Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt
comparison EURL_VTEC_WGS_PT.py @ 0:965517909457 draft
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
| author | cstrittmatter |
|---|---|
| date | Wed, 22 Jan 2020 08:41:44 -0500 |
| parents | |
| children | 0cbed1c0a762 |
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| -1:000000000000 | 0:965517909457 |
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| 1 # -*- coding: utf-8 -*- | |
| 2 """ | |
| 3 ############################################################################ | |
| 4 # Istituto Superiore di Sanita' | |
| 5 # European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) | |
| 6 # Developer: Arnold Knijn arnold.knijn@iss.it | |
| 7 ############################################################################ | |
| 8 """ | |
| 9 | |
| 10 import argparse | |
| 11 import sys | |
| 12 import os | |
| 13 import HTML | |
| 14 import datetime | |
| 15 import fileinput | |
| 16 | |
| 17 BASE_URL = 'https://galaxytrakr.org' | |
| 18 TOOL_DIR = os.path.dirname(os.path.abspath(__file__)) | |
| 19 | |
| 20 def insertFile(filename, report): | |
| 21 with open(filename) as html_in: | |
| 22 for line in html_in: | |
| 23 report.write(line) | |
| 24 | |
| 25 def insertFileAsTable(filename, report, hasheader=False, tabclass="table table-rep"): | |
| 26 with open(filename) as table_in: | |
| 27 table_data = [[str(col) for col in row.split('\t')] for row in table_in] | |
| 28 insertTable(table_data, report, hasheader, tabclass) | |
| 29 | |
| 30 def insertTable(table_data, report, hasheader=False, tabclass="table table-rep"): | |
| 31 if hasheader: | |
| 32 htmlcode = HTML.table(table_data[1:], attribs={'class':tabclass}, header_row=table_data[0]) | |
| 33 else: | |
| 34 htmlcode = HTML.table(table_data, attribs={'class':tabclass}) | |
| 35 report.write(htmlcode) | |
| 36 | |
| 37 def openFileAsTable(filename): | |
| 38 with open(filename) as table_in: | |
| 39 table_data = [[str(col) for col in row.split('\t')] for row in table_in] | |
| 40 return table_data | |
| 41 | |
| 42 def __main__(): | |
| 43 parser = argparse.ArgumentParser() | |
| 44 parser.add_argument('--serotyping', dest='serotyping', help='perform serotyping', action='store_true') | |
| 45 parser.add_argument('--virulotyping', dest='virulotyping', help='perform virulotyping', action='store_true') | |
| 46 parser.add_argument('--shigatoxintyping', dest='shigatoxintyping', help='perform shigatoxintyping', action='store_true') | |
| 47 parser.add_argument('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format') | |
| 48 parser.add_argument('--input1_ext', dest='input1_ext', help='extension of forward or single-end reads file in Sanger FASTQ format') | |
| 49 parser.add_argument('--input1_name', dest='input1_name', help='name of forward or single-end reads file in Sanger FASTQ format') | |
| 50 parser.add_argument('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format') | |
| 51 parser.add_argument('--input2_ext', dest='input2_ext', help='extension of reverse reads file in Sanger FASTQ format') | |
| 52 parser.add_argument('--input2_name', dest='input2_name', help='name of reverse reads file in Sanger FASTQ format') | |
| 53 parser.add_argument('--html1', dest='html1', help='html FASTQC file') | |
| 54 parser.add_argument('--html1_id', dest='html1_id', help='html FASTQC file id') | |
| 55 parser.add_argument('--html1_path', dest='html1_path', help='html FASTQC file path') | |
| 56 parser.add_argument('--text1', dest='text1', help='text FASTQC file') | |
| 57 parser.add_argument('--html2', dest='html2', help='html FASTQC file') | |
| 58 parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id') | |
| 59 parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path') | |
| 60 parser.add_argument('--text2', dest='text2', help='text FASTQC file') | |
| 61 parser.add_argument('--trimmed1', dest='trimmed1', help='trimmed forward FASTQ file') | |
| 62 parser.add_argument('--trimmed2', dest='trimmed2', help='trimmed reverse FASTQ file') | |
| 63 parser.add_argument('--trimmedunpaired', dest='trimmedunpaired', help='trimmed unpaired FASTQ file') | |
| 64 parser.add_argument('--log', dest='logfile', help='log file') | |
| 65 parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads') | |
| 66 parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id') | |
| 67 parser.add_argument('--blastn_STX', dest='blastn_STX', help='Blastn for Shiga toxin') | |
| 68 parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table') | |
| 69 parser.add_argument('--spades_log', dest='spades_log', help='SPAdes log') | |
| 70 parser.add_argument('--blastn_O', dest='blastn_O', help='Blastn for O') | |
| 71 parser.add_argument('--blastn_H', dest='blastn_H', help='Blastn for H') | |
| 72 parser.add_argument('--output', dest='output', help='output report html file') | |
| 73 args = parser.parse_args() | |
| 74 | |
| 75 os.system("printf 'EURL VTEC WGS PT v2.3\n\nTool versions\n=============\n' > " + args.logfile) | |
| 76 if args.input2: | |
| 77 # FASTQC | |
| 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") | |
| 79 os.system("rm -r " + args.html1_path) | |
| 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") | |
| 81 os.system("rm -r " + args.html2_path) | |
| 82 os.system("fastqc -v >> " + args.logfile) | |
| 83 # TRIMMING | |
| 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) | |
| 85 os.system("ln -s " + args.trimmed1 + " input_1.fq") | |
| 86 os.system("ln -s " + args.trimmed2 + " input_2.fq") | |
| 87 os.system("printf '\nfastq_positional_quality_trimming v1.0\n' >> " + args.logfile) | |
| 88 os.system("printf 'parameters: maxlt=300, lt=17, rt=0, minqt=25, avgqt=27.0, minlf=-1\n' >> " + args.logfile) | |
| 89 if args.virulotyping: | |
| 90 # VIRULOTYPER | |
| 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'") | |
| 92 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper) | |
| 93 os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile) | |
| 94 os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile) | |
| 95 os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile) | |
| 96 if args.shigatoxintyping: | |
| 97 # SHIGATOXIN FILTERING | |
| 98 os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq") | |
| 99 os.system(TOOL_DIR + "/scripts/duk -m filtered2STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_2.fq") | |
| 100 os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq filtered2STX.fq") | |
| 101 os.system(TOOL_DIR + "/scripts/fastq_pair filtered1STX.fq.single.fq input_2.fq") | |
| 102 os.system(TOOL_DIR + "/scripts/fastq_pair filtered2STX.fq.single.fq input_1.fq") | |
| 103 os.system("cat filtered1STX.fq.paired.fq > filtered1STX_paired.fq") | |
| 104 os.system("cat filtered1STX.fq.single.fq.paired.fq >> filtered1STX_paired.fq") | |
| 105 os.system("cat input_1.fq.paired.fq >> filtered1STX_paired.fq") | |
| 106 os.system("cat filtered2STX.fq.paired.fq > filtered2STX_paired.fq") | |
| 107 os.system("cat input_2.fq.paired.fq >> filtered2STX_paired.fq") | |
| 108 os.system("cat filtered2STX.fq.single.fq.paired.fq >> filtered2STX_paired.fq") | |
| 109 os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile) | |
| 110 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) | |
| 111 # SHIGATOXIN ASSEMBLY: SPADES | |
| 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") | |
| 113 os.system("spades.py -v >> " + args.logfile) | |
| 114 os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile) | |
| 115 # SHIGATOXIN NCBI BLAST+ blastn | |
| 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") | |
| 117 os.system("blastn -version >> " + args.logfile) | |
| 118 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) | |
| 119 os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile) | |
| 120 # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT | |
| 121 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct") | |
| 122 os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc") | |
| 123 shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc") | |
| 124 os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct") | |
| 125 if os.stat('blastn_shigatoxin_fc').st_size == 0: | |
| 126 os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") | |
| 127 # SEQUENCETYPER | |
| 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") | |
| 129 os.system("mv mentalist_out.byvote " + args.mlstsevenloci) | |
| 130 sequence_typing = openFileAsTable(args.mlstsevenloci) | |
| 131 sequence_qc = openFileAsTable("mentalist_out.coverage.txt") | |
| 132 os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile) | |
| 133 os.system("mentalist -v | grep MentaLiST >> " + args.logfile) | |
| 134 os.system("printf '\n' >> " + args.logfile) | |
| 135 os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile) | |
| 136 if args.serotyping: | |
| 137 # SEROTYPE FILTERING | |
| 138 os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq") | |
| 139 os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq") | |
| 140 os.system("cat filteredO1.fq > filteredOH1.fq") | |
| 141 os.system("cat filteredH1.fq >> filteredOH1.fq") | |
| 142 os.system(TOOL_DIR + "/scripts/duk -m filteredO2.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_2.fq") | |
| 143 os.system(TOOL_DIR + "/scripts/duk -m filteredH2.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_2.fq") | |
| 144 os.system("cat filteredO2.fq > filteredOH2.fq") | |
| 145 os.system("cat filteredH2.fq >> filteredOH2.fq") | |
| 146 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq filteredOH2.fq") | |
| 147 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH1.fq.single.fq input_2.fq") | |
| 148 os.system(TOOL_DIR + "/scripts/fastq_pair filteredOH2.fq.single.fq input_1.fq") | |
| 149 os.system("cat filteredOH1.fq.paired.fq > filteredOH1_paired.fq") | |
| 150 os.system("cat filteredOH1.fq.single.fq.paired.fq >> filteredOH1_paired.fq") | |
| 151 os.system("cat input_1.fq.paired.fq >> filteredOH1_paired.fq") | |
| 152 os.system("cat filteredOH2.fq.paired.fq > filteredOH2_paired.fq") | |
| 153 os.system("cat input_2.fq.paired.fq >> filteredOH2_paired.fq") | |
| 154 os.system("cat filteredOH2.fq.single.fq.paired.fq >> filteredOH2_paired.fq") | |
| 155 os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile) | |
| 156 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) | |
| 157 # SEROTYPE ASSEMBLY: SPADES | |
| 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") | |
| 159 os.system("spades.py -v >> " + args.logfile) | |
| 160 os.system("printf 'parameters: careful, k=21,33,55, pe1-ff, pe1-1, pe1-2\n\n' >> " + args.logfile) | |
| 161 # SEROTYPE NCBI BLAST+ blastn | |
| 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") | |
| 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") | |
| 164 os.system("blastn -version >> " + args.logfile) | |
| 165 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) | |
| 166 os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile) | |
| 167 # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT | |
| 168 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc") | |
| 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") | |
| 170 sero_typing_o = openFileAsTable("blastn_O_fc") | |
| 171 os.system("cat blastn_O_fc >> blastn_OH_fc") | |
| 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") | |
| 173 sero_typing_h = openFileAsTable("blastn_H_fc") | |
| 174 os.system("cat blastn_H_fc >> blastn_OH_fc") | |
| 175 if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0: | |
| 176 os.system("echo '-\t-\t-\t-' >> blastn_OH_fc") | |
| 177 else: | |
| 178 # FASTQC | |
| 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") | |
| 180 os.system("rm -r " + args.html1_path) | |
| 181 os.system("fastqc -v >> " + args.logfile) | |
| 182 # TRIMMING | |
| 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") | |
| 184 os.system("ln -s " + args.trimmed1 + " input_1.fq") | |
| 185 os.system("echo 'fastq_positional_quality_trimming v1.0' >> " + args.logfile) | |
| 186 os.system("printf 'parameters: maxlt=360, lt=10, rt=0, minqt=25, avgqt=27.0, minlf=50\n' >> " + args.logfile) | |
| 187 if args.virulotyping: | |
| 188 # VIRULOTYPER | |
| 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'") | |
| 190 os.system("cat pathotyper_rep_tot_tab > " + args.virulotyper) | |
| 191 os.system("printf '\n\nViruloTyper\n===========\npatho_typing v0.3\n' >> " + args.logfile) | |
| 192 os.system("printf 'parameters: minGeneCoverage=90, minGeneIdentity=90, minGeneDepth=15\n\n' >> " + args.logfile) | |
| 193 os.system("cat " + TOOL_DIR + "/data/ViruloTyping_db.txt >> " + args.logfile) | |
| 194 if args.shigatoxintyping: | |
| 195 # SHIGATOXIN FILTERING | |
| 196 os.system(TOOL_DIR + "/scripts/duk -m filtered1STX.fq -k 23 " + TOOL_DIR + "/data/stx.fa input_1.fq") | |
| 197 os.system("printf '\n\nShigatoxinTyper\n===============\nduk v20110303\n' >> " + args.logfile) | |
| 198 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) | |
| 199 # SHIGATOXIN ASSEMBLY: SPADES | |
| 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") | |
| 201 os.system("spades.py -v >> " + args.logfile) | |
| 202 os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile) | |
| 203 # SHIGATOXIN NCBI BLAST+ blastn | |
| 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") | |
| 205 os.system("blastn -version >> " + args.logfile) | |
| 206 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) | |
| 207 os.system("cat " + TOOL_DIR + "/data/ShigatoxinTyping_db.txt >> " + args.logfile) | |
| 208 # SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT | |
| 209 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_shigatoxin_fct") | |
| 210 os.system("awk -F '\t' '($3>99 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' " + args.blastn_STX + " > blastn_shigatoxin_fc") | |
| 211 shigatoxin_typing = openFileAsTable("blastn_shigatoxin_fc") | |
| 212 os.system("cat blastn_shigatoxin_fc >> blastn_shigatoxin_fct") | |
| 213 if os.stat('blastn_shigatoxin_fc').st_size == 0: | |
| 214 os.system("echo '-\t-\t-\t-' >> blastn_shigatoxin_fct") | |
| 215 # SEQUENCETYPER | |
| 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") | |
| 217 os.system("mv mentalist_out.byvote " + args.mlstsevenloci) | |
| 218 sequence_typing = openFileAsTable(args.mlstsevenloci) | |
| 219 sequence_qc = openFileAsTable("mentalist_out.coverage.txt") | |
| 220 os.system("printf '\n\nSequenceTyper\n=============\n' >> " + args.logfile) | |
| 221 os.system("mentalist -v | grep MentaLiST >> " + args.logfile) | |
| 222 os.system("printf '\n' >> " + args.logfile) | |
| 223 os.system("cat " + TOOL_DIR + "/data/SequenceTyping_db.txt >> " + args.logfile) | |
| 224 if args.serotyping: | |
| 225 # SEROTYPE FILTERING | |
| 226 os.system(TOOL_DIR + "/scripts/duk -m filteredO1.fq -k 23 " + TOOL_DIR + "/data/O_type.fsa input_1.fq") | |
| 227 os.system(TOOL_DIR + "/scripts/duk -m filteredH1.fq -k 23 " + TOOL_DIR + "/data/H_type.fsa input_1.fq") | |
| 228 os.system("cat filteredO1.fq > filteredOH1.fq") | |
| 229 os.system("cat filteredH1.fq >> filteredOH1.fq") | |
| 230 os.system("printf '\n\nSeroTyper\n=========\nduk v20110303\n' >> " + args.logfile) | |
| 231 os.system("printf 'parameters: k=23\n\n' >> " + args.logfile) | |
| 232 # SEROTYPE ASSEMBLY: SPADES | |
| 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") | |
| 234 os.system("spades.py -v >> " + args.logfile) | |
| 235 os.system("printf 'parameters: careful, k=21,33,55, iontorrent, pe1-ff, pe1-s\n\n' >> " + args.logfile) | |
| 236 # SEROTYPE NCBI BLAST+ blastn | |
| 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") | |
| 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") | |
| 239 os.system("blastn -version >> " + args.logfile) | |
| 240 os.system("printf 'parameters: evalue=0.001, strand=both, dust=yes, max_target_seqs=10, perc_identity=95.0\n\n' >> " + args.logfile) | |
| 241 os.system("cat " + TOOL_DIR + "/data/SeroTyping_db.txt >> " + args.logfile) | |
| 242 # SEROTYPER: FILTER, CUT AND CONCATENATE BLASTN OUTPUT | |
| 243 os.system("echo 'sseqid\tpident\tlength\tpositive' > blastn_OH_fc") | |
| 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") | |
| 245 sero_typing_o = openFileAsTable("blastn_O_fc") | |
| 246 os.system("cat blastn_O_fc >> blastn_OH_fc") | |
| 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") | |
| 248 sero_typing_h = openFileAsTable("blastn_H_fc") | |
| 249 os.system("cat blastn_H_fc >> blastn_OH_fc") | |
| 250 if os.stat('blastn_O_fc').st_size == 0 and os.stat('blastn_H_fc').st_size == 0: | |
| 251 os.system("echo '-\t-\t-\t-' >> blastn_OH_fc") | |
| 252 try: | |
| 253 report = open(args.output, 'w') | |
| 254 # write head html | |
| 255 insertFile(TOOL_DIR + "/report_head.html", report) | |
| 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"))) | |
| 257 insertFile(TOOL_DIR + "/report_head2.html", report) | |
| 258 # write results | |
| 259 report.write("<h3>Summary</h3>\n") | |
| 260 if args.serotyping: | |
| 261 report.write("<p>Serotype: ") | |
| 262 if len(sero_typing_o) == 0: | |
| 263 report.write("O?") | |
| 264 else: | |
| 265 report.write("%s" % sero_typing_o[0][0][sero_typing_o[0][0].rfind("O"):]) | |
| 266 if len(sero_typing_h) == 0: | |
| 267 report.write(":H?") | |
| 268 else: | |
| 269 report.write(":%s" % sero_typing_h[0][0][sero_typing_h[0][0].rfind("H"):]) | |
| 270 report.write("</p>\n") | |
| 271 report.write("<p>Sequence type: ") | |
| 272 if len(sequence_typing) < 2: | |
| 273 report.write("Sequence typing failed") | |
| 274 elif sequence_typing[1][1] == "failed": | |
| 275 report.write("Sequence typing failed") | |
| 276 else: | |
| 277 report.write("ST%s" % sequence_typing[1][8]) | |
| 278 report.write("</p>\n") | |
| 279 if args.virulotyping: | |
| 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") | |
| 281 for line in fileinput.input("virulotyper_rep", inplace=True): | |
| 282 print line.replace("1a", "1"), | |
| 283 for line in fileinput.input("virulotyper_rep", inplace=True): | |
| 284 print line.replace("2a", "2"), | |
| 285 for line in fileinput.input("virulotyper_rep", inplace=True): | |
| 286 print line.replace("1b", "1"), | |
| 287 for line in fileinput.input("virulotyper_rep", inplace=True): | |
| 288 print line.replace("2b", "2"), | |
| 289 report.write("<p>Virulotypes: ") | |
| 290 insertFile("virulotyper_rep", report) | |
| 291 report.write("</p>\n") | |
| 292 if args.shigatoxintyping: | |
| 293 report.write("<p>Stx Subtypes: ") | |
| 294 if len(shigatoxin_typing) == 0: | |
| 295 report.write("No subtype match found") | |
| 296 else: | |
| 297 shigatoxin_subtype = "" | |
| 298 shigatoxin_types = openFileAsTable(TOOL_DIR + "/data/stx_subtypes") | |
| 299 for subtype in shigatoxin_typing: | |
| 300 blast_pident_100 = float(subtype[1]) == 100 | |
| 301 if (blast_pident_100): | |
| 302 for item in shigatoxin_types: | |
| 303 if item[0] == subtype[0]: | |
| 304 shigatoxin_subtype = item[1] + " " + shigatoxin_subtype | |
| 305 if len(shigatoxin_subtype) == 0: | |
| 306 shigatoxin_subtype = "No complete subtype match found" | |
| 307 report.write("%s" % shigatoxin_subtype) | |
| 308 report.write("</p>\n") | |
| 309 # Quality Check | |
| 310 disclaimer = False | |
| 311 sequence_qc_cov = 0 | |
| 312 for x in range(7): | |
| 313 if float(sequence_qc[x+1][2]) < 1: | |
| 314 disclaimer = True | |
| 315 sequence_qc_cov = sequence_qc_cov + float(sequence_qc[x+1][3]) | |
| 316 if sequence_qc_cov < 210: | |
| 317 disclaimer = True | |
| 318 if disclaimer: | |
| 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") | |
| 320 report.write("<hr/><h3>Raw data quality check</h3>\n") | |
| 321 if args.input2: | |
| 322 report.write("<p>FASTQC result forward: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id)) | |
| 323 report.write("<p>FASTQC result reverse: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html2_id)) | |
| 324 else: | |
| 325 report.write("<p>FASTQC result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id)) | |
| 326 if args.serotyping: | |
| 327 report.write("<br/><hr/><h3>Serotyping</h3>\n") | |
| 328 insertFileAsTable("blastn_OH_fc", report, True) | |
| 329 report.write("<br/><hr/><h3>Multi Locus Sequence Typing</h3>\n") | |
| 330 if len(sequence_typing) > 1: | |
| 331 insertTable(sequence_typing, report, True) | |
| 332 if args.virulotyping: | |
| 333 report.write("<br/><hr/><h3>Virulotyping</h3>\n") | |
| 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)) | |
| 335 insertFileAsTable("pathotyper_rep_tab", report, True, "table table-cross") | |
| 336 if args.shigatoxintyping: | |
| 337 report.write("<br/><hr/><h3>Shiga toxin typing</h3>\n") | |
| 338 insertFileAsTable("blastn_shigatoxin_fct", report, True) | |
| 339 # write tail html | |
| 340 insertFile(TOOL_DIR + "/report_tail.html", report) | |
| 341 finally: | |
| 342 report.close() | |
| 343 | |
| 344 if __name__ == "__main__": | |
| 345 __main__() | |
| 346 | |
| 347 |