--- a/EURL_VTEC_WGS_PT.py	Wed Jan 22 09:10:12 2020 -0500
+++ b/EURL_VTEC_WGS_PT.py	Tue Jan 28 10:42:31 2020 -0500
@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 ############################################################################
@@ -44,6 +45,7 @@
     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('--amrtyping', dest='amrtyping', help='perform amrtyping', 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')
@@ -58,197 +60,106 @@
     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('--stx', dest='stx', help='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('--amr', dest='amr', help='SPAdes log')
+    parser.add_argument('--amr_id', dest='amr_id', help='AMR file id')
+    parser.add_argument('--antigen_O', dest='antigen_O', help='Antigen for O')
+    parser.add_argument('--antigen_H', dest='antigen_H', help='Antigen 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)
+    log = open(args.logfile, 'w')
+    log.write("EURL VTEC WGS PT v3.0\n\nTool versions\n=============\n")
     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)
+        log.write(os.popen("fastqc -v").read())
         # 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)
+        os.system("python " + TOOL_DIR + "/scripts/fastq_positional_quality_trimming.py -1 " + args.input1 + " --maxlt 300 --lt 17 --rt 0 --minqt 25 --avgqt 27.0 --minlf -1 --trimmed1 input_t1.fq --log trimming_logfile -2 " + args.input2 + " --trimmed2 input_t2.fq --trimmedunpaired trimmedunpaired")
+        log.write("\nfastq_positional_quality_trimming v1.0\n")
+        log.write("parameters: maxlt=300, lt=17, rt=0, minqt=25, avgqt=27.0, minlf=-1\n")
+        if args.shigatoxintyping or args.serotyping:
+            # ASSEMBLY
+            os.system("perl " + TOOL_DIR + "/scripts/spades.pl contigs.fa spades_contig_stats spades_scaffolds spades_scaffold_stats spades_log NODE spades.py --disable-gzip-output --isolate -t \${GALAXY_SLOTS:-16} --pe1-ff --pe1-1 fastq:input_t1.fq --pe1-2 fastq:input_t2.fq")
+            log.write(os.popen("spades.py -v").read())
+            log.write("parameters: --isolate, pe1-ff, pe1-1, pe1-2\n\n")
         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("perl " + TOOL_DIR + "/scripts/patho_typing.pl 'python " + TOOL_DIR + "/scripts/patho_typing.py -s Escherichia coli -f " + args.input1 + " " + args.input2 + " -o output_dir -j 1 --minGeneCoverage 90 --minGeneIdentity 90 --minGeneDepth 15'")
             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")
+            log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n")
+            log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n")
+            log.write(os.popen("cat " +  TOOL_DIR + "/data/ViruloTyping_db.txt").read())
     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)
+        log.write(os.popen("fastqc -v").read())
         # 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)
+        os.system("python " + TOOL_DIR + "/scripts/fastq_positional_quality_trimming.py -1 " + args.input1 + " --maxlt 360 --lt 10 --rt 0 --minqt 25 --avgqt 27.0 --minlf 50 --trimmed1 input_t1.fq --log trimming_logfile")
+        log.write("\nfastq_positional_quality_trimming v1.0\n")
+        log.write("parameters: maxlt=360, lt=10, rt=0, minqt=25, avgqt=27.0, minlf=50\n")
+        if args.shigatoxintyping or args.serotyping:
+            # ASSEMBLY
+            os.system("perl " + TOOL_DIR + "/scripts/spades.pl contigs.fa spades_contig_stats spades_scaffolds spades_scaffold_stats spades_log NODE spades.py --disable-gzip-output --isolate -t ${GALAXY_SLOTS:-16} --iontorrent -s fastq:input_t1.fq")
+            log.write(os.popen("spades.py -v").read())
+            log.write("parameters: --isolate, --iontorrent\n\n")
         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("perl " + TOOL_DIR + "/scripts/patho_typing.pl 'python " + TOOL_DIR + "/scripts/patho_typing.py -s Escherichia coli -f " + args.input1 + " -o output_dir -j 1 --minGeneCoverage 90 --minGeneIdentity 90 --minGeneDepth 15'")
             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")
+            log.write("\n\nViruloTyper\n===========\npatho_typing v1.0\n")
+            log.write("parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n")
+            log.write(os.popen("cat " +  TOOL_DIR + "/data/ViruloTyping_db.txt").read())
+    # SEQUENCETYPER
+    if args.input2:
+        os.system("mentalist call --output_votes -o 'mentalist_out' --db '" + TOOL_DIR + "/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_t1.fq -2 input_t2.fq")
+    else:
+        os.system("mentalist call --output_votes -o 'mentalist_out' --db '" + TOOL_DIR + "/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld' -1 input_t1.fq")
+    os.system("mv mentalist_out.byvote " + args.mlstsevenloci)
+    sequence_typing = openFileAsTable(args.mlstsevenloci)
+    sequence_qc = openFileAsTable("mentalist_out.coverage.txt")
+    log.write("\n\nSequenceTyper\n=============\n")
+    log.write(os.popen("mentalist -v | grep MentaLiST").read())
+    log.write("\n")
+    log.write(os.popen("cat " +  TOOL_DIR + "/data/SequenceTyping_db.txt").read())
+    if args.shigatoxintyping:
+        # SHIGATOXIN TYPER
+        os.system("echo 'sseqid\tpident\tlength\tpositive' > mmseqs_shigatoxin_fct")
+        os.system("mmseqs easy-search --search-type 3 --format-output query,target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/stxDB mmseqs_STX /tmp")
+        os.system(TOOL_DIR + "/scripts/extract_shigatoxin.sh")
+        os.system("cat mmseqs_shigatoxin_fc >> mmseqs_shigatoxin_fct")
+        shigatoxin_typing = openFileAsTable("mmseqs_shigatoxin_fc")
+        log.write("\n\nShigatoxinTyper\n=============\n")
+        log.write(os.popen("cat " +  TOOL_DIR + "/data/ShigatoxinTyping_db.txt").read())
+    if args.serotyping:        
+        # SEROTYPER
+        os.system("echo 'sseqid\tpident\tlength\tpositive' > mmseqs_OH_fc")
+        # SEROTYPER O
+        os.system("mmseqs easy-search --search-type 3 --format-output target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/O_typeDB mmseqs_O /tmp")
+        os.system("awk -F '\t' '($3>800 && $4>800) { print $1 FS $2 FS $3 FS $4 }' mmseqs_O | sort -nrk 2 -nrk 3 > mmseqs_O_fc")
+        sero_typing_o = openFileAsTable("mmseqs_O_fc")
+        os.system("cat mmseqs_O_fc >> mmseqs_OH_fc")
+        # SEROTYPER H
+        os.system("mmseqs easy-search --search-type 3 --format-output target,pident,alnlen,tlen contigs.fa " + TOOL_DIR + "/data/H_typeDB mmseqs_H /tmp")
+        os.system("awk -F '\t' '($3>800 && $4>800) { print $1 FS $2 FS $3 FS $4 }' mmseqs_H | sort -nrk 2 -nrk 3 > mmseqs_H_fc")
+        sero_typing_h = openFileAsTable("mmseqs_H_fc")
+        os.system("cat mmseqs_H_fc >> mmseqs_OH_fc")    
+        if os.stat('mmseqs_O_fc').st_size == 0 and os.stat('mmseqs_H_fc').st_size == 0:
+            os.system("echo '-\t-\t-\t-' >> mmseqs_OH_fc")
+        log.write("\n\nSeroTyper\n=============\n")
+        log.write(os.popen("cat " +  TOOL_DIR + "/data/SeroTyping_db.txt").read())
+    if args.amrtyping:
+        # AMRGENES
+        os.system("amrfinder --threads 4 --database " + TOOL_DIR + "/data/amrfinder -n contigs.fa -O Escherichia -o " + args.amr)
+    # REPORT
     try:
         report = open(args.output, 'w')
         # write head html
@@ -279,13 +190,13 @@
         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"),
+                print(line.replace("1a", "1"),)
             for line in fileinput.input("virulotyper_rep", inplace=True):
-                print line.replace("2a", "2"),
+                print(line.replace("2a", "2"),)
             for line in fileinput.input("virulotyper_rep", inplace=True):
-                print line.replace("1b", "1"),
+                print(line.replace("1b", "1"),)
             for line in fileinput.input("virulotyper_rep", inplace=True):
-                print line.replace("2b", "2"),
+                print(line.replace("2b", "2"),)
             report.write("<p>Virulotypes: ")
             insertFile("virulotyper_rep", report)
             report.write("</p>\n")
@@ -325,7 +236,7 @@
             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)
+            insertFileAsTable("mmseqs_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)
@@ -335,7 +246,10 @@
             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)
+            insertFileAsTable("mmseqs_shigatoxin_fct", report, True)
+        if args.amrtyping:
+            report.write("<br/><hr/><h3>AMR typing</h3>\n")
+            report.write("<p>AMR result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.amr_id))
         # write tail html
         insertFile(TOOL_DIR + "/report_tail.html", report)
     finally:
@@ -343,5 +257,3 @@
 
 if __name__ == "__main__":
     __main__()
-
-