Mercurial > repos > mcharles > rapsosnp
changeset 1:7f36bd129321 draft
Uploaded
author | mcharles |
---|---|
date | Wed, 10 Sep 2014 10:24:01 -0400 |
parents | 442a7c88b886 |
children | 761fecc07fa9 |
files | rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga 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/MergeFile2x.pl rapsodyn/MergeFile2x.xml rapsodyn/MergeFile4x.pl rapsodyn/MergeFile4x.xml rapsodyn/rapsosnp_stats.pl rapsodyn/rapsosnp_stats.xml |
diffstat | 12 files changed, 3534 insertions(+), 3168 deletions(-) [+] |
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28, + "output_name": "output_file4" + } + }, + "inputs": [], + "name": "ParseBlastForUniqueMatch", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + } + ], + "position": { + "left": 4281.5, + "top": 1305 + }, + "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": [] + }, + "41": { + "annotation": "", + "id": 41, + "input_connections": { + "input_file1": { + "id": 37, + "output_name": "output_file" + }, + "input_file2": { + "id": 38, + "output_name": "output_file" + }, + "input_file3": { + "id": 39, + "output_name": "output_file" + }, + "input_file4": { + "id": 40, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "MergeFile4x", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 4700, + "top": 841.8833312988281 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "MergeFile4x", + "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file4\": \"null\", \"input_file1\": \"null\", \"input_file2\": \"null\", \"input_file3\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + }, + "42": { + "annotation": "", + "id": 42, + "input_connections": { + "input_file": { + "id": 41, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "mpileupfilterandstat", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 5056, + "top": 886.8833312988281 + }, + "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\": \"\\\"0.8\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}", + "tool_version": "0.08", + "type": "tool", + "user_outputs": [] + }, + "43": { + "annotation": "", + "id": 43, + "input_connections": { + "input_blast_filtered_part1_file": { + "id": 37, + "output_name": "output_file" + }, + "input_blast_filtered_part2_file": { + "id": 38, + "output_name": "output_file" + }, + "input_blast_filtered_part3_file": { + "id": 39, + "output_name": "output_file" + }, + "input_blast_filtered_part4_file": { + "id": 40, + "output_name": "output_file" + }, + "input_list_filtered_file": { + "id": 27, + "output_name": "output_file" + }, + "input_mpileup_variant_file": { + "id": 26, + "output_name": "output_file" + }, + "input_read1_part1_trimmed_file": { + "id": 7, + "output_name": "output_read1_file" + }, + "input_read1_part2_trimmed_file": { + "id": 8, + "output_name": "output_read1_file" + }, + "input_read1_part3_trimmed_file": { + "id": 9, + "output_name": "output_read1_file" + }, + "input_read1_part4_trimmed_file": { + "id": 10, + "output_name": "output_read1_file" + }, + "input_read1_row_file": { + "id": 0, + "output_name": "output" + }, + "input_read2_part1_trimmed_file": { + "id": 7, + "output_name": "output_read2_file" + }, + "input_read2_part2_trimmed_file": { + "id": 8, + "output_name": "output_read2_file" + }, + "input_read2_part3_trimmed_file": { + "id": 9, + "output_name": "output_read2_file" + }, + "input_read2_part4_trimmed_file": { + "id": 10, + "output_name": "output_read2_file" + }, + "input_read2_row_file": { + "id": 1, + "output_name": "output" + }, + "input_sam_filtered_part1_file": { + "id": 16, + "output_name": "output_file" + }, + "input_sam_filtered_part2_file": { + "id": 17, + "output_name": "output_file" + }, + "input_sam_filtered_part3_file": { + "id": 18, + "output_name": "output_file" + }, + "input_sam_filtered_part4_file": { + "id": 19, + "output_name": "output_file" + }, + "input_sam_row_part1_file": { + "id": 12, + "output_name": "output" + }, + "input_sam_row_part2_file": { + "id": 13, + "output_name": "output" + }, + "input_sam_row_part3_file": { + "id": 14, + "output_name": "output" + }, + "input_sam_row_part4_file": { + "id": 15, + "output_name": "output" + }, + "input_snp_selected_file": { + "id": 42, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "rapsosnp_stats4x", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 5447.5, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "rapsosnp_stats4x", + "tool_state": "{\"input_blast_filtered_part2_file\": \"null\", \"input_blast_filtered_part3_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_read1_part4_trimmed_file\": \"null\", \"input_read1_part3_trimmed_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_mpileup_variant_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_blast_filtered_part1_file\": \"null\", \"input_sam_row_part4_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\", \"input_read2_part3_trimmed_file\": \"null\", \"input_read2_part4_trimmed_file\": \"null\", \"input_sam_filtered_part3_file\": \"null\", \"input_sam_filtered_part4_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_blast_filtered_part4_file\": \"null\", \"input_sam_row_part3_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeFile2x.pl Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,21 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $in1 = $ARGV[0]; +my $in2 = $ARGV[1]; + +open(IN1, $in1) or die ("Can't open $in1\n"); +while (my $line = <IN1>){ + print $line; +} +close (IN1); + +open(IN2, $in2) or die ("Can't open $in2\n"); +while (my $line = <IN2>){ + print $line; +} +close (IN2); + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeFile2x.xml Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,34 @@ +<tool id="MergeFile2x" name="MergeFile2x" version="0.01"> +<description>Merge splitted file</description> +<command interpreter="perl"> + MergeFile2x.pl $input_file1 $input_file2 > $output_file +</command> +<inputs> +<param name="out_format" type="select" label="Format"> + <option value="pileup">pileup</option> + <option value="fastq">fastq</option> + <option value="fastqsanger">fastqsanger</option> + <option value="sam">sam</option> + <option value="fasta">fasta</option> +</param> +<param name="input_file1" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 1st file from your history"/> +<param name="input_file2" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 2nd file from your history"/> +</inputs> +<outputs> +<data name="output_file" format="txt" label="MERGE"> + <change_format> + <when input="out_format" value="pileup" format="pileup" /> + <when input="out_format" value="fastq" format="fastq" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + <when input="out_format" value="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + </change_format> +</data> +</outputs> + +<help> + + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeFile4x.pl Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,34 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $in1 = $ARGV[0]; +my $in2 = $ARGV[1]; +my $in3 = $ARGV[2]; +my $in4 = $ARGV[3]; + +open(IN1, $in1) or die ("Can't open $in1\n"); +while (my $line = <IN1>){ + print $line; +} +close (IN1); + +open(IN2, $in2) or die ("Can't open $in2\n"); +while (my $line = <IN2>){ + print $line; +} +close (IN2); + +open(IN3, $in3) or die ("Can't open $in3\n"); +while (my $line = <IN3>){ + print $line; +} +close (IN3); + +open(IN4, $in4) or die ("Can't open $in4\n"); +while (my $line = <IN4>){ + print $line; +} +close (IN4); + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeFile4x.xml Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,36 @@ +<tool id="MergeFile4x" name="MergeFile4x" version="0.01"> +<description>Merge splitted file</description> +<command interpreter="perl"> + MergeFile4x.pl $input_file1 $input_file2 $input_file3 $input_file4 > $output_file +</command> +<inputs> +<param name="out_format" type="select" label="Format"> + <option value="pileup">pileup</option> + <option value="fastq">fastq</option> + <option value="fastqsanger">fastqsanger</option> + <option value="sam">sam</option> + <option value="fasta">fasta</option> +</param> +<param name="input_file1" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 1st file from your history"/> +<param name="input_file2" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 2nd file from your history"/> +<param name="input_file3" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 3rd file from your history"/> +<param name="input_file4" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable 4th file from your history"/> +</inputs> +<outputs> +<data name="output_file" format="txt" label="MERGE on ${on_string}"> + <change_format> + <when input="out_format" value="pileup" format="pileup" /> + <when input="out_format" value="fastq" format="fastq" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + <when input="out_format" value="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + </change_format> +</data> +</outputs> + +<help> + + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsosnp_stats.pl Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,215 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $read1_row = $ARGV[0]; +my $read2_row = $ARGV[1]; + +my $read1_trimmed = $ARGV[2]; +my $read2_trimmed = $ARGV[3]; + +my $sam_row = $ARGV[4]; +my $sam_filtered = $ARGV[5]; + +my $mpileup_variant = $ARGV[6]; + +my $list_filtered = $ARGV[7]; + +my $blast_filtered = $ARGV[8]; + +my $snp_selected = $ARGV[9]; + + +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(INR1T, $read1_trimmed) or die ("Can't open $read1_trimmed\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR1T>){ + my $line2 = <INR1T>; + my $line3 = <INR1T>; + my $line4 = <INR1T>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1T); + +open(INR2T, $read2_trimmed) or die ("Can't open $read2_trimmed\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2T>){ + my $line2 = <INR2T>; + my $line3 = <INR2T>; + my $line4 = <INR2T>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2T); + +print "\nSAM row\n"; +open(SAM, $sam_row) or die ("Can't open $sam_row\n"); +my %bitscore; +while (my $line=<SAM>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} + +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"; +close (SAM); + +print "\nSAM filtered\n"; +open(SAMF, $sam_filtered) or die ("Can't open $sam_filtered\n"); +undef %bitscore; +while (my $line=<SAMF>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} + +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"; +close (SAMF); + +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(BF, $blast_filtered) or die ("Can't open $blast_filtered\n"); +$nbvariant=0; +while (my $line=<BF>){ + $nbvariant++; +} + +print "Variant selected :\t$nbvariant\n"; +close (BF); + + +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_stats.xml Wed Sep 10 10:24:01 2014 -0400 @@ -0,0 +1,26 @@ +<tool id="rapsosnp_stats" name="rapsosnp_stats" version="0.01"> +<description>Merge best results from Blast</description> +<command interpreter="perl"> + rapsosnp_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_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_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/> +<param name="input_read2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/> +<param name="input_sam_row_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/> +<param name="input_sam_filtered_file" type="data" format="sam" label="Select a suitable input SAM 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_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED 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>