--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EURL_VTEC_WGS_PT.py	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,347 @@
+# -*- 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__()
+
+