Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate EURL_VTEC_WGS_PT.py @ 3:0cbed1c0a762 draft default tip

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author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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3
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1 #!/usr/bin/env python3
0
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2 # -*- coding: utf-8 -*-
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3 """
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4 ############################################################################
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5 # Istituto Superiore di Sanita'
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6 # European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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7 # Developer: Arnold Knijn arnold.knijn@iss.it
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8 ############################################################################
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9 """
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10
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11 import argparse
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12 import sys
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13 import os
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14 import HTML
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15 import datetime
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16 import fileinput
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17
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18 BASE_URL = 'https://galaxytrakr.org'
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19 TOOL_DIR = os.path.dirname(os.path.abspath(__file__))
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20
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21 def insertFile(filename, report):
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22 with open(filename) as html_in:
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23 for line in html_in:
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24 report.write(line)
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25
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26 def insertFileAsTable(filename, report, hasheader=False, tabclass="table table-rep"):
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27 with open(filename) as table_in:
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28 table_data = [[str(col) for col in row.split('\t')] for row in table_in]
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29 insertTable(table_data, report, hasheader, tabclass)
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30
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31 def insertTable(table_data, report, hasheader=False, tabclass="table table-rep"):
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32 if hasheader:
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33 htmlcode = HTML.table(table_data[1:], attribs={'class':tabclass}, header_row=table_data[0])
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34 else:
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35 htmlcode = HTML.table(table_data, attribs={'class':tabclass})
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36 report.write(htmlcode)
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37
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38 def openFileAsTable(filename):
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39 with open(filename) as table_in:
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40 table_data = [[str(col) for col in row.split('\t')] for row in table_in]
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41 return table_data
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42
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43 def __main__():
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44 parser = argparse.ArgumentParser()
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45 parser.add_argument('--serotyping', dest='serotyping', help='perform serotyping', action='store_true')
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46 parser.add_argument('--virulotyping', dest='virulotyping', help='perform virulotyping', action='store_true')
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47 parser.add_argument('--shigatoxintyping', dest='shigatoxintyping', help='perform shigatoxintyping', action='store_true')
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48 parser.add_argument('--amrtyping', dest='amrtyping', help='perform amrtyping', action='store_true')
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49 parser.add_argument('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format')
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50 parser.add_argument('--input1_ext', dest='input1_ext', help='extension of forward or single-end reads file in Sanger FASTQ format')
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51 parser.add_argument('--input1_name', dest='input1_name', help='name of forward or single-end reads file in Sanger FASTQ format')
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52 parser.add_argument('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format')
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53 parser.add_argument('--input2_ext', dest='input2_ext', help='extension of reverse reads file in Sanger FASTQ format')
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54 parser.add_argument('--input2_name', dest='input2_name', help='name of reverse reads file in Sanger FASTQ format')
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55 parser.add_argument('--html1', dest='html1', help='html FASTQC file')
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56 parser.add_argument('--html1_id', dest='html1_id', help='html FASTQC file id')
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57 parser.add_argument('--html1_path', dest='html1_path', help='html FASTQC file path')
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58 parser.add_argument('--text1', dest='text1', help='text FASTQC file')
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59 parser.add_argument('--html2', dest='html2', help='html FASTQC file')
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60 parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id')
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61 parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path')
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62 parser.add_argument('--text2', dest='text2', help='text FASTQC file')
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63 parser.add_argument('--log', dest='logfile', help='log file')
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64 parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads')
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65 parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id')
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66 parser.add_argument('--stx', dest='stx', help='Shiga toxin')
0
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67 parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table')
3
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68 parser.add_argument('--amr', dest='amr', help='SPAdes log')
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69 parser.add_argument('--amr_id', dest='amr_id', help='AMR file id')
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70 parser.add_argument('--antigen_O', dest='antigen_O', help='Antigen for O')
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71 parser.add_argument('--antigen_H', dest='antigen_H', help='Antigen for H')
0
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72 parser.add_argument('--output', dest='output', help='output report html file')
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73 args = parser.parse_args()
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74
3
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75 log = open(args.logfile, 'w')
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76 log.write("EURL VTEC WGS PT v3.0\n\nTool versions\n=============\n")
0
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77 if args.input2:
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78 # FASTQC
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79 os.system("python " + TOOL_DIR + "/scripts/rgFastQC.py -i " + args.input1 + " -d " + args.html1_path + " -o " + args.html1 + " -t " + args.text1 + " -f " + args.input1_ext + " -j " + args.input1_name + " -e " + "fastqc")
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80 os.system("rm -r " + args.html1_path)
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81 os.system("python " + TOOL_DIR + "/scripts/rgFastQC.py -i " + args.input2 + " -d " + args.html2_path + " -o " + args.html2 + " -t " + args.text2 + " -f " + args.input2_ext + " -j " + args.input2_name + " -e " + "fastqc")
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82 os.system("rm -r " + args.html2_path)
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83 log.write(os.popen("fastqc -v").read())
0
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84 # TRIMMING
3
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85 os.system("python " + TOOL_DIR + "/scripts/fastq_positional_quality_trimming.py -1 " + args.input1 + " --maxlt 300 --lt 17 --rt 0 --minqt 25 --avgqt 27.0 --minlf -1 --trimmed1 input_t1.fq --log trimming_logfile -2 " + args.input2 + " --trimmed2 input_t2.fq --trimmedunpaired trimmedunpaired")
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86 log.write("\nfastq_positional_quality_trimming v1.0\n")
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87 log.write("parameters: maxlt=300, lt=17, rt=0, minqt=25, avgqt=27.0, minlf=-1\n")
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88 if args.shigatoxintyping or args.serotyping:
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89 # ASSEMBLY
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90 os.system("perl " + TOOL_DIR + "/scripts/spades.pl contigs.fa spades_contig_stats spades_scaffolds spades_scaffold_stats spades_log NODE spades.py --disable-gzip-output --isolate -t \${GALAXY_SLOTS:-16} --pe1-ff --pe1-1 fastq:input_t1.fq --pe1-2 fastq:input_t2.fq")
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91 log.write(os.popen("spades.py -v").read())
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92 log.write("parameters: --isolate, pe1-ff, pe1-1, pe1-2\n\n")
0
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93 if args.virulotyping:
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94 # VIRULOTYPER
3
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95 os.system("perl " + TOOL_DIR + "/scripts/patho_typing.pl 'python " + TOOL_DIR + "/scripts/patho_typing.py -s Escherichia coli -f " + args.input1 + " " + args.input2 + " -o output_dir -j 1 --minGeneCoverage 90 --minGeneIdentity 90 --minGeneDepth 15'")
0
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96 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper)
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97 log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n")
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98 log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n")
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99 log.write(os.popen("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt").read())
0
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100 else:
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101 # FASTQC
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102 os.system("python " + TOOL_DIR + "/scripts/rgFastQC.py -i " + args.input1 + " -d " + args.html1_path + " -o " + args.html1 + " -t " + args.text1 + " -f " + args.input1_ext + " -j " + args.input1_name + " -e " + "fastqc")
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103 os.system("rm -r " + args.html1_path)
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104 log.write(os.popen("fastqc -v").read())
0
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105 # TRIMMING
3
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106 os.system("python " + TOOL_DIR + "/scripts/fastq_positional_quality_trimming.py -1 " + args.input1 + " --maxlt 360 --lt 10 --rt 0 --minqt 25 --avgqt 27.0 --minlf 50 --trimmed1 input_t1.fq --log trimming_logfile")
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107 log.write("\nfastq_positional_quality_trimming v1.0\n")
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108 log.write("parameters: maxlt=360, lt=10, rt=0, minqt=25, avgqt=27.0, minlf=50\n")
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109 if args.shigatoxintyping or args.serotyping:
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110 # ASSEMBLY
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111 os.system("perl " + TOOL_DIR + "/scripts/spades.pl contigs.fa spades_contig_stats spades_scaffolds spades_scaffold_stats spades_log NODE spades.py --disable-gzip-output --isolate -t ${GALAXY_SLOTS:-16} --iontorrent -s fastq:input_t1.fq")
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112 log.write(os.popen("spades.py -v").read())
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113 log.write("parameters: --isolate, --iontorrent\n\n")
0
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114 if args.virulotyping:
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115 # VIRULOTYPER
3
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116 os.system("perl " + TOOL_DIR + "/scripts/patho_typing.pl 'python " + TOOL_DIR + "/scripts/patho_typing.py -s Escherichia coli -f " + args.input1 + " -o output_dir -j 1 --minGeneCoverage 90 --minGeneIdentity 90 --minGeneDepth 15'")
0
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117 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper)
3
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118 log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n")
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119 log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n")
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120 log.write(os.popen("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt").read())
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121 # SEQUENCETYPER
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122 if args.input2:
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123 os.system("mentalist call --output_votes -o 'mentalist_out' --db '" + TOOL_DIR + "/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_t1.fq -2 input_t2.fq")
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124 else:
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125 os.system("mentalist call --output_votes -o 'mentalist_out' --db '" + TOOL_DIR + "/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_t1.fq")
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126 os.system("mv mentalist_out.byvote " + args.mlstsevenloci)
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127 sequence_typing = openFileAsTable(args.mlstsevenloci)
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128 sequence_qc = openFileAsTable("mentalist_out.coverage.txt")
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129 log.write("\n\nSequenceTyper\n=============\n")
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130 log.write(os.popen("mentalist -v | grep MentaLiST").read())
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131 log.write("\n")
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132 log.write(os.popen("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt").read())
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133 if args.shigatoxintyping:
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134 # SHIGATOXIN TYPER
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135 os.system("echo 'sseqid\tpident\tlength\tpositive' > mmseqs_shigatoxin_fct")
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136 os.system("mmseqs easy-search --search-type 3 --format-output query,target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/stxDB mmseqs_STX /tmp")
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137 os.system(TOOL_DIR + "/scripts/extract_shigatoxin.sh")
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138 os.system("cat mmseqs_shigatoxin_fc >> mmseqs_shigatoxin_fct")
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139 shigatoxin_typing = openFileAsTable("mmseqs_shigatoxin_fc")
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140 log.write("\n\nShigatoxinTyper\n=============\n")
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141 log.write(os.popen("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt").read())
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142 if args.serotyping:
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143 # SEROTYPER
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144 os.system("echo 'sseqid\tpident\tlength\tpositive' > mmseqs_OH_fc")
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145 # SEROTYPER O
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146 os.system("mmseqs easy-search --search-type 3 --format-output target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/O_typeDB mmseqs_O /tmp")
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147 os.system("awk -F '\t' '($3>800 && $4>800) { print $1 FS $2 FS $3 FS $4 }' mmseqs_O | sort -nrk 2 -nrk 3 > mmseqs_O_fc")
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148 sero_typing_o = openFileAsTable("mmseqs_O_fc")
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149 os.system("cat mmseqs_O_fc >> mmseqs_OH_fc")
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150 # SEROTYPER H
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151 os.system("mmseqs easy-search --search-type 3 --format-output target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/H_typeDB mmseqs_H /tmp")
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152 os.system("awk -F '\t' '($3>800 && $4>800) { print $1 FS $2 FS $3 FS $4 }' mmseqs_H | sort -nrk 2 -nrk 3 > mmseqs_H_fc")
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153 sero_typing_h = openFileAsTable("mmseqs_H_fc")
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154 os.system("cat mmseqs_H_fc >> mmseqs_OH_fc")
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155 if os.stat('mmseqs_O_fc').st_size == 0 and os.stat('mmseqs_H_fc').st_size == 0:
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156 os.system("echo '-\t-\t-\t-' >> mmseqs_OH_fc")
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157 log.write("\n\nSeroTyper\n=============\n")
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158 log.write(os.popen("cat " + TOOL_DIR + "/data/SeroTyping_db.txt").read())
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159 if args.amrtyping:
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160 # AMRGENES
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161 os.system("amrfinder --threads 4 --database " + TOOL_DIR + "/data/amrfinder -n contigs.fa -O Escherichia -o " + args.amr)
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162 # REPORT
0
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163 try:
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164 report = open(args.output, 'w')
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165 # write head html
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166 insertFile(TOOL_DIR + "/report_head.html", report)
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167 report.write("<td><h1>EURL VTEC WGS PT</h1><h2>Report for %s</h2>%s</td>" % (args.input1_name, datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M UTC")))
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168 insertFile(TOOL_DIR + "/report_head2.html", report)
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169 # write results
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170 report.write("<h3>Summary</h3>\n")
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171 if args.serotyping:
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172 report.write("<p>Serotype: ")
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173 if len(sero_typing_o) == 0:
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174 report.write("O?")
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175 else:
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176 report.write("%s" % sero_typing_o[0][0][sero_typing_o[0][0].rfind("O"):])
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177 if len(sero_typing_h) == 0:
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178 report.write(":H?")
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179 else:
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180 report.write(":%s" % sero_typing_h[0][0][sero_typing_h[0][0].rfind("H"):])
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181 report.write("</p>\n")
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182 report.write("<p>Sequence type: ")
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183 if len(sequence_typing) < 2:
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184 report.write("Sequence typing failed")
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185 elif sequence_typing[1][1] == "failed":
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186 report.write("Sequence typing failed")
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187 else:
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188 report.write("ST%s" % sequence_typing[1][8])
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189 report.write("</p>\n")
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190 if args.virulotyping:
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191 os.system("sort " + args.virulotyper + " | awk '/eae_|stx1._|stx2._|ehxa_/ && $2>50 && !seen[substr($1, 1, index($1, \"_\")-2)]++ { printf(\"%s%s\",sep,substr($1, 1, index($1, \"_\")-1));sep=\", \" }END{print \"\"}' > virulotyper_rep")
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192 for line in fileinput.input("virulotyper_rep", inplace=True):
3
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193 print(line.replace("1a", "1"),)
0
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194 for line in fileinput.input("virulotyper_rep", inplace=True):
3
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195 print(line.replace("2a", "2"),)
0
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196 for line in fileinput.input("virulotyper_rep", inplace=True):
3
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197 print(line.replace("1b", "1"),)
0
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198 for line in fileinput.input("virulotyper_rep", inplace=True):
3
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199 print(line.replace("2b", "2"),)
0
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200 report.write("<p>Virulotypes: ")
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201 insertFile("virulotyper_rep", report)
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202 report.write("</p>\n")
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203 if args.shigatoxintyping:
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204 report.write("<p>Stx Subtypes: ")
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205 if len(shigatoxin_typing) == 0:
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206 report.write("No subtype match found")
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207 else:
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208 shigatoxin_subtype = ""
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209 shigatoxin_types = openFileAsTable(TOOL_DIR + "/data/stx_subtypes")
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210 for subtype in shigatoxin_typing:
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211 blast_pident_100 = float(subtype[1]) == 100
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212 if (blast_pident_100):
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213 for item in shigatoxin_types:
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214 if item[0] == subtype[0]:
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215 shigatoxin_subtype = item[1] + " " + shigatoxin_subtype
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216 if len(shigatoxin_subtype) == 0:
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217 shigatoxin_subtype = "No complete subtype match found"
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218 report.write("%s" % shigatoxin_subtype)
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219 report.write("</p>\n")
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220 # Quality Check
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221 disclaimer = False
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222 sequence_qc_cov = 0
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223 for x in range(7):
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224 if float(sequence_qc[x+1][2]) < 1:
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225 disclaimer = True
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226 sequence_qc_cov = sequence_qc_cov + float(sequence_qc[x+1][3])
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227 if sequence_qc_cov < 210:
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228 disclaimer = True
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229 if disclaimer:
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230 report.write("<p style='font-weight:bold;color:red'>Disclaimer: The data analysed do not fulfill minimum quality parameters, please consider repeating the sequencing.</p>\n")
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231 report.write("<hr/><h3>Raw data quality check</h3>\n")
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232 if args.input2:
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233 report.write("<p>FASTQC result forward: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id))
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234 report.write("<p>FASTQC result reverse: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html2_id))
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235 else:
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236 report.write("<p>FASTQC result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id))
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237 if args.serotyping:
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238 report.write("<br/><hr/><h3>Serotyping</h3>\n")
3
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239 insertFileAsTable("mmseqs_OH_fc", report, True)
0
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240 report.write("<br/><hr/><h3>Multi Locus Sequence Typing</h3>\n")
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241 if len(sequence_typing) > 1:
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242 insertTable(sequence_typing, report, True)
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243 if args.virulotyping:
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244 report.write("<br/><hr/><h3>Virulotyping</h3>\n")
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245 report.write("<p>This table is filtered for results with >90%% gene coverage, unfiltered results can be found <a href='%s/datasets/%s/display/?preview=True'>here</a></p>\n" % (BASE_URL, args.virulotyper_id))
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246 insertFileAsTable("pathotyper_rep_tab", report, True, "table table-cross")
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247 if args.shigatoxintyping:
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248 report.write("<br/><hr/><h3>Shiga toxin typing</h3>\n")
3
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249 insertFileAsTable("mmseqs_shigatoxin_fct", report, True)
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250 if args.amrtyping:
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251 report.write("<br/><hr/><h3>AMR typing</h3>\n")
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252 report.write("<p>AMR result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.amr_id))
0
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253 # write tail html
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254 insertFile(TOOL_DIR + "/report_tail.html", report)
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255 finally:
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256 report.close()
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257
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258 if __name__ == "__main__":
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259 __main__()