Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt
view EURL_VTEC_WGS_PT.py @ 1:bf3194a789a2 draft
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author | cstrittmatter |
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date | Wed, 22 Jan 2020 08:45:40 -0500 |
parents | 965517909457 |
children | 0cbed1c0a762 |
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# -*- coding: utf-8 -*- """ ############################################################################ # Istituto Superiore di Sanita' # European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) # Developer: Arnold Knijn arnold.knijn@iss.it ############################################################################ """ import argparse import sys import os import HTML import datetime import fileinput BASE_URL = 'https://galaxytrakr.org' TOOL_DIR = os.path.dirname(os.path.abspath(__file__)) def insertFile(filename, report): with open(filename) as html_in: for line in html_in: report.write(line) def insertFileAsTable(filename, report, hasheader=False, tabclass="table table-rep"): with open(filename) as table_in: table_data = [[str(col) for col in row.split('\t')] for row in table_in] insertTable(table_data, report, hasheader, tabclass) def insertTable(table_data, report, hasheader=False, tabclass="table table-rep"): if hasheader: htmlcode = HTML.table(table_data[1:], attribs={'class':tabclass}, header_row=table_data[0]) else: htmlcode = HTML.table(table_data, attribs={'class':tabclass}) report.write(htmlcode) def openFileAsTable(filename): with open(filename) as table_in: table_data = [[str(col) for col in row.split('\t')] for row in table_in] return table_data def __main__(): parser = argparse.ArgumentParser() parser.add_argument('--serotyping', dest='serotyping', help='perform serotyping', action='store_true') parser.add_argument('--virulotyping', dest='virulotyping', help='perform virulotyping', action='store_true') parser.add_argument('--shigatoxintyping', dest='shigatoxintyping', help='perform shigatoxintyping', action='store_true') parser.add_argument('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format') parser.add_argument('--input1_ext', dest='input1_ext', help='extension of forward or single-end reads file in Sanger FASTQ format') parser.add_argument('--input1_name', dest='input1_name', help='name of forward or single-end reads file in Sanger FASTQ format') parser.add_argument('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format') parser.add_argument('--input2_ext', dest='input2_ext', help='extension of reverse reads file in Sanger FASTQ format') parser.add_argument('--input2_name', dest='input2_name', help='name of reverse reads file in Sanger FASTQ format') parser.add_argument('--html1', dest='html1', help='html FASTQC file') parser.add_argument('--html1_id', dest='html1_id', help='html FASTQC file id') parser.add_argument('--html1_path', dest='html1_path', help='html FASTQC file path') parser.add_argument('--text1', dest='text1', help='text FASTQC file') parser.add_argument('--html2', dest='html2', help='html FASTQC file') parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id') parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path') parser.add_argument('--text2', dest='text2', help='text FASTQC file') parser.add_argument('--trimmed1', dest='trimmed1', help='trimmed forward FASTQ file') parser.add_argument('--trimmed2', dest='trimmed2', help='trimmed reverse FASTQ file') parser.add_argument('--trimmedunpaired', dest='trimmedunpaired', help='trimmed unpaired FASTQ file') parser.add_argument('--log', dest='logfile', help='log file') parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads') parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id') parser.add_argument('--blastn_STX', dest='blastn_STX', help='Blastn for Shiga toxin') parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table') parser.add_argument('--spades_log', dest='spades_log', help='SPAdes log') parser.add_argument('--blastn_O', dest='blastn_O', help='Blastn for O') parser.add_argument('--blastn_H', dest='blastn_H', help='Blastn for H') parser.add_argument('--output', dest='output', help='output report html file') args = parser.parse_args() os.system("printf 'EURL VTEC WGS PT v2.3\n\nTool versions\n=============\n' > " + args.logfile) if args.input2: # FASTQC 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") os.system("rm -r " + args.html1_path) 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") os.system("rm -r " + args.html2_path) os.system("fastqc -v >> " + args.logfile) # TRIMMING 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) os.system("ln -s " + args.trimmed1 + " input_1.fq") os.system("ln -s " + args.trimmed2 + " input_2.fq") os.system("printf '\nfastq_positional_quality_trimming v1.0\n' >> " + args.logfile) os.system("printf 'parameters: maxlt=300, lt=17, rt=0, minqt=25, avgqt=27.0, minlf=-1\n' >> " + args.logfile) if args.virulotyping: # VIRULOTYPER 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'") os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper) os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile) os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile) if args.shigatoxintyping: # SHIGATOXIN FILTERING os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq") os.system(TOOL_DIR + "/scripts/duk -m filtered2STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_2.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq filtered2STX.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq.single.fq input_2.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filtered2STX.fq.single.fq input_1.fq") os.system("cat filtered1STX.fq.paired.fq > filtered1STX_paired.fq") os.system("cat filtered1STX.fq.single.fq.paired.fq >> filtered1STX_paired.fq") os.system("cat input_1.fq.paired.fq >> filtered1STX_paired.fq") os.system("cat filtered2STX.fq.paired.fq > filtered2STX_paired.fq") os.system("cat input_2.fq.paired.fq >> filtered2STX_paired.fq") os.system("cat filtered2STX.fq.single.fq.paired.fq >> filtered2STX_paired.fq") os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile) os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) # SHIGATOXIN ASSEMBLY: SPADES 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") os.system("spades.py -v >> " + args.logfile) os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile) # SHIGATOXIN NCBI BLAST+ blastn 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") os.system("blastn -version >> " + args.logfile) os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile) # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct") os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc") shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc") os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct") if os.stat('blastn_shigatoxin_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") # SEQUENCETYPER 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") os.system("mv mentalist_out.byvote " + args.mlstsevenloci) sequence_typing = openFileAsTable(args.mlstsevenloci) sequence_qc = openFileAsTable("mentalist_out.coverage.txt") os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile) os.system("mentalist -v | grep MentaLiST >> " + args.logfile) os.system("printf '\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile) if args.serotyping: # SEROTYPE FILTERING os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq") os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq") os.system("cat filteredO1.fq > filteredOH1.fq") os.system("cat filteredH1.fq >> filteredOH1.fq") os.system(TOOL_DIR + "/scripts/duk -m filteredO2.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_2.fq") os.system(TOOL_DIR + "/scripts/duk -m filteredH2.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_2.fq") os.system("cat filteredO2.fq > filteredOH2.fq") os.system("cat filteredH2.fq >> filteredOH2.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq filteredOH2.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq.single.fq input_2.fq") os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH2.fq.single.fq input_1.fq") os.system("cat filteredOH1.fq.paired.fq > filteredOH1_paired.fq") os.system("cat filteredOH1.fq.single.fq.paired.fq >> filteredOH1_paired.fq") os.system("cat input_1.fq.paired.fq >> filteredOH1_paired.fq") os.system("cat filteredOH2.fq.paired.fq > filteredOH2_paired.fq") os.system("cat input_2.fq.paired.fq >> filteredOH2_paired.fq") os.system("cat filteredOH2.fq.single.fq.paired.fq >> filteredOH2_paired.fq") os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile) os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) # SEROTYPE ASSEMBLY: SPADES 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") os.system("spades.py -v >> " + args.logfile) os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile) # SEROTYPE NCBI BLAST+ blastn 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") 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") os.system("blastn -version >> " + args.logfile) os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile) # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc") 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") sero_typing_o = openFileAsTable("blastn_O_fc") os.system("cat blastn_O_fc >> blastn_OH_fc") 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") sero_typing_h = openFileAsTable("blastn_H_fc") os.system("cat blastn_H_fc >> blastn_OH_fc") if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_OH_fc") else: # FASTQC 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") os.system("rm -r " + args.html1_path) os.system("fastqc -v >> " + args.logfile) # TRIMMING 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") os.system("ln -s " + args.trimmed1 + " input_1.fq") os.system("echo 'fastq_positional_quality_trimming v1.0' >> " + args.logfile) os.system("printf 'parameters: maxlt=360, lt=10, rt=0, minqt=25, avgqt=27.0, minlf=50\n' >> " + args.logfile) if args.virulotyping: # VIRULOTYPER 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'") os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper) os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile) os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile) if args.shigatoxintyping: # SHIGATOXIN FILTERING os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq") os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile) os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) # SHIGATOXIN ASSEMBLY: SPADES 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") os.system("spades.py -v >> " + args.logfile) os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile) # SHIGATOXIN NCBI BLAST+ blastn 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") os.system("blastn -version >> " + args.logfile) os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile) # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct") os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc") shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc") os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct") if os.stat('blastn_shigatoxin_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") # SEQUENCETYPER 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") os.system("mv mentalist_out.byvote " + args.mlstsevenloci) sequence_typing = openFileAsTable(args.mlstsevenloci) sequence_qc = openFileAsTable("mentalist_out.coverage.txt") os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile) os.system("mentalist -v | grep MentaLiST >> " + args.logfile) os.system("printf '\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile) if args.serotyping: # SEROTYPE FILTERING os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq") os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq") os.system("cat filteredO1.fq > filteredOH1.fq") os.system("cat filteredH1.fq >> filteredOH1.fq") os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile) os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) # SEROTYPE ASSEMBLY: SPADES 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") os.system("spades.py -v >> " + args.logfile) os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile) # SEROTYPE NCBI BLAST+ blastn 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") 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") os.system("blastn -version >> " + args.logfile) os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile) # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc") 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") sero_typing_o = openFileAsTable("blastn_O_fc") os.system("cat blastn_O_fc >> blastn_OH_fc") 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") sero_typing_h = openFileAsTable("blastn_H_fc") os.system("cat blastn_H_fc >> blastn_OH_fc") if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0: os.system("echo '-\t-\t-\t-' >> blastn_OH_fc") try: report = open(args.output, 'w') # write head html insertFile(TOOL_DIR + "/report_head.html", report) 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"))) insertFile(TOOL_DIR + "/report_head2.html", report) # write results report.write("<h3>Summary</h3>\n") if args.serotyping: report.write("<p>Serotype: ") if len(sero_typing_o) == 0: report.write("O?") else: report.write("%s" % sero_typing_o[0][0][sero_typing_o[0][0].rfind("O"):]) if len(sero_typing_h) == 0: report.write(":H?") else: report.write(":%s" % sero_typing_h[0][0][sero_typing_h[0][0].rfind("H"):]) report.write("</p>\n") report.write("<p>Sequence type: ") if len(sequence_typing) < 2: report.write("Sequence typing failed") elif sequence_typing[1][1] == "failed": report.write("Sequence typing failed") else: report.write("ST%s" % sequence_typing[1][8]) report.write("</p>\n") if args.virulotyping: 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") for line in fileinput.input("virulotyper_rep", inplace=True): print line.replace("1a", "1"), for line in fileinput.input("virulotyper_rep", inplace=True): print line.replace("2a", "2"), for line in fileinput.input("virulotyper_rep", inplace=True): print line.replace("1b", "1"), for line in fileinput.input("virulotyper_rep", inplace=True): print line.replace("2b", "2"), report.write("<p>Virulotypes: ") insertFile("virulotyper_rep", report) report.write("</p>\n") if args.shigatoxintyping: report.write("<p>Stx Subtypes: ") if len(shigatoxin_typing) == 0: report.write("No subtype match found") else: shigatoxin_subtype = "" shigatoxin_types = openFileAsTable(TOOL_DIR + "/data/stx_subtypes") for subtype in shigatoxin_typing: blast_pident_100 = float(subtype[1]) == 100 if (blast_pident_100): for item in shigatoxin_types: if item[0] == subtype[0]: shigatoxin_subtype = item[1] + " " + shigatoxin_subtype if len(shigatoxin_subtype) == 0: shigatoxin_subtype = "No complete subtype match found" report.write("%s" % shigatoxin_subtype) report.write("</p>\n") # Quality Check disclaimer = False sequence_qc_cov = 0 for x in range(7): if float(sequence_qc[x+1][2]) < 1: disclaimer = True sequence_qc_cov = sequence_qc_cov + float(sequence_qc[x+1][3]) if sequence_qc_cov < 210: disclaimer = True if disclaimer: 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") report.write("<hr/><h3>Raw data quality check</h3>\n") if args.input2: report.write("<p>FASTQC result forward: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id)) report.write("<p>FASTQC result reverse: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html2_id)) else: report.write("<p>FASTQC result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id)) if args.serotyping: report.write("<br/><hr/><h3>Serotyping</h3>\n") insertFileAsTable("blastn_OH_fc", report, True) report.write("<br/><hr/><h3>Multi Locus Sequence Typing</h3>\n") if len(sequence_typing) > 1: insertTable(sequence_typing, report, True) if args.virulotyping: report.write("<br/><hr/><h3>Virulotyping</h3>\n") 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)) insertFileAsTable("pathotyper_rep_tab", report, True, "table table-cross") if args.shigatoxintyping: report.write("<br/><hr/><h3>Shiga toxin typing</h3>\n") insertFileAsTable("blastn_shigatoxin_fct", report, True) # write tail html insertFile(TOOL_DIR + "/report_tail.html", report) finally: report.close() if __name__ == "__main__": __main__()