Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate EURL_VTEC_WGS_PT.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
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children 0cbed1c0a762
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1 # -*- coding: utf-8 -*-
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2 """
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3 ############################################################################
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4 # Istituto Superiore di Sanita'
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5 # European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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6 # Developer: Arnold Knijn arnold.knijn@iss.it
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7 ############################################################################
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8 """
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9
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10 import argparse
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11 import sys
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12 import os
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13 import HTML
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14 import datetime
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15 import fileinput
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16
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17 BASE_URL = 'https://galaxytrakr.org'
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18 TOOL_DIR = os.path.dirname(os.path.abspath(__file__))
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19
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20 def insertFile(filename, report):
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21 with open(filename) as html_in:
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22 for line in html_in:
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23 report.write(line)
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24
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25 def insertFileAsTable(filename, report, hasheader=False, tabclass="table table-rep"):
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26 with open(filename) as table_in:
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27 table_data = [[str(col) for col in row.split('\t')] for row in table_in]
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28 insertTable(table_data, report, hasheader, tabclass)
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29
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30 def insertTable(table_data, report, hasheader=False, tabclass="table table-rep"):
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31 if hasheader:
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32 htmlcode = HTML.table(table_data[1:], attribs={'class':tabclass}, header_row=table_data[0])
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33 else:
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34 htmlcode = HTML.table(table_data, attribs={'class':tabclass})
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35 report.write(htmlcode)
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36
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37 def openFileAsTable(filename):
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38 with open(filename) as table_in:
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39 table_data = [[str(col) for col in row.split('\t')] for row in table_in]
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40 return table_data
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41
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42 def __main__():
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43 parser = argparse.ArgumentParser()
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44 parser.add_argument('--serotyping', dest='serotyping', help='perform serotyping', action='store_true')
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45 parser.add_argument('--virulotyping', dest='virulotyping', help='perform virulotyping', action='store_true')
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46 parser.add_argument('--shigatoxintyping', dest='shigatoxintyping', help='perform shigatoxintyping', action='store_true')
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47 parser.add_argument('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format')
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48 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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49 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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50 parser.add_argument('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format')
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51 parser.add_argument('--input2_ext', dest='input2_ext', help='extension of reverse reads file in Sanger FASTQ format')
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52 parser.add_argument('--input2_name', dest='input2_name', help='name of reverse reads file in Sanger FASTQ format')
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53 parser.add_argument('--html1', dest='html1', help='html FASTQC file')
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54 parser.add_argument('--html1_id', dest='html1_id', help='html FASTQC file id')
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55 parser.add_argument('--html1_path', dest='html1_path', help='html FASTQC file path')
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56 parser.add_argument('--text1', dest='text1', help='text FASTQC file')
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57 parser.add_argument('--html2', dest='html2', help='html FASTQC file')
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58 parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id')
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59 parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path')
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60 parser.add_argument('--text2', dest='text2', help='text FASTQC file')
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61 parser.add_argument('--trimmed1', dest='trimmed1', help='trimmed forward FASTQ file')
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62 parser.add_argument('--trimmed2', dest='trimmed2', help='trimmed reverse FASTQ file')
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63 parser.add_argument('--trimmedunpaired', dest='trimmedunpaired', help='trimmed unpaired FASTQ file')
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64 parser.add_argument('--log', dest='logfile', help='log file')
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65 parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads')
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66 parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id')
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67 parser.add_argument('--blastn_STX', dest='blastn_STX', help='Blastn for Shiga toxin')
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68 parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table')
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69 parser.add_argument('--spades_log', dest='spades_log', help='SPAdes log')
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70 parser.add_argument('--blastn_O', dest='blastn_O', help='Blastn for O')
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71 parser.add_argument('--blastn_H', dest='blastn_H', help='Blastn for H')
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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
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75 os.system("printf 'EURL VTEC WGS PT v2.3\n\nTool versions\n=============\n' > " + args.logfile)
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76 if args.input2:
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77 # FASTQC
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78 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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79 os.system("rm -r " + args.html1_path)
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80 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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81 os.system("rm -r " + args.html2_path)
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82 os.system("fastqc -v >> " + args.logfile)
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83 # TRIMMING
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84 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 " + args.trimmed1 + " --log trimming_logfile -2 " + args.input2 + " --trimmed2 " + args.trimmed2 + " --trimmedunpaired " + args.trimmedunpaired)
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85 os.system("ln -s " + args.trimmed1 + " input_1.fq")
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86 os.system("ln -s " + args.trimmed2 + " input_2.fq")
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87 os.system("printf '\nfastq_positional_quality_trimming v1.0\n' >> " + args.logfile)
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88 os.system("printf 'parameters: maxlt=300, lt=17, rt=0, minqt=25, avgqt=27.0, minlf=-1\n' >> " + args.logfile)
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89 if args.virulotyping:
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90 # VIRULOTYPER
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91 os.system("perl " + TOOL_DIR + "/scripts/patho_typing_pt.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'")
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92 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper)
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93 os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile)
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94 os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile)
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95 os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile)
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96 if args.shigatoxintyping:
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97 # SHIGATOXIN FILTERING
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98 os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq")
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99 os.system(TOOL_DIR + "/scripts/duk -m filtered2STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_2.fq")
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100 os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq filtered2STX.fq")
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101 os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq.single.fq input_2.fq")
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102 os.system(TOOL_DIR + "/scripts/fastq_pair filtered2STX.fq.single.fq input_1.fq")
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103 os.system("cat filtered1STX.fq.paired.fq > filtered1STX_paired.fq")
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104 os.system("cat filtered1STX.fq.single.fq.paired.fq >> filtered1STX_paired.fq")
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105 os.system("cat input_1.fq.paired.fq >> filtered1STX_paired.fq")
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106 os.system("cat filtered2STX.fq.paired.fq > filtered2STX_paired.fq")
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107 os.system("cat input_2.fq.paired.fq >> filtered2STX_paired.fq")
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108 os.system("cat filtered2STX.fq.single.fq.paired.fq >> filtered2STX_paired.fq")
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109 os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile)
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110 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile)
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111 # SHIGATOXIN ASSEMBLY: SPADES
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112 os.system("perl " + TOOL_DIR + "/scripts/spades.pl spades_contigs_stx spades_contig_stats_stx spades_scaffolds_stx spades_scaffold_stats_stx spades_log_stx NODE spades.py --disable-gzip-output --careful -t \${GALAXY_SLOTS:-16} -k '21,33,55' --pe1-ff --pe1-1 fastq:filtered1STX_paired.fq --pe1-2 fastq:filtered2STX_paired.fq")
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113 os.system("spades.py -v >> " + args.logfile)
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114 os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile)
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115 # SHIGATOXIN NCBI BLAST+ blastn
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116 os.system("blastn -query 'spades_contigs_stx' -db '" + TOOL_DIR + "/data/stx' -task blastn -evalue 0.001 -out '" + args.blastn_STX + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0")
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117 os.system("blastn -version >> " + args.logfile)
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118 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile)
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119 os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile)
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120 # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT
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121 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct")
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122 os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc")
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123 shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc")
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124 os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct")
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125 if os.stat('blastn_shigatoxin_fc').st_size == 0:
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126 os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct")
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127 # SEQUENCETYPER
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128 os.system("mentalist call --output_votes -o 'mentalist_out' --db '/afs/galaxy/tool-data/mentalist_databases/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq -2 input_2.fq")
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129 os.system("mv mentalist_out.byvote " + args.mlstsevenloci)
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130 sequence_typing = openFileAsTable(args.mlstsevenloci)
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131 sequence_qc = openFileAsTable("mentalist_out.coverage.txt")
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132 os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile)
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133 os.system("mentalist -v | grep MentaLiST >> " + args.logfile)
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134 os.system("printf '\n' >> " + args.logfile)
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135 os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile)
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136 if args.serotyping:
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137 # SEROTYPE FILTERING
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138 os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq")
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139 os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq")
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140 os.system("cat filteredO1.fq > filteredOH1.fq")
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141 os.system("cat filteredH1.fq >> filteredOH1.fq")
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142 os.system(TOOL_DIR + "/scripts/duk -m filteredO2.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_2.fq")
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143 os.system(TOOL_DIR + "/scripts/duk -m filteredH2.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_2.fq")
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144 os.system("cat filteredO2.fq > filteredOH2.fq")
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145 os.system("cat filteredH2.fq >> filteredOH2.fq")
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146 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq filteredOH2.fq")
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147 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq.single.fq input_2.fq")
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148 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH2.fq.single.fq input_1.fq")
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149 os.system("cat filteredOH1.fq.paired.fq > filteredOH1_paired.fq")
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150 os.system("cat filteredOH1.fq.single.fq.paired.fq >> filteredOH1_paired.fq")
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151 os.system("cat input_1.fq.paired.fq >> filteredOH1_paired.fq")
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152 os.system("cat filteredOH2.fq.paired.fq > filteredOH2_paired.fq")
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153 os.system("cat input_2.fq.paired.fq >> filteredOH2_paired.fq")
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154 os.system("cat filteredOH2.fq.single.fq.paired.fq >> filteredOH2_paired.fq")
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155 os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile)
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156 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile)
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157 # SEROTYPE ASSEMBLY: SPADES
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158 os.system("perl " + TOOL_DIR + "/scripts/spades.pl spades_contigs_oh spades_contig_stats_oh spades_scaffolds_oh spades_scaffold_stats_oh " + args.spades_log + " NODE spades.py --disable-gzip-output --careful -t \${GALAXY_SLOTS:-16} -k '21,33,55' --pe1-ff --pe1-1 fastq:filteredOH1_paired.fq --pe1-2 fastq:filteredOH2_paired.fq")
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159 os.system("spades.py -v >> " + args.logfile)
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160 os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile)
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161 # SEROTYPE NCBI BLAST+ blastn
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162 os.system("blastn -query 'spades_contigs_oh' -db '" + TOOL_DIR + "/data/O_type' -task blastn -evalue 0.001 -out '" + args.blastn_O + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0")
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163 os.system("blastn -query 'spades_contigs_oh' -db '" + TOOL_DIR + "/data/H_type' -task blastn -evalue 0.001 -out '" + args.blastn_H + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0 -ungapped")
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164 os.system("blastn -version >> " + args.logfile)
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165 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile)
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166 os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile)
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167 # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT
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168 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc")
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169 os.system("awk -F '\t' '$4>800 { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_O + " | sort -nrk 2 -nrk 3 > blastn_O_fc")
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170 sero_typing_o = openFileAsTable("blastn_O_fc")
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171 os.system("cat blastn_O_fc >> blastn_OH_fc")
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172 os.system("awk -F '\t' '$4>800 { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_H + " | sort -nrk 2 -nrk 3 > blastn_H_fc")
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173 sero_typing_h = openFileAsTable("blastn_H_fc")
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174 os.system("cat blastn_H_fc >> blastn_OH_fc")
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175 if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0:
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176 os.system("echo '-\t-\t-\t-' >> blastn_OH_fc")
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177 else:
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178 # FASTQC
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179 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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180 os.system("rm -r " + args.html1_path)
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181 os.system("fastqc -v >> " + args.logfile)
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182 # TRIMMING
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183 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 " + args.trimmed1 + " --log trimming_logfile")
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184 os.system("ln -s " + args.trimmed1 + " input_1.fq")
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185 os.system("echo 'fastq_positional_quality_trimming v1.0' >> " + args.logfile)
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186 os.system("printf 'parameters: maxlt=360, lt=10, rt=0, minqt=25, avgqt=27.0, minlf=50\n' >> " + args.logfile)
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187 if args.virulotyping:
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188 # VIRULOTYPER
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189 os.system("perl " + TOOL_DIR + "/scripts/patho_typing_pt.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'")
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190 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper)
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191 os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile)
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192 os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile)
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193 os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile)
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194 if args.shigatoxintyping:
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195 # SHIGATOXIN FILTERING
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196 os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq")
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197 os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile)
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198 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile)
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199 # SHIGATOXIN ASSEMBLY: SPADES
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200 os.system("perl " + TOOL_DIR + "/scripts/spades.pl spades_contigs_stx spades_contig_stats_stx spades_scaffolds_stx spades_scaffold_stats_stx spades_log_stx NODE spades.py --disable-gzip-output --careful -t \${GALAXY_SLOTS:-16} -k '21,33,55' --iontorrent --pe1-ff --pe1-s fastq:filtered1STX.fq")
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201 os.system("spades.py -v >> " + args.logfile)
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202 os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile)
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203 # SHIGATOXIN NCBI BLAST+ blastn
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204 os.system("blastn -query 'spades_contigs_stx' -db '" + TOOL_DIR + "/data/stx' -task blastn -evalue 0.001 -out '" + args.blastn_STX + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0")
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205 os.system("blastn -version >> " + args.logfile)
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206 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile)
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207 os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile)
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208 # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT
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209 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct")
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210 os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc")
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211 shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc")
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212 os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct")
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213 if os.stat('blastn_shigatoxin_fc').st_size == 0:
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214 os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct")
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215 # SEQUENCETYPER
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216 os.system("mentalist call --output_votes -o 'mentalist_out' --db '/afs/galaxy/tool-data/mentalist_databases/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_1.fq")
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217 os.system("mv mentalist_out.byvote " + args.mlstsevenloci)
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218 sequence_typing = openFileAsTable(args.mlstsevenloci)
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219 sequence_qc = openFileAsTable("mentalist_out.coverage.txt")
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220 os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile)
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221 os.system("mentalist -v | grep MentaLiST >> " + args.logfile)
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222 os.system("printf '\n' >> " + args.logfile)
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223 os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile)
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224 if args.serotyping:
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225 # SEROTYPE FILTERING
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226 os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq")
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227 os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq")
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228 os.system("cat filteredO1.fq > filteredOH1.fq")
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229 os.system("cat filteredH1.fq >> filteredOH1.fq")
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230 os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile)
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231 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile)
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232 # SEROTYPE ASSEMBLY: SPADES
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233 os.system("perl " + TOOL_DIR + "/scripts/spades.pl spades_contigs_oh spades_contig_stats_oh spades_scaffolds_oh spades_scaffold_stats_oh " + args.spades_log + " NODE spades.py --disable-gzip-output --careful -t \${GALAXY_SLOTS:-16} -k '21,33,55' --iontorrent --pe1-ff --pe1-s fastq:filteredOH1.fq")
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234 os.system("spades.py -v >> " + args.logfile)
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235 os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile)
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236 # SEROTYPE NCBI BLAST+ blastn
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237 os.system("blastn -query 'spades_contigs_oh' -db '" + TOOL_DIR + "/data/O_type' -task blastn -evalue 0.001 -out '" + args.blastn_O + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0")
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238 os.system("blastn -query 'spades_contigs_oh' -db '" + TOOL_DIR + "/data/H_type' -task blastn -evalue 0.001 -out '" + args.blastn_H + "' -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads ${GALAXY_SLOTS:-8} -strand both -dust yes -max_target_seqs 10 -perc_identity 95.0 -ungapped")
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239 os.system("blastn -version >> " + args.logfile)
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240 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile)
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241 os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile)
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242 # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT
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243 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc")
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244 os.system("awk -F '\t' '$4>800 { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_O + " | sort -nrk 2 -nrk 3 > blastn_O_fc")
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245 sero_typing_o = openFileAsTable("blastn_O_fc")
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246 os.system("cat blastn_O_fc >> blastn_OH_fc")
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247 os.system("awk -F '\t' '$4>800 { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_H + " | sort -nrk 2 -nrk 3 > blastn_H_fc")
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248 sero_typing_h = openFileAsTable("blastn_H_fc")
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249 os.system("cat blastn_H_fc >> blastn_OH_fc")
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250 if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0:
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251 os.system("echo '-\t-\t-\t-' >> blastn_OH_fc")
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252 try:
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253 report = open(args.output, 'w')
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254 # write head html
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255 insertFile(TOOL_DIR + "/report_head.html", report)
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256 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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257 insertFile(TOOL_DIR + "/report_head2.html", report)
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258 # write results
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259 report.write("<h3>Summary</h3>\n")
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260 if args.serotyping:
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261 report.write("<p>Serotype: ")
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262 if len(sero_typing_o) == 0:
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263 report.write("O?")
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264 else:
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265 report.write("%s" % sero_typing_o[0][0][sero_typing_o[0][0].rfind("O"):])
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266 if len(sero_typing_h) == 0:
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267 report.write(":H?")
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268 else:
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269 report.write(":%s" % sero_typing_h[0][0][sero_typing_h[0][0].rfind("H"):])
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270 report.write("</p>\n")
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271 report.write("<p>Sequence type: ")
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272 if len(sequence_typing) < 2:
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273 report.write("Sequence typing failed")
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274 elif sequence_typing[1][1] == "failed":
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275 report.write("Sequence typing failed")
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276 else:
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277 report.write("ST%s" % sequence_typing[1][8])
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278 report.write("</p>\n")
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279 if args.virulotyping:
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280 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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281 for line in fileinput.input("virulotyper_rep", inplace=True):
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282 print line.replace("1a", "1"),
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283 for line in fileinput.input("virulotyper_rep", inplace=True):
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284 print line.replace("2a", "2"),
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285 for line in fileinput.input("virulotyper_rep", inplace=True):
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286 print line.replace("1b", "1"),
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287 for line in fileinput.input("virulotyper_rep", inplace=True):
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288 print line.replace("2b", "2"),
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289 report.write("<p>Virulotypes: ")
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290 insertFile("virulotyper_rep", report)
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291 report.write("</p>\n")
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292 if args.shigatoxintyping:
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293 report.write("<p>Stx Subtypes: ")
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294 if len(shigatoxin_typing) == 0:
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295 report.write("No subtype match found")
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296 else:
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297 shigatoxin_subtype = ""
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298 shigatoxin_types = openFileAsTable(TOOL_DIR + "/data/stx_subtypes")
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299 for subtype in shigatoxin_typing:
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300 blast_pident_100 = float(subtype[1]) == 100
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301 if (blast_pident_100):
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302 for item in shigatoxin_types:
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303 if item[0] == subtype[0]:
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304 shigatoxin_subtype = item[1] + " " + shigatoxin_subtype
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305 if len(shigatoxin_subtype) == 0:
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306 shigatoxin_subtype = "No complete subtype match found"
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307 report.write("%s" % shigatoxin_subtype)
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308 report.write("</p>\n")
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309 # Quality Check
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310 disclaimer = False
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311 sequence_qc_cov = 0
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312 for x in range(7):
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313 if float(sequence_qc[x+1][2]) < 1:
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314 disclaimer = True
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315 sequence_qc_cov = sequence_qc_cov + float(sequence_qc[x+1][3])
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316 if sequence_qc_cov < 210:
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317 disclaimer = True
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318 if disclaimer:
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319 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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320 report.write("<hr/><h3>Raw data quality check</h3>\n")
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321 if args.input2:
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322 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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323 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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324 else:
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325 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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326 if args.serotyping:
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327 report.write("<br/><hr/><h3>Serotyping</h3>\n")
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328 insertFileAsTable("blastn_OH_fc", report, True)
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329 report.write("<br/><hr/><h3>Multi Locus Sequence Typing</h3>\n")
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330 if len(sequence_typing) > 1:
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331 insertTable(sequence_typing, report, True)
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332 if args.virulotyping:
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333 report.write("<br/><hr/><h3>Virulotyping</h3>\n")
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334 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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335 insertFileAsTable("pathotyper_rep_tab", report, True, "table table-cross")
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336 if args.shigatoxintyping:
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337 report.write("<br/><hr/><h3>Shiga toxin typing</h3>\n")
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338 insertFileAsTable("blastn_shigatoxin_fct", report, True)
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339 # write tail html
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340 insertFile(TOOL_DIR + "/report_tail.html", report)
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341 finally:
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342 report.close()
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343
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344 if __name__ == "__main__":
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345 __main__()
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346
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347