Mercurial > repos > mcharles > rapsosnp
changeset 2:761fecc07fa9 draft
Uploaded
| author | mcharles |
|---|---|
| date | Thu, 11 Sep 2014 03:10:47 -0400 |
| parents | 7f36bd129321 |
| children | 9332b9da7491 |
| files | rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-1x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_4x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.17.ga rapsodyn/rapsosnp_stats2x.pl rapsodyn/rapsosnp_stats2x.xml rapsodyn/rapsosnp_stats4x.pl rapsodyn/rapsosnp_stats4x.xml |
| diffstat | 8 files changed, 1418 insertions(+), 3168 deletions(-) [+] |
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+ "name": "listfiltering", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 2235, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "listfiltering", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "input_assembly_file": { + "id": 0, + "output_name": "output" + }, + "input_variant_file": { + "id": 12, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "extractseq", + "outputs": [ + { + "name": "output_file", + "type": "fasta" + } + ], + "position": { + "left": 2563, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "extractseq", + "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}", + "tool_version": "0.03", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "db_opts|histdb": { + "id": 6, + "output_name": "outfile" + }, + "query": { + "id": 13, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "NCBI BLAST+ blastn", + "outputs": [ + { + "name": "output1", + "type": "tabular" + } + ], + "position": { + "left": 2891, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00", + "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}", + "tool_version": "0.1.00", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "input_blast_file": { + "id": 14, + "output_name": "output1" + }, + "input_variant_file": { + "id": 12, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "ParseBlastForUniqueMatch", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 3193, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "ParseBlastForUniqueMatch", + "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input_file": { + "id": 15, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "mpileupfilterandstat", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 3521, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "mpileupfilterandstat", + "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"1.0\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"50\\\"\"}", + "tool_version": "0.08", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "input_blast_filtered_file": { + "id": 15, + "output_name": "output_file" + }, + "input_list_filtered_file": { + "id": 12, + "output_name": "output_file" + }, + "input_mpileup_variant_file": { + "id": 11, + "output_name": "output_file" + }, + "input_read1_row_file": { + "id": 1, + "output_name": "output" + }, + "input_read1_trimmed_file": { + "id": 5, + "output_name": "output_read1_file" + }, + "input_read2_row_file": { + "id": 2, + "output_name": "output" + }, + "input_read2_trimmed_file": { + "id": 5, + "output_name": "output_read2_file" + }, + "input_sam_filtered_file": { + "id": 8, + "output_name": "output_file" + }, + "input_sam_row_file": { + "id": 7, + "output_name": "output" + }, + "input_snp_selected_file": { + "id": 16, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "rapsosnp_stats", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 3849, + "top": 200 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "rapsosnp_stats", + "tool_state": "{\"input_read1_trimmed_file\": \"null\", \"__page__\": 0, \"input_read2_trimmed_file\": \"null\", \"input_sam_row_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_sam_filtered_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\", \"input_blast_filtered_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsosnp_stats2x.pl Thu Sep 11 03:10:47 2014 -0400 @@ -0,0 +1,307 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $read1_row = $ARGV[0]; +my $read2_row = $ARGV[1]; + +my $read1_trimmed_part1 = $ARGV[2]; +my $read1_trimmed_part2 = $ARGV[3]; +my $read2_trimmed_part1 = $ARGV[4]; +my $read2_trimmed_part2 = $ARGV[5]; + +my $sam_row_part1 = $ARGV[6]; +my $sam_row_part2 = $ARGV[7]; +my $sam_filtered_part1 = $ARGV[8]; +my $sam_filtered_part2 = $ARGV[9]; + +my $mpileup_variant = $ARGV[10]; + +my $list_filtered = $ARGV[11]; + +my $blast_filtered_part1 = $ARGV[12]; +my $blast_filtered_part2 = $ARGV[13]; + +my $snp_selected = $ARGV[14]; + + +open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); +my $nbread=0; +my $nbbase =0; +while (my $line1=<INR1R>){ + my $line2 = <INR1R>; + my $line3 = <INR1R>; + my $line4 = <INR1R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1R); + + + + +open(INR2R, $read2_row) or die ("Can't open $read2_row\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2R>){ + my $line2 = <INR2R>; + my $line3 = <INR2R>; + my $line4 = <INR2R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2R); + + + + + +open(INR1TP1, $read1_trimmed_part1) or die ("Can't open $read1_trimmed_part1\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR1TP1>){ + my $line2 = <INR1TP1>; + my $line3 = <INR1TP1>; + my $line4 = <INR1TP1>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP1); +open(INR1TP2, $read1_trimmed_part2) or die ("Can't open $read1_trimmed_part2\n"); +while (my $line1=<INR1TP2>){ + my $line2 = <INR1TP2>; + my $line3 = <INR1TP2>; + my $line4 = <INR1TP2>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP2); +print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; + + + + +open(INR2TP1, $read2_trimmed_part1) or die ("Can't open $read2_trimmed_part1\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2TP1>){ + my $line2 = <INR2TP1>; + my $line3 = <INR2TP1>; + my $line4 = <INR2TP1>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP2); +open(INR2TP2, $read2_trimmed_part2) or die ("Can't open $read2_trimmed_part2\n"); +while (my $line1=<INR2TP2>){ + my $line2 = <INR2TP2>; + my $line3 = <INR2TP2>; + my $line4 = <INR2TP2>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP2); +print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; + + + + +print "\nSAM row\n"; +open(SAMP1, $sam_row_part1) or die ("Can't open $sam_row_part1\n"); +my %bitscore; +while (my $line=<SAMP1>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP1); +open(SAMP2, $sam_row_part2) or die ("Can't open $sam_row_part2\n"); +while (my $line=<SAMP2>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP2); +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; + + + + +print "\nSAM filtered\n"; +open(SAMFP1, $sam_filtered_part1) or die ("Can't open $sam_filtered_part1\n"); +undef %bitscore; +while (my $line=<SAMFP1>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP1); +open(SAMFP2, $sam_filtered_part2) or die ("Can't open $sam_filtered_part2\n"); +while (my $line=<SAMFP2>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP2); +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; + + + + +print "\nMPILEUP variant\n"; +open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n"); +my $nbvariant=0; +while (my $line=<MPV>){ + my @fields = split(/\s+/,$line); + if ($#fields >= 4){ + my $match = $fields[4]; + $match =~ s/\$//g; #the read start at this position + $match =~ s/\^.//g; #the read end at this position followed by quality char + if ($match =~/[ACGTNacgtn]+/){ + $nbvariant++; + } + } + else { + #print STDERR "Erreur : $line\n"; + } +} +print "Variant detected :\t$nbvariant\n"; +close (MPV); + + + + + + +print "\nMPILEUP filtered without dubious position\n"; +open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); +$nbvariant=0; +while (my $line=<LF>){ + $nbvariant++; +} +print "Variant selected :\t$nbvariant\n"; +close (LF); + + + + + +print "\nMPILEUP filtered without dubious position and BLAST\n"; +open(BFP1, $blast_filtered_part1) or die ("Can't open $blast_filtered_part1\n"); +$nbvariant=0; +while (my $line=<BFP1>){ + $nbvariant++; +} +close (BFP1); +open(BFP2, $blast_filtered_part2) or die ("Can't open $blast_filtered_part2\n"); +while (my $line=<BFP2>){ + $nbvariant++; +} +close (BFP2); +print "Variant selected :\t$nbvariant\n"; + + + + + +print "\nSNP selected after mpileup filtering : \t"; +open(SNP, $snp_selected) or die ("Can't open $snp_selected\n"); +$nbvariant=0; +while (my $line=<SNP>){ + $nbvariant++; +} + +print "$nbvariant\n"; +close (SNP); + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsosnp_stats2x.xml Thu Sep 11 03:10:47 2014 -0400 @@ -0,0 +1,31 @@ +<tool id="rapsosnp_stats2x" name="rapsosnp_stats2x" version="0.01"> +<description>Stats for rapsosnp workflow</description> +<command interpreter="perl"> + rapsosnp_stats2x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_snp_selected_file > $output_file +</command> +<inputs> +<param name="input_read1_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/> +<param name="input_read2_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/> +<param name="input_read1_part1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART1 TRIMMED file from your history"/> +<param name="input_read1_part2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART2 TRIMMED file from your history"/> +<param name="input_read2_part1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART1 TRIMMED file from your history"/> +<param name="input_read2_part2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART2 TRIMMED file from your history"/> +<param name="input_sam_row_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/> +<param name="input_sam_row_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/> +<param name="input_sam_filtered_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/> +<param name="input_sam_filtered_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/> +<param name="input_mpileup_variant_file" type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/> +<param name="input_list_filtered_file" type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/> +<param name="input_blast_filtered_part1_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/> +<param name="input_blast_filtered_part2_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/> +<param name="input_snp_selected_file" type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="STATS"/> +</outputs> + + +<help> + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsosnp_stats4x.pl Thu Sep 11 03:10:47 2014 -0400 @@ -0,0 +1,447 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $read1_row = $ARGV[0]; +my $read2_row = $ARGV[1]; + +my $read1_trimmed_part1 = $ARGV[2]; +my $read1_trimmed_part2 = $ARGV[3]; +my $read1_trimmed_part3 = $ARGV[4]; +my $read1_trimmed_part4 = $ARGV[5]; +my $read2_trimmed_part1 = $ARGV[6]; +my $read2_trimmed_part2 = $ARGV[7]; +my $read2_trimmed_part3 = $ARGV[8]; +my $read2_trimmed_part4 = $ARGV[9]; + +my $sam_row_part1 = $ARGV[10]; +my $sam_row_part2 = $ARGV[11]; +my $sam_row_part3 = $ARGV[12]; +my $sam_row_part4 = $ARGV[13]; +my $sam_filtered_part1 = $ARGV[14]; +my $sam_filtered_part2 = $ARGV[15]; +my $sam_filtered_part3 = $ARGV[16]; +my $sam_filtered_part4 = $ARGV[17]; + +my $mpileup_variant = $ARGV[18]; + +my $list_filtered = $ARGV[19]; + +my $blast_filtered_part1 = $ARGV[20]; +my $blast_filtered_part2 = $ARGV[21]; +my $blast_filtered_part3 = $ARGV[22]; +my $blast_filtered_part4 = $ARGV[23]; + +my $snp_selected = $ARGV[24]; + + +open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); +my $nbread=0; +my $nbbase =0; +while (my $line1=<INR1R>){ + my $line2 = <INR1R>; + my $line3 = <INR1R>; + my $line4 = <INR1R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1R); + + + + +open(INR2R, $read2_row) or die ("Can't open $read2_row\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2R>){ + my $line2 = <INR2R>; + my $line3 = <INR2R>; + my $line4 = <INR2R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2R); + + + + + +open(INR1TP1, $read1_trimmed_part1) or die ("Can't open $read1_trimmed_part1\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR1TP1>){ + my $line2 = <INR1TP1>; + my $line3 = <INR1TP1>; + my $line4 = <INR1TP1>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP1); +open(INR1TP2, $read1_trimmed_part2) or die ("Can't open $read1_trimmed_part2\n"); +while (my $line1=<INR1TP2>){ + my $line2 = <INR1TP2>; + my $line3 = <INR1TP2>; + my $line4 = <INR1TP2>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP2); +open(INR1TP3, $read1_trimmed_part3) or die ("Can't open $read1_trimmed_part3\n"); +while (my $line1=<INR1TP3>){ + my $line2 = <INR1TP3>; + my $line3 = <INR1TP3>; + my $line4 = <INR1TP3>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP3); +open(INR1TP4, $read1_trimmed_part4) or die ("Can't open $read1_trimmed_part4\n"); +while (my $line1=<INR1TP4>){ + my $line2 = <INR1TP4>; + my $line3 = <INR1TP4>; + my $line4 = <INR1TP4>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR1TP4); +print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; + + + + +open(INR2TP1, $read2_trimmed_part1) or die ("Can't open $read2_trimmed_part1\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2TP1>){ + my $line2 = <INR2TP1>; + my $line3 = <INR2TP1>; + my $line4 = <INR2TP1>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP2); +open(INR2TP2, $read2_trimmed_part2) or die ("Can't open $read2_trimmed_part2\n"); +while (my $line1=<INR2TP2>){ + my $line2 = <INR2TP2>; + my $line3 = <INR2TP2>; + my $line4 = <INR2TP2>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP2); +open(INR2TP3, $read2_trimmed_part3) or die ("Can't open $read2_trimmed_part3\n"); +while (my $line1=<INR2TP3>){ + my $line2 = <INR2TP3>; + my $line3 = <INR2TP3>; + my $line4 = <INR2TP3>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP3); +open(INR2TP4, $read2_trimmed_part4) or die ("Can't open $read2_trimmed_part4\n"); +while (my $line1=<INR2TP4>){ + my $line2 = <INR2TP4>; + my $line3 = <INR2TP4>; + my $line4 = <INR2TP4>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +close (INR2TP4); +print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; + + + + +print "\nSAM row\n"; +open(SAMP1, $sam_row_part1) or die ("Can't open $sam_row_part1\n"); +my %bitscore; +while (my $line=<SAMP1>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP1); +open(SAMP2, $sam_row_part2) or die ("Can't open $sam_row_part2\n"); +while (my $line=<SAMP2>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP2); +open(SAMP3, $sam_row_part3) or die ("Can't open $sam_row_part3\n"); +while (my $line=<SAMP3>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP3); +open(SAMP4, $sam_row_part4) or die ("Can't open $sam_row_part4\n"); +while (my $line=<SAMP4>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMP4); +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; + + + + +print "\nSAM filtered\n"; +open(SAMFP1, $sam_filtered_part1) or die ("Can't open $sam_filtered_part1\n"); +undef %bitscore; +while (my $line=<SAMFP1>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP1); +open(SAMFP2, $sam_filtered_part2) or die ("Can't open $sam_filtered_part2\n"); +while (my $line=<SAMFP2>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP2); +open(SAMFP3, $sam_filtered_part3) or die ("Can't open $sam_filtered_part3\n"); +while (my $line=<SAMFP3>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP3); +open(SAMFP4, $sam_filtered_part4) or die ("Can't open $sam_filtered_part4\n"); +while (my $line=<SAMFP4>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} +close (SAMFP4); +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; + + + + +print "\nMPILEUP variant\n"; +open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n"); +my $nbvariant=0; +while (my $line=<MPV>){ + my @fields = split(/\s+/,$line); + if ($#fields >= 4){ + my $match = $fields[4]; + $match =~ s/\$//g; #the read start at this position + $match =~ s/\^.//g; #the read end at this position followed by quality char + if ($match =~/[ACGTNacgtn]+/){ + $nbvariant++; + } + } + else { + #print STDERR "Erreur : $line\n"; + } +} +print "Variant detected :\t$nbvariant\n"; +close (MPV); + + + + + + +print "\nMPILEUP filtered without dubious position\n"; +open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); +$nbvariant=0; +while (my $line=<LF>){ + $nbvariant++; +} +print "Variant selected :\t$nbvariant\n"; +close (LF); + + + + + +print "\nMPILEUP filtered without dubious position and BLAST\n"; +open(BFP1, $blast_filtered_part1) or die ("Can't open $blast_filtered_part1\n"); +$nbvariant=0; +while (my $line=<BFP1>){ + $nbvariant++; +} +close (BFP1); +open(BFP2, $blast_filtered_part2) or die ("Can't open $blast_filtered_part2\n"); +while (my $line=<BFP2>){ + $nbvariant++; +} +close (BFP2); +open(BFP3, $blast_filtered_part3) or die ("Can't open $blast_filtered_part3\n"); +while (my $line=<BFP3>){ + $nbvariant++; +} +close (BFP3); +open(BFP4, $blast_filtered_part4) or die ("Can't open $blast_filtered_part4\n"); +while (my $line=<BFP4>){ + $nbvariant++; +} +close (BFP4); +print "Variant selected :\t$nbvariant\n"; + + + + + +print "\nSNP selected after mpileup filtering : \t"; +open(SNP, $snp_selected) or die ("Can't open $snp_selected\n"); +$nbvariant=0; +while (my $line=<SNP>){ + $nbvariant++; +} + +print "$nbvariant\n"; +close (SNP); + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsosnp_stats4x.xml Thu Sep 11 03:10:47 2014 -0400 @@ -0,0 +1,47 @@ +<tool id="rapsosnp_stats4x" name="rapsosnp_stats4x" version="0.01"> +<description>Stats for rapsosnp workflow</description> +<command interpreter="perl"> + rapsosnp_stats4x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read1_part3_trimmed_file $input_read1_part4_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_read2_part3_trimmed_file $input_read2_part4_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_row_part3_file $input_sam_row_part4_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_sam_filtered_part3_file $input_sam_filtered_part4_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_blast_filtered_part3_file $input_blast_filtered_part4_file $input_snp_selected_file > $output_file +</command> +<inputs> +<param name="input_read1_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/> +<param name="input_read2_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/> + +<param name="input_read1_part1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART1 TRIMMED file from your history"/> +<param name="input_read1_part2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART2 TRIMMED file from your history"/> +<param name="input_read1_part3_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART3 TRIMMED file from your history"/> +<param name="input_read1_part4_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART4 TRIMMED file from your history"/> +<param name="input_read2_part1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART1 TRIMMED file from your history"/> +<param name="input_read2_part2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART2 TRIMMED file from your history"/> +<param name="input_read2_part3_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART3 TRIMMED file from your history"/> +<param name="input_read2_part4_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART4 TRIMMED file from your history"/> + +<param name="input_sam_row_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/> +<param name="input_sam_row_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/> +<param name="input_sam_row_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 file from your history"/> +<param name="input_sam_row_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 file from your history"/> +<param name="input_sam_filtered_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/> +<param name="input_sam_filtered_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/> +<param name="input_sam_filtered_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 FILTERED file from your history"/> +<param name="input_sam_filtered_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 FILTERED file from your history"/> + + +<param name="input_mpileup_variant_file" type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/> +<param name="input_list_filtered_file" type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/> + +<param name="input_blast_filtered_part1_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/> +<param name="input_blast_filtered_part2_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/> +<param name="input_blast_filtered_part3_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART3 file from your history"/> +<param name="input_blast_filtered_part4_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART4 file from your history"/> + +<param name="input_snp_selected_file" type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="STATS"/> +</outputs> + + +<help> + +</help> +</tool>