the input arguments, use '-h' for help."
8 357e38526e2a planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 7 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
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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.
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	31 parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	35 parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	36 parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	37 return parser.parse_args()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	38
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	39 ### check paths of dependencies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	40 check_dependencies = parse_args().check
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	41 dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py']
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	42 if check_dependencies:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	43 for item in dependencies:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	44 ext_path = find_executable(item)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	45 if ext_path is not None:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	46 print ("Using "+item+" - "+ext_path)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	47 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	48 print ("ERROR: can not find "+item+" in PATH")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	49 sys.exit()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	50 ### end of --check
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	51
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	52 def reverse_complement(sequence):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	53 complement = {
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	54 'A': 'T',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	55 'C': 'G',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	56 'G': 'C',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	57 'T': 'A',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	58 'N': 'N',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	59 'M': 'K',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	60 'R': 'Y',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	61 'W': 'W',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	62 'S': 'S',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	63 'Y': 'R',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	64 'K': 'M',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	65 'V': 'B',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	66 'H': 'D',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	67 'D': 'H',
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	68 'B': 'V'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	69 }
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	70 return "".join(complement[base] for base in reversed(sequence))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	71
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	72
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	73 def createKmerDict_reads(list_of_strings, kmer):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	74 kmer_table = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	75 for string in list_of_strings:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	76 sequence = string.strip('\n')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	77 for i in range(len(sequence) - kmer + 1):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	78 new_mer = sequence[i:i + kmer].upper()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	79 new_mer_rc = reverse_complement(new_mer)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	80 if new_mer in kmer_table:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	81 kmer_table[new_mer.upper()] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	82 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	83 kmer_table[new_mer.upper()] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	84 if new_mer_rc in kmer_table:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	85 kmer_table[new_mer_rc.upper()] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	86 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	87 kmer_table[new_mer_rc.upper()] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	88 return kmer_table
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	89
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	90
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	91 def multifasta_dict(multifasta):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	92 multifasta_list = [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	93 line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	94 ]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	95 headers = [i for i in multifasta_list if i[0] == '>']
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	96 multifasta_dict = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	97 for h in headers:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	98 start = multifasta_list.index(h)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	99 for element in multifasta_list[start + 1:]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	100 if element[0] == '>':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	101 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	102 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	103 if h[1:] in multifasta_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	104 multifasta_dict[h[1:]] += element
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	105 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	106 multifasta_dict[h[1:]] = element
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	107 return multifasta_dict
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	108
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	109
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	110 def multifasta_single_string(multifasta):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	111 multifasta_list = [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	112 line.strip() for line in open(multifasta, 'r')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	113 if (len(line.strip()) > 0) and (line.strip()[0] != '>')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	114 ]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	115 return ''.join(multifasta_list)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	116
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	117
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	118 def chunk_a_long_sequence(long_sequence, chunk_size=60):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	119 chunk_list = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	120 steps = len(long_sequence) // 60 #how many chunks
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	121 for i in range(steps):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	122 chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	123 chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	124 return chunk_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	125
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	126
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	127 def target_multifasta_kmerizer(multifasta, k, kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	128 forward_length = 300 #if find the target, put forward 300 bases
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	129 reverse_length = 2200 #if find the target, put backward 2200 bases
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	131 target_mers = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	132 long_single_string = multifasta_single_string(multifasta)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	133 multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	134 unit_length = len(multifasta_list[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	135 forward_lines = int(forward_length / unit_length) + 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	136 reverse_lines = int(forward_length / unit_length) + 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	137 start_num = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	138 end_num = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	139 for i in range(len(multifasta_list)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	140 if i not in range(start_num, end_num): #avoid computational repetition
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	141 line = multifasta_list[i]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	142 start = int((len(line) - k) // 2)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	143 s1 = line[start:k + start]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	144 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	145 if i - forward_lines >= 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	146 start_num = i - forward_lines
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	147 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	148 start_num = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	149 if i + reverse_lines <= len(multifasta_list) - 1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	150 end_num = i + reverse_lines
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	151 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	152 end_num = len(multifasta_list) - 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	153 target_list = [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	154 x.strip() for x in multifasta_list[start_num:end_num]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	155 ]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	156 target_line = "".join(target_list)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	157 target_mers += [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	158 k1 for k1 in createKmerDict_reads([str(target_line)], k)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	160 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	161 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	162 return set(target_mers)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	163
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	164
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	165 def target_read_kmerizer(file, k, kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	166 i = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	167 n_reads = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	168 total_coverage = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	169 target_mers = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	170 if file.endswith(".gz"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	171 file_content = io.BufferedReader(gzip.open(file))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	172 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	173 file_content = open(file, "r").readlines()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	174 for line in file_content:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	175 start = int((len(line) - k) // 2)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	176 if i % 4 == 2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	177 if file.endswith(".gz"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	178 s1 = line[start:k + start].decode()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	179 line = line.decode()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	180 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	181 s1 = line[start:k + start]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	182 if s1 in kmerDict: #detect it is a potential read or not (use the middle part)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	183 n_reads += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	184 total_coverage += len(line)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	185 target_mers += [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	186 k1 for k1 in createKmerDict_reads([str(line)], k)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	188 i += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	189 if total_coverage >= 4000000:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	190 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	191 return set(target_mers)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	192
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	193
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	194 def minion_fasta_kmerizer(file, k, kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	195 i = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	196 n_reads = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	197 total_coverage = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	198 target_mers = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	199 for line in open(file):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	200 if i % 2 == 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	201 for kmer, rc_kmer in kmers(line.strip().upper(), k):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	202 if (kmer in kmerDict) or (rc_kmer in kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	203 if kmer in target_mers:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	204 target_mers[kmer] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	205 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	206 target_mers[kmer] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	207 if rc_kmer in target_mers:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	208 target_mers[rc_kmer] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	209 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	210 target_mers[rc_kmer] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	211 i += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	212 return set([h for h in target_mers])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	213
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	214
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	215 def minion_fastq_kmerizer(file, k, kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	216 i = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	217 n_reads = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	218 total_coverage = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	219 target_mers = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	220 for line in open(file):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	221 if i % 4 == 2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	222 for kmer, rc_kmer in kmers(line.strip().upper(), k):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	223 if (kmer in kmerDict) or (rc_kmer in kmerDict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	224 if kmer in target_mers:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	225 target_mers[kmer] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	226 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	227 target_mers[kmer] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	228 if rc_kmer in target_mers:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	229 target_mers[rc_kmer] += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	230 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	231 target_mers[rc_kmer] = 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	232 i += 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	233 return set([h for h in target_mers])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	234
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	235
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	236 def multifasta_single_string2(multifasta):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	237 single_string = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	238 with open(multifasta, 'r') as f:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	239 for line in f:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	240 if line.strip()[0] == '>':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	241 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	242 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	243 single_string += line.strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	244 return single_string
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	245
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	246
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	247 def kmers(seq, k):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	248 rev_comp = reverse_complement(seq)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	249 for start in range(1, len(seq) - k + 1):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	250 yield seq[start:start + k], rev_comp[-(start + k):-start]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	251
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	252
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	253 def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	254 multi_seq_dict = multifasta_dict(multifasta)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	255 lib_dict = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	256 for h in multi_seq_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	257 lib_dict[h] = set(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	258 [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	259 return lib_dict
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	260
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	261
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	262 def Combine(b, c):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	263 fliC_combinations = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	264 fliC_combinations.append(",".join(c))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	265 temp_combinations = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	266 for i in range(len(b)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	267 for x in itertools.combinations(b, i + 1):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	268 temp_combinations.append(",".join(x))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	269 for x in temp_combinations:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	270 temp = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	271 for y in c:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	272 temp.append(y)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	273 temp.append(x)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	274 temp = ",".join(temp)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	275 temp = temp.split(",")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	276 temp.sort()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	277 temp = ",".join(temp)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	278 fliC_combinations.append(temp)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	279 return fliC_combinations
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	280
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	281
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	282 def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	283 #like test_output_06012017.txt
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	285 from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	286 rename_dict_not_anymore=[rename_dict[x] for x in rename_dict]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	287 rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	288 seronames = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	289 seronames_none_subspecies=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	290 for i in range(len(phase1)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	291 fliC_combine = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	292 fljB_combine = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	293 if phaseO[i] == Otype: # no VII in KW, but it's there
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	294 ### for fliC, detect every possible combinations to avoid the effect of "["
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	295 if phase1[i].count("[") == 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	296 fliC_combine.append(phase1[i])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	297 elif phase1[i].count("[") >= 1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	298 c = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	299 b = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	300 if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	301 "[") == 1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	302 content = phase1[i].replace("[", "").replace("]", "")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	303 fliC_combine.append(content)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	304 fliC_combine.append("-")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	305 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	306 for x in phase1[i].split(","):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	307 if "[" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	308 b.append(x.replace("[", "").replace("]", ""))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	309 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	310 c.append(x)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	311 fliC_combine = Combine(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	312 b, c
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	313 ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	314 ### end of fliC "[" detect
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	315 ### for fljB, detect every possible combinations to avoid the effect of "["
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	316 if phase2[i].count("[") == 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	317 fljB_combine.append(phase2[i])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	318 elif phase2[i].count("[") >= 1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	319 d = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	320 e = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	321 if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	322 "[") == 1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	323 content = phase2[i].replace("[", "").replace("]", "")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	324 fljB_combine.append(content)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	325 fljB_combine.append("-")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	326 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	327 for x in phase2[i].split(","):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	328 if "[" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	329 d.append(x.replace("[", "").replace("]", ""))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	330 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	331 e.append(x)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	332 fljB_combine = Combine(d, e)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	333 ### end of fljB "[" detect
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	334 new_fliC = fliC.split(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	335 ","
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	337 new_fliC.sort()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	338 new_fliC = ",".join(new_fliC)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	339 new_fljB = fljB.split(",")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	340 new_fljB.sort()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	341 new_fljB = ",".join(new_fljB)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	342 if (new_fliC in fliC_combine
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	343 or fliC in fliC_combine) and (new_fljB in fljB_combine
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	344 or fljB in fljB_combine):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	345 ######start, remove_list,rename_dict, added on 11/11/2018
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	346 if sero[i] not in remove_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	347 temp_sero=sero[i]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	348 if temp_sero in rename_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	349 temp_sero=rename_dict[temp_sero] #rename if in the rename list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	350 if temp_sero not in seronames:#the new sero may already included, if yes, then not consider
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	351 if subs[i] == subspecies:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	352 seronames.append(temp_sero)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	353 seronames_none_subspecies.append(temp_sero)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	354 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	355 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	356 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	357 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	358 ######end, added on 11/11/2018
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	359 #analyze seronames
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	360 subspecies_pointer=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	361 if len(seronames) == 0 and len(seronames_none_subspecies)!=0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	362 # ed_SL_12182019: modified to fix the subspecies output problem
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	363 #seronames=seronames_none_subspecies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	364 seronames=["N/A"]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	365 #subspecies_pointer="1"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	366 subspecies_pointer="0"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	367 if len(seronames) == 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	368 seronames = [
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	369 "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	370 ]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	371 star = ""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	372 star_line = ""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	373 if len(seronames) > 1: #there are two possible predictions for serotypes
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	374 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	375 #changed 04072019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	376 #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	377 if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	378 star="*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	381 if Otype=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	382 Otype="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	383 predict_form = Otype + ":" + fliC + ":" + fljB
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	384 predict_sero = (" or ").join(seronames)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	385 ###special test for Enteritidis
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	386 if predict_form == "9:g,m:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	387 sdf = "-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	388 for x in special_gene_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	389 if x.startswith("sdf"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	390 sdf = "+"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	391 #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	392 star_line="sdf gene detected. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	393 #predict_form = predict_form + " Sdf prediction:" + sdf
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	394 predict_form = predict_form #changed 04072019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	395 if sdf == "-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	396 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	397 #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	398 star_line="sdf gene not detected. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	399 #changed in 04072019, for new output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	401 #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	402 predict_sero = "Gallinarum or Enteritidis"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	403 ###end of special test for Enteritidis
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	404 elif predict_form == "4:i:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	405 predict_sero = "I 4,[5],12:i:-" # change serotype name
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	406 elif predict_form == "4:r:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	407 predict_sero = "N/A (4:r:-)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	408 elif predict_form == "4:b:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	409 predict_sero = "N/A (4:b:-)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	410 #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	411 #predict_sero = "Newport"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	412 #star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	413 #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	415 if "N/A" in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	416 claim = ""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	417 #special test for Typhimurium
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	418 if "Typhimurium" in predict_sero or predict_form == "4:i:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	419 normal = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	420 mutation = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	421 for x in special_gene_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	422 if "oafA-O-4_full" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	423 normal = float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	424 elif "oafA-O-4_5-" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	425 mutation = float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	426 if normal > mutation:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	427 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	428 elif normal < mutation:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	429 #predict_sero = predict_sero.strip() + "(O5-)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	430 predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	431 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	432 #star_line = "Detected the deletion of O5-."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	433 star_line = "Detected a deletion that causes O5- variant of Typhimurium. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	434 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	435 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	436 #special test for Paratyphi B
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	437 if "Paratyphi B" in predict_sero or predict_form == "4:b:-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	438 normal = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	439 mutation = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	440 for x in special_gene_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	441 if "gntR-family-regulatory-protein_dt-positive" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	442 normal = float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	443 elif "gntR-family-regulatory-protein_dt-negative" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	444 mutation = float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	445 #print(normal,mutation)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	446 if normal > mutation:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	447 #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	448 predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	449 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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(+)."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	451 star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	452 elif normal < mutation:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	453 #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	454 predict_sero = predict_sero.strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	455 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	456 #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	457 star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	458 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	459 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	461 star_line = " " ## ed_SL_05152019: do not report this situation.
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	462 #special test for O13,22 and O13,23
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	463 if Otype=="13":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	464 #ex_dir = os.path.dirname(os.path.realpath(__file__))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	466 f = open(ex_dir + '/special.pickle', 'rb')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	467 special = pickle.load(f)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	468 O22_O23=special['O22_O23']
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	470 O22_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	471 O23_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	472 for x in special_gene_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	473 if "O:22" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	474 O22_score = O22_score+float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	475 elif "O:23" in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	476 O23_score = O23_score+float(special_gene_list[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	477 #print(O22_score,O23_score)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	478 for z in O22_O23[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	479 if predict_sero.split(" or ")[0] in z:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	480 if O22_score > O23_score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	481 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	482 #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	483 predict_sero = z[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	484 elif O22_score < O23_score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	485 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	486 #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	487 predict_sero = z[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	488 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	489 star = "*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	490 #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	491 if " or " in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	492 star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	493 #special test for O6,8
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	494 #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	495 #for x in merge_O68_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	496 # if x in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	497 # predict_sero=x
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	498 # star=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	499 # star_line=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	500 #special test for Montevideo; most of them are monophasic
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	502 #star="*"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	504 return predict_form, predict_sero, star, star_line, claim
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	505 ### End of SeqSero Kmer part
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	506
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	507 ### Begin of SeqSero2 allele prediction and output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	508 def xml_parse_score_comparision_seqsero(xmlfile):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	509 #used to do seqsero xml analysis
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	510 from Bio.Blast import NCBIXML
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	511 handle=open(xmlfile)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	512 handle=NCBIXML.parse(handle)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	513 handle=list(handle)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	514 List=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	515 List_score=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	516 List_ids=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	517 List_query_region=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	518 for i in range(len(handle)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	519 if len(handle[i].alignments)>0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	520 for j in range(len(handle[i].alignments)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	521 score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	522 ids=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	523 cover_region=set() #fixed problem that repeated calculation leading percentage > 1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	524 List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	525 for z in range(len(handle[i].alignments[j].hsps)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	526 hsp=handle[i].alignments[j].hsps[z]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	527 temp=set(range(hsp.query_start,hsp.query_end))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	528 if len(cover_region)==0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	529 cover_region=cover_region\|temp
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	530 fraction=1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	531 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	532 fraction=1-len(cover_region&temp)/float(len(temp))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	533 cover_region=cover_region\|temp
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	534 if "last" in handle[i].query or "first" in handle[i].query:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	535 score+=hsp.bits*fraction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	536 ids+=float(hsp.identities)/handle[i].query_length*fraction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	537 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	538 score+=hsp.bits*fraction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	539 ids+=float(hsp.identities)/handle[i].query_length*fraction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	540 List_score.append(score)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	541 List_ids.append(ids)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	542 List_query_region.append(cover_region)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	543 temp=zip(List,List_score,List_ids,List_query_region)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	544 Final_list=sorted(temp, key=lambda d:d[1], reverse = True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	545 return Final_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	546
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	547
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	548 def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	549 Old=L
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	550 L.sort()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	551 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	552 count=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	553 for j in range(len(L)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	554 y=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	555 for x in Old:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	556 if L[j]==x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	557 y+=1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	558 count.append(y)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	559 if sort_on_fre!="none":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	560 d=zip(*sorted(zip(count, L)))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	561 L=d[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	562 count=d[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	563 return (L,count)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	564
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	565 def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	567 #this is mainly used for
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	568 a=nodes_vs_score_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	569 fliC_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	570 fljB_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	571 for z in a:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	572 if "fliC" in z[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	573 fliC_score+=z[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	574 elif "fljB" in z[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	575 fljB_score+=z[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	576 if fliC_score>=fljB_score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	577 role="fliC"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	578 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	579 role="fljB"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	580 return (role,abs(fliC_score-fljB_score))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	581
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	582 def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	584 #also used when no head or tail got blasted score for the contig
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	585 role=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	586 for z in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	587 if node_name in z[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	588 role=z[0].split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	589 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	590 return role
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	591
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	592 def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	593 #nodes_list is the c created by c,d=Uniq(nodes) in below function
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	594 first_target=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	595 role_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	596 for x in nodes_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	597 a=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	598 role=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	599 for y in tail_head_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	600 if x in y[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	601 a.append(y)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	602 if len(a)==4:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	603 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	604 if diff<20:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	605 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	606 elif len(a)==3:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	607 ###however, if the one with highest score is the fewer one, compare their accumulation score
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	608 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	609 if diff<20:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	610 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	611 ###end of above score comparison
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	612 elif len(a)==2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	614 temp=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	615 for z in a:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	616 temp.append(z[0].split("_")[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	617 m,n=Uniq(temp)#should only have one choice, but weird situation might occur too
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	618 if len(m)==1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	619 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	620 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	621 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	622 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	623 if diff<20:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	624 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	625 ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	626 elif len(a)==1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	627 #that one
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	628 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	629 if diff<20:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	630 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	632 else:#a==0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	633 #use Final_list_passed best match
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	634 for z in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	635 if x in z[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	636 role=z[0].split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	637 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	638 #print x,role,len(a)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	639 role_list.append((role,x))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	640 if len(role_list)==2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	642 #just use score to do a final test
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	643 role_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	644 for x in nodes_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	645 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	646 role_list.append((role,x))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	647 return role_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	648
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	649 def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	650 #used to decide which contig is FliC and which one is fljB
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	651 contigs=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	652 nodes=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	653 for x in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	654 if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	655 nodes.append(x[0].split("___")[1].strip())
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	656 c,d=Uniq(nodes)#c is node_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	657 #print c
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	658 tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	659 roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	660 return roles
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	661
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	662 def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	663 #decide O based on Final_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	664 O_choice="?"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	665 O_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	666 special_genes={}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	667 nodes=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	668 for x in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	669 if x[0].startswith("O-"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	670 nodes.append(x[0].split("___")[1].strip())
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	671 elif not x[0].startswith("fl"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	672 special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	673 #print "special_genes:",special_genes
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	674 c,d=Uniq(nodes)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	675 #print "potential O antigen contig",c
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	676 final_O=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	677 O_nodes_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	678 for x in c:#c is the list for contigs
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	679 temp=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	680 for y in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	681 if x in y[0] and y[0].startswith("O-"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	682 final_O.append(y)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	683 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	684 ### O contig has the problem of two genes on same contig, so do additional test
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	685 potenial_new_gene=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	686 for x in final_O:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	687 pointer=0 #for genes merged or not
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	688 #not consider O-1,3,19_not_in_3,10, too short compared with others
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	690 pointer=x[0].split("___")[1].strip()#store the contig name
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	691 print(pointer)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	692 if pointer!=0:#it has potential merge event
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	693 for y in Final_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	695 potenial_new_gene=y
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	696 #print(potenial_new_gene)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	697 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	698 if potenial_new_gene!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	699 print("two differnt genes in same contig, fix it for O antigen")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	700 print(potenial_new_gene[:3])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	701 pointer=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	702 for y in final_O:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	703 if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	704 pointer=1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	705 if pointer!=0: #changed to consider two genes in same contig
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	706 final_O.append(potenial_new_gene)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	707 ### end of the two genes on same contig test
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	708 final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	710 #print "$$$No Otype, due to no hit"#may need to be changed
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	711 O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	712 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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]])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	714 O_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	715 O_list_less_contamination=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	716 for x in final_O:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	718 O_list.append(x[0].split("__")[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	719 O_nodes_list.append(x[0].split("___")[1])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	720 if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	721 O_list_less_contamination.append(x[0].split("__")[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	722 ### special test for O9,46 and O3,10 family
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	725 O_choice="O-9,46"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	726 #print "$$$Most possilble Otype: O-9,46"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	727 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	728 O_choice="O-9,46,27"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	729 #print "$$$Most possilble Otype: O-9,46,27"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	730 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	731 O_choice="O-9"#next, detect O9 vs O2?
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	732 O2=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	733 O9=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	734 for z in special_genes:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	735 if "tyr-O-9" in z:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	736 O9=special_genes[z]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	737 elif "tyr-O-2" in z:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	738 O2=special_genes[z]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	739 if O2>O9:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	740 O_choice="O-2"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	741 elif O2<O9:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	742 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	743 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	744 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	748 O_choice="O-3,10"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	749 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	750 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	751 O_choice="O-1,3,19"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	752 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	753 ### end of special test for O9,46 and O3,10 family
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	754 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	755 try:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	756 max_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	757 for x in final_O:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	759 max_score=x[2]#change from x[-1] to x[2],08172018
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	760 O_choice=x[0].split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	761 if O_choice=="O-1,3,19":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	762 O_choice=final_O[1][0].split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	763 #print "$$$Most possilble Otype: ",O_choice
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	764 except:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	765 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	766 #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	768 O_choice="O-4"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	769 #print "O:",O_choice,O_nodes_list
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	770 Otypes=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	771 for x in O_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	772 if x!="O-1,3,19_not_in_3,10":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	773 if "O-9,46_" not in x:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	774 Otypes.append(x.split("_")[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	775 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	776 Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	777 #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	778 Otypes_uniq,Otypes_fre=Uniq(Otypes)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	779 contamination_O=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	781 if len(Otypes_uniq)>2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	782 contamination_O="potential contamination from O antigen signals"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	783 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	784 if len(Otypes_uniq)>1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	786 contamination_O=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	788 contamination_O=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	789 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	790 contamination_O="potential contamination from O antigen signals"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	791 return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	792 ### End of SeqSero2 allele prediction and output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	793
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	794 def get_input_files(make_dir,input_file,data_type,dirpath):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	795 #tell input files from datatype
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	797 for_fq=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	798 rev_fq=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	799 os.chdir(make_dir)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	800 if data_type=="1":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	801 input_file=input_file[0].split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	802 if input_file.endswith(".sra"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	803 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	804 for_fq=input_file.replace(".sra","_1.fastq")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	805 rev_fq=input_file.replace(".sra","_2.fastq")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	806 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	807 core_id=input_file.split(".fastq")[0].split(".fq")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	808 for_fq=core_id+"_1.fastq"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	809 rev_fq=core_id+"_2.fastq"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	810 if input_file.endswith(".gz"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	811 subprocess.check_call("gzip -dc "+input_file+" \| "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	812 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	813 subprocess.check_call("cat "+input_file+" \| "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	814 elif data_type=="2":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	815 for_fq=input_file[0].split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	816 rev_fq=input_file[1].split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	817 elif data_type=="3":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	818 input_file=input_file[0].split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	819 if input_file.endswith(".sra"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	820 subprocess.check_call("fastq-dump --split-files "+input_file,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	821 for_fq=input_file.replace(".sra","_1.fastq")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	822 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	823 for_fq=input_file
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	824 elif data_type in ["4","5","6"]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	825 for_fq=input_file[0].split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	826 os.chdir("..")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	827 return for_fq,rev_fq
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	828
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	829 def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	830 #get O and H types from Final_list from blast parsing; allele mode
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	831 from Bio import SeqIO
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	832 fliC_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	833 fljB_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	834 fliC_contig="NA"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	835 fljB_contig="NA"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	836 fliC_region=set([0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	837 fljB_region=set([0,])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	838 fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	839 fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	840 O_choice="-"#no need to decide O contig for now, should be only one
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	842 O_choice=O_choice.split("-")[-1].strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	844 O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	846 #add alignment locations, used for further selection, 03312019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	847 for i in range(len(H_contig_roles)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	848 x=H_contig_roles[i]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	849 for y in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	850 if x[1] in y[0] and y[0].startswith(x[0]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	851 H_contig_roles[i]+=H_contig_roles[i]+(y[-1],)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	852 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	853 log_file=open("SeqSero_log.txt","a")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	854 extract_file=open("Extracted_antigen_alleles.fasta","a")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	855 handle_fasta=list(SeqIO.parse(new_fasta,"fasta"))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	856
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	857 #print("O_contigs:")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	858 log_file.write("O_contigs:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	860 extract_file.write("#O_contigs:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	861 for x in O_nodes_roles:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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])))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	866 seqs=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	867 for z in handle_fasta:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	868 if x[0].split("___")[-1]==z.description:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	869 seqs=str(z.seq)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	870 extract_file.write(title+seqs+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	871 if len(H_contig_roles)!=0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	873 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	874 highest_H_coverage=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	875 for x in H_contig_roles:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	876 #if multiple choices, temporately select the one with longest length for now, will revise in further change
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	878 fliC_contig=x[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	879 fliC_length=len(x[-1])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	881 fljB_contig=x[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	882 fljB_length=len(x[-1])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	883 for x in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	884 if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	885 fliC_choice=x[0].split("_")[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	886 elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	887 fljB_choice=x[0].split("_")[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	888 elif fliC_choice!="-" and fljB_choice!="-":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	889 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	890 #now remove contigs not in middle core part
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	891 first_allele="NA"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	892 first_allele_percentage=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	893 for x in Final_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	894 if x[0].startswith("fliC") or x[0].startswith("fljB"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	895 first_allele=x[0].split("__")[0] #used to filter those un-middle contigs
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	896 first_allele_percentage=x[2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	897 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	898 additional_contigs=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	899 for x in Final_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	900 if first_allele in x[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	901 if (fliC_contig == x[0].split("___")[-1]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	902 fliC_region=x[3]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	903 elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	904 fljB_region=x[3]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	905 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	906 if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	907 additional_contigs.append(x)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	908 #else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	909 #print x[:3]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	911 if first_allele_percentage>0.9:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	912 if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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))))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	914 elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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))))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	916 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	917 target_region=set()#doesn't do anything
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	918 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	919 target_region=set()#doesn't do anything
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	920 #print(target_region)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	921 #print(additional_contigs)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	923 target_region=target_region2\|target_region
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	924 for x in additional_contigs:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	925 removal=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	926 contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	928 removal=1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	929 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	931 removal=1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	932 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	933 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	934 if removal==1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	935 for y in H_contig_roles:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	936 if y[1] in x[0]:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	937 H_contig_roles.remove(y)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	938 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	939 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	941 #end of removing none-middle contigs
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	942 #print("H_contigs:")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	943 log_file.write("H_contigs:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	944 extract_file.write("#H_contigs:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	945 H_contig_stat=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	946 H1_cont_stat={}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	947 H2_cont_stat={}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	948 for i in range(len(H_contig_roles)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	949 x=H_contig_roles[i]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	950 a=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	951 for y in Final_list_passed:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	952 if x[1] in y[0] and y[0].startswith(x[0]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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])))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	958 H_contig_roles[i]="can't decide fliC or fljB, may be third phase"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	960 seqs=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	961 for z in handle_fasta:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	962 if x[1]==z.description:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	963 seqs=str(z.seq)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	964 extract_file.write(title+seqs+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	965 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	966 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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])))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	970 seqs=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	971 for z in handle_fasta:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	972 if x[1]==z.description:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	973 seqs=str(z.seq)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	974 extract_file.write(title+seqs+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	975 if x[0]=="fliC":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	976 if y[0].split("_")[1] not in H1_cont_stat:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	977 H1_cont_stat[y[0].split("_")[1]]=y[2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	978 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	979 H1_cont_stat[y[0].split("_")[1]]+=y[2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	980 if x[0]=="fljB":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	981 if y[0].split("_")[1] not in H2_cont_stat:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	982 H2_cont_stat[y[0].split("_")[1]]=y[2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	983 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	984 H2_cont_stat[y[0].split("_")[1]]+=y[2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	985 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	986 #detect contaminations
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	987 #print(H1_cont_stat)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	988 #print(H2_cont_stat)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	989 H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	990 H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	991 contamination_H=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	992 if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	993 contamination_H="potential contamination from H antigen signals"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	994 elif len(H2_cont_stat_list)==1 and fljB_contig=="NA":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	995 contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	996 #get additional antigens
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	997 """
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	999 if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1000 O_choice="O-9,46"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1001 #print "$$$Most possilble Otype: O-9,46"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1002 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1003 O_choice="O-9,46,27"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1004 #print "$$$Most possilble Otype: O-9,46,27"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1007 O_choice="O-3,10"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1008 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1009 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1010 O_choice="O-1,3,19"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1011 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1012 ### end of special test for O9,46 and O3,10 family
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1013
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1015 if len(Otypes_uniq)>2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1016 contamination_O="potential contamination from O antigen signals"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1017 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1018 if len(Otypes_uniq)>1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1020 contamination_O=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1022 contamination_O=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1023 """
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1024 additonal_antigents=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1025 #print(contamination_O)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1026 #print(contamination_H)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1027 log_file.write(contamination_O+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1028 log_file.write(contamination_H+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1029 log_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1031
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1032 def get_input_K(input_file,lib_dict,data_type,k_size):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1033 #kmer mode; get input_Ks from dict and data_type
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1034 kmers = []
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1035 for h in lib_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1036 kmers += lib_dict[h]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1037 if data_type == '4':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1038 input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1039 elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1040 input_Ks = target_read_kmerizer(input_file, k_size, set(kmers))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1041 elif data_type == '5':#minion_2d_fasta
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1042 input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1043 if data_type == '6':#minion_2d_fastq
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1044 input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1045 return input_Ks
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1046
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1047 def get_kmer_dict(lib_dict,input_Ks):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1048 #kmer mode; get predicted types
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1049 O_dict = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1050 H_dict = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1051 Special_dict = {}
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1052 for h in lib_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1053 score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1055 if h.startswith('O-') and score > 25:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1056 O_dict[h] = score
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1057 if h.startswith('fl') and score > 40:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1058 H_dict[h] = score
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1059 if (h[:2] != 'fl') and (h[:2] != 'O-'):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1060 Special_dict[h] = score
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1061 return O_dict,H_dict,Special_dict
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1062
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1063 def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1064 log_file=open("SeqSero_log.txt","a")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1065 log_file.write("O_scores:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1066 #call O:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1067 highest_O = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1068 if len(O_dict) == 0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1069 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1070 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1071 for x in O_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1072 log_file.write(x+"\t"+str(O_dict[x])+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1075 #modified to fix miscall of O-9,46
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1077 highest_O = "O-9,46"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1078 elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1079 highest_O = "O-9,46,27"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1080 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1081 highest_O = "O-9" # next, detect O9 vs O2?
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1082 O2 = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1083 O9 = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1084 for z in Special_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1085 if "tyr-O-9" in z:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1086 O9 = float(Special_dict[z])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1087 if "tyr-O-2" in z:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1088 O2 = float(Special_dict[z])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1089 if O2 > O9:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1090 highest_O = "O-2"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1091 elif ("O-3,10_wzx__1539" in O_dict) and (
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1092 "O-9,46_wzy__1191" in O_dict
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1093 ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1095 highest_O = "O-3,10"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1096 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1097 highest_O = "O-1,3,19"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1098 ### end of special test for O9,46 and O3,10 family
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1099 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1100 try:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1101 max_score = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1102 for x in O_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1103 if float(O_dict[x]) >= max_score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1104 max_score = float(O_dict[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1105 #highest_O = x.split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1106 # ed_SL_12182019: modified to fix the O-9,46 error example1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1108 highest_O = "O-9"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1109 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1110 highest_O = x.split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1111 if highest_O == "O-1,3,19":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1112 highest_O = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1113 max_score = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1114 for x in O_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1115 if x == 'O-1,3,19_not_in_3,10__130':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1116 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1117 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1118 if float(O_dict[x]) >= max_score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1119 max_score = float(O_dict[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1120 #highest_O = x.split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1121 # ed_SL_12182019: modified to fix the O-9,46 error example1
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1123 highest_O = "O-9"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1124 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1125 highest_O = x.split("_")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1126 except:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1127 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1128 #call_fliC:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1129 if len(H_dict)!=0:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1131 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1132 highest_H_score_both_BC=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1133 highest_fliC = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1134 highest_fliC_raw = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1135 highest_Score = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1136 log_file.write("\nH_scores:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1137 for s in H_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1138 log_file.write(s+"\t"+str(H_dict[s])+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1139 if s.startswith('fliC'):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1140 if float(H_dict[s]) > highest_Score:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1141 highest_fliC = s.split('_')[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1142 highest_fliC_raw = s
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1143 highest_Score = float(H_dict[s])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1144 #call_fljB
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1145 highest_fljB = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1146 highest_fljB_raw = '-'
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1147 highest_Score = 0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1148 for s in H_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1149 if s.startswith('fljB'):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1151 #highest_fljB = s.split('_')[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1152 #highest_fljB_raw = s
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1153 #highest_Score = float(H_dict[s])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1154 if s.split('_')[1]!=highest_fliC:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1155 highest_fljB = s.split('_')[1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1156 highest_fljB_raw = s
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1157 highest_Score = float(H_dict[s])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1158 log_file.write("\nSpecial_scores:\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1159 for s in Special_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1160 log_file.write(s+"\t"+str(Special_dict[s])+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1161 log_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1162 return highest_O,highest_fliC,highest_fljB
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1163
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1164 def get_temp_file_names(for_fq,rev_fq):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1165 #seqsero2 -a; get temp file names
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1166 sam=for_fq+".sam"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1167 bam=for_fq+".bam"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1168 sorted_bam=for_fq+"_sorted.bam"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1169 mapped_fq1=for_fq+"_mapped.fq"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1170 mapped_fq2=rev_fq+"_mapped.fq"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1171 combined_fq=for_fq+"_combined.fq"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1172 for_sai=for_fq+".sai"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1173 rev_sai=rev_fq+".sai"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1174 return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1175
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1176 def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1177 #seqsero2 -a; do mapping and sort
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1178 print("building database...")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1179 subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1180 print("mapping...")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1181 if mapping_mode=="mem":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1182 subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1183 elif mapping_mode=="sam":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1184 if fnameB!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1185 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1186 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1187 subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1188 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1189 subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1190 subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1191 subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1192 ### check the version of samtools then use differnt commands
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1193 samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1194 out, err = samtools_version.communicate()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1195 version = str(err).split("ersion:")[1].strip().split(" ")[0].strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1196 print("check samtools version:",version)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1197 ### end of samtools version check and its analysis
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1198 if LooseVersion(version)<=LooseVersion("1.2"):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1199 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1200 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1201 subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1202
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1204 #seqsero2 -a; extract, assembly and blast
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1205 subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1206 #print("fnameA:",fnameA)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1207 #print("fnameB:",fnameB)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1208 if fnameB!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1210 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1211 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1212 outdir=current_time+"_temp"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1213 print("assembling...")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1214 if int(threads)>4:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1215 t="4"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1216 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1217 t=threads
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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 "-:-:-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1219 if fnameB!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1221 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1223 new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1224 #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1225 subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1226 #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1227 subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1228 print("blasting...","\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1229 xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a 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"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1232 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1233 xmlfile="NA"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1234 return xmlfile,new_fasta
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1235
7 aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1236 def judge_subspecies(fnameA,dirpath):
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1237 #seqsero2 -a; judge subspecies on just forward raw reads fastq
7 aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1238 samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA
aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1239 #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True)
aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1240 print(samid_strcmd)
aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1241 salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1242 out, err = salmID_output.communicate()
8 357e38526e2a planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 7 diff changeset	1243 print("judge_subspecies -> err = salmID_output.communicate() " + err)
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1244 out=out.decode("utf-8")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1245 file=open("data_log.txt","a")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1246 file.write(out)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1247 file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1248 salm_species_scores=out.split("\n")[1].split("\t")[6:]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1249 salm_species_results=out.split("\n")[0].split("\t")[6:]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1250 max_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1251 max_score_index=1 #default is 1, means "I"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1252 for i in range(len(salm_species_scores)):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1253 if max_score<float(salm_species_scores[i]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1254 max_score=float(salm_species_scores[i])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1255 max_score_index=i
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1256 prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1257 #if float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1258 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1259 prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1260 #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1261 if max_score<60:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1262 prediction="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1263 return prediction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1264
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1265 def judge_subspecies_Kmer(Special_dict):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1266 #seqsero2 -k;
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1267 max_score=0
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1268 prediction="-" #default should be I
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1269 for x in Special_dict:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1270 #if "mer" in x: ## ed_SL_0318: change ssp_threshold
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1271 if "mer" in x and float(Special_dict[x]) > 60:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1272 if max_score<float(Special_dict[x]):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1273 max_score=float(Special_dict[x])
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1274 prediction=x.split("_")[-1].strip()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1275 if x.split("_")[-1].strip()=="bongori" and float(Special_dict[x])>95:#if bongori already, then no need to test enterica
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1276 prediction="bongori"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1277 break
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1278 return prediction
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1279
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1280 ## ed_SL_11232019: add notes for missing antigen
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1281 def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1282 antigen_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1283 if ssp != '-':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1284 if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:-
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1285 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. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1286 NA_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1287 elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1288 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. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1289 NA_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1290 elif O_antigen == '-' and H1_antigen != '-': # -:H1:X
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1291 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. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1292 NA_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1293 elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:-
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1294 antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1295 NA_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1296 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1297 antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1298 NA_note = ''
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1299 # if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1300 # 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. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1301 # else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1302 # antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. '
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1303 return (antigen_note,NA_note)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1304
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1305 def main():
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1306 #combine SeqSeroK and SeqSero2, also with SalmID
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1307 args = parse_args()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1308 input_file = args.i
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1309 data_type = args.t
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1310 analysis_mode = args.m
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1311 mapping_mode=args.b
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1312 threads=args.p
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1313 make_dir=args.d
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1314 clean_mode=args.c
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1315 sample_name=args.n
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1316 ingore_header=args.s
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1317 k_size=27 #will change for bug fixing
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1318 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1319 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1320 seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1321 database="H_and_O_and_specific_genes.fasta"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1322 note="Note: "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1323 NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1324 if len(sys.argv)==1:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1325 subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1326 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1327 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1328 request_id += str(random.randint(1, 10000000))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1329 if make_dir is None:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1330 make_dir="SeqSero_result_"+request_id
8 357e38526e2a planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 7 diff changeset	1331 make_dir=os.path.abspath(make_dir)
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1332 if os.path.isdir(make_dir):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1333 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1334 else:
8 357e38526e2a planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 7 diff changeset	1335 subprocess.check_call("mkdir -p "+make_dir,shell=True)
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1336 #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1337 #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1338 subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1339 #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).
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1340 ############################begin the real analysis
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1341 if analysis_mode=="a":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1342 if data_type in ["1","2","3"]:#use allele mode
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1343 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1344 os.chdir(make_dir)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1345 ###add a function to tell input files
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1346 fnameA=for_fq.split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1347 fnameB=rev_fq.split("/")[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1348 current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime())
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1349 sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1350 map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1351 ### avoid error out when micro assembly fails. ed_SL_03172020
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1352 try:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1353 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1354 except (UnboundLocalError, subprocess.CalledProcessError):
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1355 xmlfile="NA"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1356 H1_cont_stat_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1357 H2_cont_stat_list=[]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1358 ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1359 if xmlfile=="NA":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1360 O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1361 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1362 Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1363 file=open("data_log.txt","a")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1364 for x in Final_list:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1365 file.write("\t".join(str(y) for y in x)+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1366 file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1367 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)]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1368 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
7 aa54a94b9aeb planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty cstrittmatter parents: 0 diff changeset	1369 subspecies=judge_subspecies(fnameA,dirpath) #predict subspecies
0 fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1370 ###output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1371 predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1372 claim="" #04132019, disable claim for new report requirement
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1373 contamination_report=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1374 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]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1375 if contamination_O!="" and contamination_H=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1376 contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1377 elif contamination_O=="" and contamination_H!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1378 contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1379 elif contamination_O!="" and contamination_H!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1380 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)+"."
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1381 if contamination_report!="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1382 #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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1383 contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. "
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1384 #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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1385 #if contamination_report+star_line+claim=="": #0413, new output style
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1386 # note=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1387 #else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1388 # note="Note:"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1389
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1390 ### ed_SL_11232019: add notes for missing antigen
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1391 if O_choice=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1392 O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1393 antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1394 if sample_name:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1395 print ("Sample name:\t"+sample_name)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1396 ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1397
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1398 if clean_mode:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1399 subprocess.check_call("rm -rf ../"+make_dir,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1400 make_dir="none-output-directory due to '-c' flag"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1401 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1402 new_file=open("SeqSero_result.txt","w")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1403 ### ed_SL_01152020: add new output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1404 conta_note="yes" if "inter-serotype contamination" in contamination_report else "no"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1405 tsv_file=open("SeqSero_result.tsv","w")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1406 if ingore_header:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1407 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1408 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1409 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1410 if sample_name:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1411 new_file.write("Sample name:\t"+sample_name+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1412 tsv_file.write(sample_name+'\t')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1413 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1414 tsv_file.write(input_file[0].split('/')[-1]+'\t')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1415 ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1416 if "N/A" not in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1417 new_file.write("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1418 "Input files:\t"+"\t".join(input_file)+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1419 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1420 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1421 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1422 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1423 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1424 "Predicted serotype:\t"+predict_sero+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1425 note+contamination_report+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1426 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1427 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1428 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1429 star_line="" #04132019, for new output requirement, diable star_line if "NA" in output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1430 new_file.write("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1431 "Input files:\t"+"\t".join(input_file)+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1432 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1433 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1434 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1435 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1436 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1437 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1438 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1439 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1440 new_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1441 tsv_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1442 #subprocess.check_call("cat Seqsero_result.txt",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1443 #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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1444 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)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1445 if "N/A" not in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1446 #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")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1447 print("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1448 "Input files:\t"+"\t".join(input_file)+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1449 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1450 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1451 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1452 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1453 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1454 "Predicted serotype:\t"+predict_sero+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1455 note+contamination_report+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1456 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1457 print("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1458 "Input files:\t"+"\t".join(input_file)+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1459 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1460 "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1461 "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1462 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1463 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1464 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1465 note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1466 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1467 print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1468 elif analysis_mode=="k":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1469 #ex_dir = os.path.dirname(os.path.realpath(__file__))
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1470 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
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1471 #output_mode = args.mode
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1472 for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1473 input_file = for_fq #-k will just use forward because not all reads were used
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1474 os.chdir(make_dir)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1475 f = open(ex_dir + '/antigens.pickle', 'rb')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1476 lib_dict = pickle.load(f)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1477 f.close
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1478 input_Ks=get_input_K(input_file,lib_dict,data_type,k_size)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1479 O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1480 highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1481 subspecies=judge_subspecies_Kmer(Special_dict)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1482 if subspecies=="IIb" or subspecies=="IIa":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1483 subspecies="II"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1484 predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes(
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1485 highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1486 claim="" #no claim any more based on new output requirement
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1487 #if star_line+claim=="": #0413, new output style
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1488 # note=""
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1489 #else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1490 # note="Note:"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1491
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1492 ### ed_SL_11232019: add notes for missing antigen
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1493 if highest_O.split('-')[-1]=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1494 O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1495 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1496 O_choice=highest_O.split('-')[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1497 antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1498 if sample_name:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1499 print ("Sample name:\t"+sample_name)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1500 ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1501
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1502 if clean_mode:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1503 subprocess.check_call("rm -rf ../"+make_dir,shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1504 make_dir="none-output-directory due to '-c' flag"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1505 # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1506 # if highest_O.split('-')[-1]=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1507 # O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1508 # else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1509 # O_choice=highest_O.split('-')[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1510 # ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1511 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1512 # if highest_O.split('-')[-1]=="":
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1513 # O_choice="-"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1514 # else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1515 # O_choice=highest_O.split('-')[-1]
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1516 #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1517 new_file=open("SeqSero_result.txt","w")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1518 #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")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1519 ### ed_SL_01152020: add new output
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1520 tsv_file=open("SeqSero_result.tsv","w")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1521 if ingore_header:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1522 pass
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1523 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1524 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1525 if sample_name:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1526 new_file.write("Sample name:\t"+sample_name+"\n")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1527 tsv_file.write(sample_name+'\t')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1528 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1529 tsv_file.write(input_file.split('/')[-1]+'\t')
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1530 ###
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1531 if "N/A" not in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1532 new_file.write("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1533 "Input files:\t"+input_file+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1534 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1535 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1536 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1537 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1538 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1539 "Predicted serotype:\t"+predict_sero+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1540 note+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1541 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1542 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1543 #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1544 star_line = "" #changed for new output requirement, 04132019
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1545 new_file.write("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1546 "Input files:\t"+input_file+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1547 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1548 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1549 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1550 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1551 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1552 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1553 note+NA_note+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1554 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")
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1555 new_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1556 tsv_file.close()
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1557 subprocess.call("rm .fasta .fastq .gz .fq temp.txt .sra 2> /dev/null",shell=True)
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1558 if "N/A" not in predict_sero:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1559 print("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1560 "Input files:\t"+input_file+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1561 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1562 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1563 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1564 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1565 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1566 "Predicted serotype:\t"+predict_sero+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1567 note+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1568 else:
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1569 print("Output directory:\t"+make_dir+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1570 "Input files:\t"+input_file+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1571 "O antigen prediction:\t"+O_choice+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1572 "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1573 "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1574 "Predicted subspecies:\t"+subspecies+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1575 "Predicted antigenic profile:\t"+predict_form+"\n"+
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1576 "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1577 note+NA_note+star_line+claim+antigen_note+"\n")#+##
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1578
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1579 if __name__ == '__main__':
fc22ec8e924e planemo upload commit 6b0a9d0f0ef4bdb0c2e2c54070b510ff28125f7a cstrittmatter parents: diff changeset	1580 main()

Mercurial > repos > cstrittmatter > ss2v110

annotate bin/SeqSero2_package.py @ 8:357e38526e2a draft