Mercurial > repos > mcharles > rapsodyn
changeset 29:7b8646f46010 draft
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} + }, + "inputs": [], + "name": "MPileup", + "outputs": [ + { + "name": "output_mpileup", + "type": "pileup" + }, + { + "name": "output_log", + "type": "txt" + } + ], + "position": { + "left": 1638.8333129882812, + "top": 221 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", + "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"0\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", + "tool_version": "0.0.3", + "type": "tool", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "input_pileup_file": { + "id": 10, + "output_name": "output_mpileup" + } + }, + "inputs": [], + "name": "PileupVariant", + "outputs": [ + { + "name": "output_pileup_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 1964.5999755859375, + "top": 221 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "PileupVariant", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\"}", + "tool_version": "1.01", + "type": "tool", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": { + "input_list1": { + "id": 11, + "output_name": "output_pileup_file" + }, + "input_list2": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "name": "listfiltering", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 2292.366668701172, + "top": 221 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "listfiltering", + "tool_state": "{\"__page__\": 0, \"input_list2\": \"null\", \"input_list1\": \"null\", \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"type\": \"\\\"specific\\\"\"}", + "tool_version": "1.01", + "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": 2561.133331298828, + "top": 221 + }, + "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": "1.01", + "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": 2888.8999938964844, + "top": 221 + }, + "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_variant_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 3190.6666870117188, + "top": 221 + }, + "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": "1.01", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input_file": { + "id": 15, + "output_name": "output_variant_file" + } + }, + "inputs": [], + "name": "mpileupfilterandstat", + "outputs": [ + { + "name": "output_file", + "type": "pileup" + }, + { + "name": "log_file", + "type": "txt" + } + ], + "position": { + "left": 3518.433349609375, + "top": 221 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "mpileupfilterandstat", + "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}", + "tool_version": "1.00", + "type": "tool", + "user_outputs": [] + }, + "17": { + "annotation": "", + "id": 17, + "input_connections": { + "input_files": [ + { + "id": 16, + "output_name": "log_file" + }, + { + "id": 15, + "output_name": "log_file" + }, + { + "id": 12, + "output_name": "log_file" + }, + { + "id": 11, + "output_name": "log_file" + }, + { + "id": 8, + "output_name": "log_file" + }, + { + "id": 5, + "output_name": "log_file" + } + ] + }, + "inputs": [], + "name": "MergeMultiFile", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 3846.199951171875, + "top": 221 + }, + "post_job_actions": { + "RenameDatasetActionoutput_file": { + "action_arguments": { + "newname": "LOGS" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_file" + } + }, + "tool_errors": null, + "tool_id": "MergeMultiFile", + "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", + "tool_version": "1.00", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeMultiFile.pl Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,15 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; + +my @files = split(/,/,$ARGV[0]); +for (my $i=0;$i<=$#files;$i++){ + + open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n"); + while (my $line = <IN>){ + print $line; + } + close (IN); +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeMultiFile.xml Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,34 @@ +<tool id="MergeMultiFile" name="MergeMultiFile" version="1.00"> +<description>Merge multiple files</description> +<command interpreter="perl"> + MergeMultiFile.pl $input_files > $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> + <option value="txt">txt</option> +</param> +<param name="input_files" type="data" format="txt,fastq,fastqsanger,fastqillumina,pileup,sam,fasta" multiple="true" label="Select suitable files 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/MergeSamFiles.pl Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,32 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; + +my $header_done = 0; +my @files = split(/,/,$ARGV[0]); +for (my $i=0;$i<=$#files;$i++){ + open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n"); + while (my $line = <IN>){ + if ($line =~ /^\@PG\s/){ + if ($header_done == 0){ + $header_done = 1; + print $line; + } + else { + } + } + elsif ($line =~ /^\@SQ\s/){ + if ($header_done == 0){ + print $line; + } + else { + } + } + else{ + print $line; + } + } + close (IN); +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeSamFiles.xml Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,18 @@ +<tool id="MergeSamFiles" name="MergeSamFiles" version="1.00"> +<description>Merge multiple SAM files</description> +<command interpreter="perl"> + MergeSamFiles.pl $input_files > $output_file +</command> +<inputs> +<param name="input_files" type="data" format="sam" multiple="true" label="Select suitable SAM files from your history"/> +</inputs> +<outputs> +<data name="output_file" format="sam" label="MERGE on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/ParseBlastForUniqueMatch.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,13 +1,26 @@ #!/usr/bin/perl +#V1.0.1 added log, option parameters use strict; use warnings; +use Getopt::Long; -my $input_variant_file = $ARGV[0]; -my $input_blast_file = $ARGV[1]; -my $window_length = $ARGV[2]; -my $nb_mismatch_max = $ARGV[3]; +my $input_variant_file; +my $input_blast_file; +my $log_file; +my $WINDOW_LENGTH= 50; +my $NB_MISMATCH_MAX = 3; +GetOptions ( +"input_variant_file=s" => \$input_variant_file, +"input_blast_file=s" => \$input_blast_file, +"window_length=s" => \$WINDOW_LENGTH, +"log_file=s" => \$log_file, +"nb_mismatch_max=s" => \$NB_MISMATCH_MAX +) or die("Error in command line arguments\n"); + +my $nb_variant_checked=0; +my $nb_variant_selected=0; my %hash_name; open(INB, $input_blast_file) or die ("Can't open $input_blast_file\n"); @@ -71,7 +84,7 @@ my $nb_gap_query=0; if (length($query_aln) == length($subject_aln)){ - if (length($query_aln)<$window_length-$nb_mismatch_max){ + if (length($query_aln)<$WINDOW_LENGTH-$NB_MISMATCH_MAX){ } else { my @q = split(//,$query_aln); @@ -79,27 +92,27 @@ for (my $i=0;$i<=$#q;$i++){ my $global_idx = $query_start-1+$i-$nb_gap_query; if ($q[$i] eq "-"){ - if ($global_idx < $window_length){ + if ($global_idx < $WINDOW_LENGTH){ $compt_mismatch_5p++; } - elsif ($global_idx > $window_length){ + elsif ($global_idx > $WINDOW_LENGTH){ $compt_mismatch_3p++; } $nb_gap_query++; #On compte les gap dans la query pour les soustraire de l'index global } else { if ($q[$i] ne $s[$i]){ - if ($global_idx < $window_length){ + if ($global_idx < $WINDOW_LENGTH){ $compt_mismatch_5p++; } - elsif ($global_idx > $window_length){ + elsif ($global_idx > $WINDOW_LENGTH){ $compt_mismatch_3p++; } } } } $compt_mismatch_5p += $query_start-1; - $compt_mismatch_3p += $window_length *2 + 1 - $query_stop; + $compt_mismatch_3p += $WINDOW_LENGTH *2 + 1 - $query_stop; # for (my $i=0;$i<$window_length;$i++){ # if ($tbl_q_aln[$i] eq "#"){ @@ -122,7 +135,7 @@ # else { # } # } - if (($compt_mismatch_5p <= $nb_mismatch_max)||($compt_mismatch_3p <= $nb_mismatch_max)){ + if (($compt_mismatch_5p <= $NB_MISMATCH_MAX)||($compt_mismatch_3p <= $NB_MISMATCH_MAX)){ $hash_name{$name}++; } @@ -151,6 +164,7 @@ open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); while (my $ligne = <INV>) { + $nb_variant_checked++; my @champs = split (/\s+/,$ligne); my $header = $champs[0]."_".$champs[1]; @@ -158,6 +172,7 @@ if ($hash_name{$header}){ if ($hash_name{$header}==1){ print $ligne; + $nb_variant_selected++; } } else { @@ -169,6 +184,12 @@ close(INV); +open (LF,">$log_file") or die("Can't open $log_file\n"); +print LF "\n####\t Blast filtering \n"; +print LF "Variant checked :\t$nb_variant_checked\n"; +print LF "Variant selected :\t$nb_variant_selected\n"; +close (LF); + # foreach my $key (sort keys %hash_name){ # print $key,"\t",$hash_name{$key},"\n";
--- a/rapsodyn/ParseBlastForUniqueMatch.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,16 +1,17 @@ -<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01"> +<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01"> <description>Filter mpileup with blast results</description> <command interpreter="perl"> - ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file + ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file </command> <inputs> -<param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> -<param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/> -<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> -<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/> + <param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> + <param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/> + <param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> + <param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/> </inputs> <outputs> - <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> </outputs> <help>
--- a/rapsodyn/PileupVariant.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/PileupVariant.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,19 +1,41 @@ #!/usr/bin/perl +#V1.0.1 added log, option parameters use strict; +use warnings; +use Getopt::Long; -my $inputfile = $ARGV[0]; -open(IF, $inputfile) or die("Can't open $inputfile\n"); +my $input_pileup_file; +my $output_pileup_file; +my $log_file; + +my $nb_base_covered=0; +my $nb_variant=0; +GetOptions ( +"input_pileup_file=s" => \$input_pileup_file, +"log_file=s" => \$log_file +) or die("Error in command line arguments\n"); + +open(IN, $input_pileup_file) or die ("Can't open $input_pileup_file\n"); #Extraction des variants my $nb_line=0; -while (my $line=<IF>){ - my $test = $line; - $test =~ s/\$//g; #the read start at this position - $test =~ s/\^.//g; #the read end at this position followed by quality char - my @field = split(/\s+/,$test); +while (my $line=<IN>){ + #print $line; + $nb_base_covered++; + $line =~ s/\$//g; #the read start at this position + $line =~ s/\^.//g; #the read end at this position followed by quality char + #print $line; + my @field = split(/\s+/,$line); if ($field[4]=~/[ATGCN]/i){ print $line; + $nb_variant++; } } -close(IF); +close(IN); + +open (LF,">$log_file") or die("Can't open $log_file\n"); +print LF "\n####\t Variant extraction \n"; +print LF "Position covered :\t$nb_base_covered\n"; +print LF "Variant detected :\t$nb_variant\n"; +close (LF);
--- a/rapsodyn/PileupVariant.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/PileupVariant.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,13 +1,14 @@ -<tool id="PileupVariant" name="PileupVariant" version="0.01"> +<tool id="PileupVariant" name="PileupVariant" version="1.01"> <description>Keep only mpileup line with variant</description> <command interpreter="perl"> - PileupVariant.pl $input_file > $output_file + PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file </command> <inputs> -<param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> + <param name="input_pileup_file" type="data" format="pileup" label="Select a suitable input file from your history"/> </inputs> <outputs> - <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> </outputs> <help>
--- a/rapsodyn/PrepareFastqLight.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,28 +1,51 @@ #!/usr/bin/perl +#V1.0.1 added log, option parameters use strict; use warnings; - -my $read1 = $ARGV[0]; -my $read2 = $ARGV[1]; +use Getopt::Long; -my $output1 = $ARGV[2]; -my $output2 = $ARGV[3]; +my $read1_file; +my $read2_file; +my $log_file; +my $output1_file; +my $output2_file; -my $TYPE = $ARGV[4]; -my $MIN_LENGTH = $ARGV[5]; -my $MIN_QUALITY = $ARGV[6]; +my $TYPE="sanger"; +my $MIN_LENGTH=30; +my $MIN_QUALITY=30; + +my $VERBOSE = "OFF"; -my $VERBOSE = $ARGV[7]; +GetOptions ( +"read1_file=s" => \$read1_file, +"read2_file=s" => \$read2_file, +"log_file=s" => \$log_file, +"output1_file=s" => \$output1_file, +"output2_file=s" => \$output2_file, +"type=s" => \$TYPE, +"min_length=i" => \$MIN_LENGTH, +"min_quality=i" => \$MIN_QUALITY, +"verbose=s" => \$VERBOSE +) or die("Error in command line arguments\n"); -if (!$VERBOSE){ - $VERBOSE ="OFF"; -} -open(READ1, $read1) or die ("Can't open $read1\n"); -open(READ2, $read2) or die ("Can't open $read2\n"); -open(OUT1, ">$output1") or die ("Can't open $output1\n"); -open(OUT2, ">$output2") or die ("Can't open $output2\n"); +my $nb_read1=0; +my $nb_base_read1=0; +my $nb_read2=0; +my $nb_base_read2=0; +my $nb_read1_t=0; +my $nb_base_read1_t=0; +my $nb_read2_t=0; +my $nb_base_read2_t=0; + +my $nb_base_current_t=0; + + +open(READ1, $read1_file) or die ("Can't open $read1_file\n"); +open(READ2, $read2_file) or die ("Can't open $read2_file\n"); +open(OUT1, ">$output1_file") or die ("Can't open $output1_file\n"); +open(OUT2, ">$output2_file") or die ("Can't open $output2_file\n"); my $error1=0; my $error2=0; @@ -43,6 +66,9 @@ my $ligne2_r2 =<READ2>; my $ligne3_r2 =<READ2>; my $ligne4_r2 =<READ2>; + + $nb_read1++; + $nb_read2++; #@ 1 sec if ((!$ligne1_r1)||(!$ligne2_r1)||(!$ligne3_r1)||(!$ligne4_r1)||(!$ligne1_r2)||(!$ligne2_r2)||(!$ligne3_r2)||(!$ligne4_r2)){ @@ -91,6 +117,7 @@ my $header2=""; my $repheader1=""; my $repheader2=""; + if ($ligne1_r1 =~/^\@(.*?)\#/){ $header1 = $1; @@ -190,9 +217,11 @@ ### Parsing sequence & qualité if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){ $seq1 = $1; + $nb_base_read1 += length($seq1); } if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){ $seq2 = $1; + $nb_base_read2 += length($seq2); } if ($ligne4_r1 =~ /^(.*)\s*$/i){ $qual1 = $1; @@ -236,147 +265,155 @@ else { my $fastq_lines_r1=""; my $fastq_lines_r2=""; + my $nb_base_current_read1_t = 0; + my $nb_base_current_read2_t = 0; + $fastq_lines_r1 = &grooming_and_trimming($ligne1_r1,$seq1,$qual1); + $nb_base_current_read1_t = $nb_base_current_t; if ($fastq_lines_r1){ $fastq_lines_r2 = &grooming_and_trimming($ligne1_r2,$seq2,$qual2); + $nb_base_current_read2_t = $nb_base_current_t; } if ($fastq_lines_r2){ print OUT1 $fastq_lines_r1; print OUT2 $fastq_lines_r2; + + $nb_read1_t++; + $nb_read2_t++; + $nb_base_read1_t += $nb_base_current_read1_t; + $nb_base_read2_t += $nb_base_current_read2_t; + + } } } - # print OUT1 $ligne1_r1; - # print OUT1 $ligne2_r1; - # print OUT1 $ligne3_r1; - # print OUT1 $ligne4_r1; - # print OUT2 $ligne1_r2; - # print OUT2 $ligne2_r2; - # print OUT2 $ligne3_r2; - # print OUT2 $ligne4_r2; - + #@ 7 sec } } - - close (READ1); close (READ2); close (OUT1); close (OUT2); - - +open (LF,">$log_file") or die("Can't open $log_file\n"); +print LF "\n####\t Fastq preparation \n"; +print LF "## Before preparation\n"; +print LF "#Read1 :\t$nb_read1\t#Base :\t$nb_base_read1\n"; +print LF "#Read2 :\t$nb_read2\t#Base :\t$nb_base_read2\n"; +print LF "## After preparation\n"; +print LF "#Read1 :\t$nb_read1_t\t#Base :\t$nb_base_read1_t\n"; +print LF "#Read2 :\t$nb_read2_t\t#Base :\t$nb_base_read2_t\n"; +close (LF); + sub grooming_and_trimming{ my $header = shift; my $seq = shift; my $quality = shift; my $quality_converted=""; + my $quality_ori=$quality; - my $startnoN = 0; - my $stopnoN = length($quality)-1; + my $lengthseq = length($seq); + my $startTrim = 0; + my $stopTrim = length($quality)-1; + my $startnoN = $startTrim; + my $stopnoN = $stopTrim; - #print "SEQ :\n$seq\n"; my $chercheN = $seq; - my @bad_position; + my @bad_position_N; + my @bad_position_Q; my $current_index = index($chercheN,"N"); my $abs_index = $current_index; while ($current_index >=0){ - push (@bad_position,$abs_index); + push (@bad_position_N,$abs_index); if ($current_index<length($seq)){ $chercheN = substr($chercheN,$current_index+1); $current_index = index($chercheN,"N"); - $abs_index = $current_index + $bad_position[$#bad_position]+1; + $abs_index = $current_index + $bad_position_N[$#bad_position_N]+1; } else { last; } } + + my @q = split(//,$quality); + for (my $i=0;$i<=$#q;$i++){ + my $chr = $q[$i]; + my $num = ord($q[$i]); + if ($TYPE eq "illumina"){ + $num = $num - 31; # 31 comme la difference entre la plage sanger (33-> 93 / 0->60) et illumina (64->104 / 0->40) + $quality_converted .= chr($num); + } + + if ($num < $MIN_QUALITY + 33){ #33 comme le départ de la plage sanger + push(@bad_position_Q,$i); + } + } + if ($quality_converted){$quality = $quality_converted;} + my @bad_position = (@bad_position_N, @bad_position_Q); if ($#bad_position>=0){ - my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)}; - $startnoN = $coord{"start"}; - $stopnoN = $coord{"stop"}; - } - my $lengthnoN = $stopnoN - $startnoN + 1; - my $seqnoN = substr($seq,$startnoN,$lengthnoN); - #print "$seqnoN\n"; - - if ($lengthnoN >= $MIN_LENGTH){ - my $startTrim = $startnoN; - my $stopTrim = $stopnoN; - - my $quality_converted=""; - my @bad_position; + @bad_position = sort {$a <=> $b} @bad_position; + my %coord=%{&extract_longer_string_coordinates_from_bad_position(0,$stopTrim,\@bad_position)}; + $startTrim = $coord{"start"}; + $stopTrim = $coord{"stop"}; +#print "$startTrim .. $stopTrim\n"; - my @q = split(//,$quality); - #print "QUALITY\n"; - #print "$quality\n"; - for (my $i=0;$i<=$stopnoN;$i++){ - my $chr = $q[$i]; - my $num = ord($q[$i]); - if ($TYPE eq "illumina"){ - $num = $num -64+33; - $quality_converted .= chr($num); - } - - if ($num <$MIN_QUALITY + 64 - 33 ){ - push(@bad_position,$i+$startnoN); - } - } - if ($quality_converted){$quality = $quality_converted;} - #print "$quality\n"; - - - - if ($#bad_position>=0){ - # for (my $i=0;$i<=$#bad_position;$i++){ - # print $bad_position[$i]."\t"; - # } - # print "\n"; - my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)}; - $startTrim = $coord{"start"}; - $stopTrim = $coord{"stop"}; - #print "$startTrim .. $stopTrim\n"; - - } - my $lengthTrim = $stopTrim - $startTrim +1; - - - my $fastq_lines=""; - - if ($lengthTrim >= $MIN_LENGTH){ - $fastq_lines .= $header; - $fastq_lines .= substr($seq,$startTrim,$lengthTrim)."\n"; - $fastq_lines .= "+\n"; - $fastq_lines .= substr($quality,$startTrim,$lengthTrim)."\n"; - return $fastq_lines; - } - else { - return ""; - } - - + } + my $lengthTrim = $stopTrim - $startTrim +1; + + #if ($stats_length{$lengthTrim}){ + # $stats_length{$lengthTrim} = 1; + #} + #else { + # $stats_length{$lengthTrim}++; + #} + my $fastq_lines=""; + +# if ($header =~ /GA8\-EAS671_0005\:3\:1\:1043\:4432/){ +# print "HEAD:\t$header"; +# print "SEQ:\n$seq\n"; +# print "$quality_ori\n"; +# print "$quality\n"; +# for (my $i=0;$i<=$#bad_position;$i++){ +# print $bad_position[$i]."(".$q[$bad_position[$i]]." : ".ord($q[$bad_position[$i]]).")"."\t"; +# } +# print "\n"; +# print "$startTrim .. $stopTrim / $lengthTrim \n"; +# print $fastq_lines; +# print "\n"; +# } + + #for (my $i=$startTrim;$i<=$stopTrim;$i++){ + # if ($stats_quality{ord($q{$i])}){ + # $stats_quality{ord($q{$i])}=1; + # } + # else { + # $stats_quality{ord($q{$i])}++; + # } + #} + + if ($lengthTrim >= $MIN_LENGTH){ + $fastq_lines .= $header; + my $new_seq = substr($seq,$startTrim,$lengthTrim); + $nb_base_current_t = length($new_seq); + $fastq_lines .= $new_seq."\n"; + $fastq_lines .= "+\n"; + my $new_q = substr($quality,$startTrim,$lengthTrim); + $fastq_lines .= $new_q."\n"; + return $fastq_lines; } else { + #print "Insufficient length after trimming\n"; return ""; } - - - # my @s = split(//,$seq); - # my $sanger_quality=""; - - - - - # return $sanger_quality; } sub extract_longer_string_coordinates_from_bad_position{
--- a/rapsodyn/PrepareFastqLight.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,21 +1,22 @@ -<tool id="PrepareFastqLight" name="PrepareFastqLight" version="0.01"> +<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01"> <description>Fastq preparation</description> <command interpreter="perl"> - PrepareFastqLight.pl $input_read1_file $input_read2_file $output_read1_file $output_read2_file $quality_type $min_quality $min_length + PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length </command> <inputs> -<param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> -<param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> -<param name="quality_type" type="select" label="Select input quality format"> - <option value="sanger">Sanger</option> - <option value="illumina">Illumina 1.3-1.7</option> - </param> -<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> -<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> + <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> + <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> + <param name="quality_type" type="select" label="Select input quality format"> + <option value="sanger">Sanger</option> + <option value="illumina">Illumina 1.3-1.7</option> + </param> + <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> + <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> </inputs> <outputs> -<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> -<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> + <data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> + <data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> </outputs> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile10x.pl Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,94 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; + +my $in = $ARGV[0]; +my $NB_LINE_GROUP = $ARGV[1]; +my $out1 = $ARGV[2]; +my $out2 = $ARGV[3]; +my $out3 = $ARGV[4]; +my $out4 = $ARGV[5]; +my $out5 = $ARGV[6]; +my $out6 = $ARGV[7]; +my $out7 = $ARGV[8]; +my $out8 = $ARGV[9]; +my $out9 = $ARGV[10]; +my $out10 = $ARGV[11]; + +my $file_nb = 1; + +my @in; +my $current_aggregate; +open(IN, $in) or die ("Can't open $in\n"); +while (my $line =<IN>){ + $current_aggregate = $line; + my $nb_line=1; + if ($NB_LINE_GROUP>1){ + while (my $add_line = <IN>){ + $current_aggregate .= $add_line; + $nb_line++; + if ($nb_line == $NB_LINE_GROUP){ + last; + } + } + } + push (@in,$current_aggregate); +} +close (IN); + +open (OUT1,">$out1") or die ("Can't open $out1"); +open (OUT2,">$out2") or die ("Can't open $out2"); +open (OUT3,">$out3") or die ("Can't open $out3"); +open (OUT4,">$out4") or die ("Can't open $out4"); +open (OUT5,">$out5") or die ("Can't open $out5"); +open (OUT6,">$out6") or die ("Can't open $out6"); +open (OUT7,">$out7") or die ("Can't open $out7"); +open (OUT8,">$out8") or die ("Can't open $out8"); +open (OUT9,">$out9") or die ("Can't open $out9"); +open (OUT10,">$out10") or die ("Can't open $out10"); + + +for (my $i=0;$i<=$#in;$i++){ + if ($i <= $#in * 1 /10){ + print OUT1 $in[$i]; + } + elsif ($i <= $#in* 2 /10){ + print OUT2 $in[$i]; + } + elsif ($i <= $#in*3/10){ + print OUT3 $in[$i]; + } + elsif ($i <= $#in*4/10){ + print OUT4 $in[$i]; + } + elsif ($i <= $#in*5/10){ + print OUT5 $in[$i]; + } + elsif ($i <= $#in*6/10){ + print OUT6 $in[$i]; + } + elsif ($i <= $#in*7/10){ + print OUT7 $in[$i]; + } + elsif ($i <= $#in*8/10){ + print OUT8 $in[$i]; + } + elsif ($i <= $#in*9/10){ + print OUT9 $in[$i]; + } + elsif ($i <= $#in*10/10){ + print OUT10 $in[$i]; + } + else { + + } + + +} +close (OUT1); +close (OUT2); +close (OUT3); +close (OUT4); + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile10x.xml Wed Oct 08 09:06:53 2014 -0400 @@ -0,0 +1,116 @@ +<tool id="SplitFile10x" name="SplitFile10x" version="1.00"> +<description>Split file in 10</description> +<command interpreter="perl"> + SplitFile10x.pl $input_file $line_number $output_file1 $output_file2 $output_file3 $output_file4 $output_file5 $output_file6 $output_file7 $output_file8 $output_file9 $output_file10 +</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_file" type="data" format="fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable input file from your history"/> +<param name="line_number" type="integer" value="4" label="Number of line read at a time before splitting"/> +</inputs> +<outputs> +<data name="output_file1" format="txt" label="PART1 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file2" format="txt" label="PART2 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file3" format="txt" label="PART3 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file4" format="txt" label="PART4 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file5" format="txt" label="PART5 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file6" format="txt" label="PART6 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file7" format="txt" label="PART7 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file8" format="txt" label="PART8 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file9" format="txt" label="PART9 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> +<data name="output_file10" format="txt" label="PART10 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="sam" format="sam" /> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastqsanger" format="fastqsanger" /> + </change_format> +</data> + +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/SplitFile2x.pl Wed Sep 10 08:10:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $in = $ARGV[0]; -my $NB_LINE_GROUP = $ARGV[1]; -my $NB_FILE = 2; -my $out1 = $ARGV[2]; -my $out2 = $ARGV[3]; - -if (!$NB_LINE_GROUP){ - $NB_LINE_GROUP=4; -} - -if (!$NB_FILE){ - $NB_FILE=2; -} - -my $file_nb = 1; - -my @in; -my $current_aggregate; -open(IN, $in) or die ("Can't open $in\n"); -while (my $line =<IN>){ - $current_aggregate = $line; - my $nb_line=1; - if ($NB_LINE_GROUP>1){ - while (my $add_line = <IN>){ - $current_aggregate .= $add_line; - $nb_line++; - if ($nb_line == $NB_LINE_GROUP){ - last; - } - } - } - push (@in,$current_aggregate); -} -close (IN); - -open (OUT1,">$out1") or die ("Can't open $out1"); -open (OUT2,">$out2") or die ("Can't open $out2"); - -for (my $i=0;$i<=$#in;$i++){ - if ($i <= $#in/2){ - print OUT1 $in[$i]; - } - else { - print OUT2 $in[$i]; - } - - -} -close (OUT1); -close (OUT2);
--- a/rapsodyn/SplitFile2x.xml Wed Sep 10 08:10:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<tool id="SplitFile2x" name="SplitFile2x" version="0.01"> -<description>Split file in 2</description> -<command interpreter="perl"> - SplitFile2x.pl $input_file $line_number $output_file1 $output_file2 -</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_file" type="data" format="fastq,fastqsanger,fastqillumina,pileup,sam,fasta" label="Select a suitable input file from your history"/> -<param name="line_number" type="integer" value="4" label="Number of line read at a time before splitting"/> -</inputs> -<outputs> -<data name="output_file1" format="txt" label="PART1 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="sam" format="sam" /> - <when input="out_format" value="fasta" format="fasta" /> - <when input="out_format" value="fastqsanger" format="fastqsanger" /> - </change_format> -</data> -<data name="output_file2" format="txt" label="PART2 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="sam" format="sam" /> - <when input="out_format" value="fasta" format="fasta" /> - <when input="out_format" value="fastqsanger" format="fastqsanger" /> - </change_format> -</data> - -</outputs> - -<help> - - - -</help> -</tool>
--- a/rapsodyn/extractseq.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/extractseq.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,5 +1,5 @@ #!/usr/bin/perl -#V1.10 +#V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+ use strict; use warnings; @@ -129,4 +129,4 @@ else { return $second; } -} \ No newline at end of file +}
--- a/rapsodyn/extractseq.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/extractseq.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="extractseq" name="extractseq" version="0.03"> +<tool id="extractseq" name="extractseq" version="1.01"> <description>Extract Sequence around variant position</description> <command interpreter="perl"> extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file
--- a/rapsodyn/fastaGroomerForMakeBlastdb.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,5 @@ #!/usr/bin/perl +#V1.0.0 my $inputfasta = $ARGV[0]; open(IB, $inputfasta) or die ("Can't open $inputfasta \n");
--- a/rapsodyn/fastaGroomerForMakeBlastdb.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01"> +<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="1.00"> <description>fasta Groomer For MakeBlastdb</description> <command interpreter="perl"> fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta
--- a/rapsodyn/filtersam_mapped_and_unique.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,23 +1,83 @@ #!/usr/bin/perl +#V1.0.1 added log, option parameters use strict; use warnings; +use Getopt::Long; -open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); +my $input_sam_file; +my $output_sam_file; +my $log_file; + +my %bitscore_all; +my %bitscore_selected; + +GetOptions ( +"input_sam_file=s" => \$input_sam_file, +"output_sam_file=s" => \$output_sam_file, +"log_file=s" => \$log_file +) or die("Error in command line arguments\n"); + +open(IN, $input_sam_file) or die ("Can't open $input_sam_file\n"); while (my $line=<IN>){ - if ($line =~ /^\@/){ + if (($line =~ /^\@SQ/)||($line =~ /^\@PG/)){ #Header conservation print $line; } else { #Optionnal flag verification + my @fields_all = split (/\s+/,$line); + my $bit = $fields_all[1]; + if ($bitscore_all{$bit}){ + $bitscore_all{$bit}++; + } + else { + $bitscore_all{$bit}=1; + } if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ - my @fields = split (/\s+/,$line); - if (($fields[1]==83)||($fields[1]==163)||($fields[1]==147)||($fields[1]==99)){ + my @fields_selected = split (/\s+/,$line); + if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){ print $line; + my $bit = $fields_selected[1]; + if ($bitscore_selected{$bit}){ + $bitscore_selected{$bit}++; + } + else { + $bitscore_selected{$bit}=1; + } } } } } +close (IN); -close (IN); \ No newline at end of file +open (LF,">$log_file") or die("Can't open $log_file\n"); +print LF "\n####\t Sam filtering \n"; +print LF "## Before filtering\n"; +print LF "bitscore\t:\t"; +foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { + print LF $key,"\t*\t"; +} +print LF "\n number \t:\t"; +foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { + print LF $bitscore_all{$key},"\t*\t"; +} +print LF "\n"; +print LF "## After filtering\n"; +print LF "bitscore\t:\t"; +foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { + print LF $key,"\t*\t"; +} +print LF "\n number \t:\t"; +foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { + print LF $bitscore_selected{$key},"\t*\t"; +} +print LF "\n"; +close (LF); + + + + + + +
--- a/rapsodyn/filtersam_mapped_and_unique.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,13 +1,14 @@ -<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="0.01"> +<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="1.01"> <description>Filter SAM file for uniq and well mapped pair-end reads</description> <command interpreter="perl"> - filtersam_mapped_and_unique.pl $input_sam_file > $output_file + filtersam_mapped_and_unique.pl -input_sam_file $input_sam_file -log_file $log_file> $output_sam_file </command> <inputs> -<param name="input_sam_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/> + <param name="input_sam_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/> </inputs> <outputs> - <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/> + <data name="output_sam_file" format="sam" label="${tool.name} on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> </outputs> <help>
--- a/rapsodyn/listfiltering.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/listfiltering.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,47 +1,51 @@ #!/usr/bin/perl +# v1.0.1 added log, and two different type of filtering (common / specific) use strict; use Getopt::Long; -my $inputfile; -my $headerfile; -my $nb_col=1; +my $list1_file; +my $list2_file; +my $log_file; +my $NB_COL=1; +my $TYPE = "common"; my %header; +my $nb_list1 = 0; +my $nb_list2 = 0; +my $nb_common = 0; -if ($#ARGV<0){ - print "\n"; - print "perl 021_ListFiltering.pl -input_file <file> -header_file <file> -nb_col <integer>[1]\n"; - exit(0); -} GetOptions ( -"input_file=s" => \$inputfile, -"header_file=s" => \$headerfile, -"nb_col=i" => \$nb_col +"list1_file=s" => \$list1_file, +"list2_file=s" => \$list2_file, +"log_file=s" => \$log_file, +"type=s" => \$TYPE, +"nb_col=i" => \$NB_COL ) or die("Error in command line arguments\n"); -open(HF, $headerfile) or die("Can't open $headerfile\n"); -while (my $line=<HF>){ +open(L2, $list2_file) or die("Can't open $list2_file\n"); +while (my $line=<L2>){ + $nb_list2++; chomp($line); my @fields = split(/\s+/,$line); my $ref=""; my $compt=0; - while ($compt<$nb_col){ + while ($compt<$NB_COL){ if ($ref){$ref.="\t";} $ref.=$fields[$compt]; $compt++; } - # my $ref = "$fields[0]\t$fields[1]"; $header{$ref}=$line; } -close (HF); +close (L2); -open(IF, $inputfile) or die("Can't open $inputfile\n"); -while (my $line=<IF>){ +open(L1, $list1_file) or die("Can't open $list1_file\n"); +while (my $line=<L1>){ + $nb_list1++; my @fields = split(/\s+/,$line); my $ref=""; my $compt=0; - while ($compt<$nb_col){ + while ($compt<$NB_COL){ if ($ref){$ref.="\t";} $ref.=$fields[$compt]; $compt++; @@ -49,13 +53,34 @@ # my $ref = "$fields[0]\t$fields[1]"; if ($header{$ref}){ - # print $line; - # print $header{$ref},"\n"; + $nb_common++; + if ($TYPE eq "common"){ + print $line; + } + elsif ($TYPE eq "specific") { + } + else { + } } else { - print $line; + if ($TYPE eq "common"){ + } + elsif ($TYPE eq "specific") { + print $line; + } + else { + } } } -close(IF); +my $nb_list1_only = $nb_list1 - $nb_common; +my $nb_list2_only = $nb_list2 - $nb_common; +close(L1); +open (LF,">$log_file") or die("Can't open $log_file\n"); +print LF "\n####\t List Filtering \n"; +print LF "#List 1 :\t$nb_list1 ($nb_list1_only)\n"; +print LF "#List 2 :\t$nb_list2 ($nb_list2_only)\n"; +print LF "#Common :\t$nb_common\n"; +close (LF); +
--- a/rapsodyn/listfiltering.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/listfiltering.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,15 +1,20 @@ -<tool id="listfiltering" name="listfiltering" version="0.01"> -<description>Compare listA and listB first X column and remove from listA the elements present in listB</description> +<tool id="listfiltering" name="listfiltering" version="1.01"> +<description>Compare list1 and list2</description> <command interpreter="perl"> - listfiltering.pl -input_file $input_listA -header_file $input_listB -nb_col $nb_col > $output_file + listfiltering.pl -list1_file $input_list1 -list2_file $input_list2 -nb_col $nb_col -type $type -log_file $log_file > $output_file </command> <inputs> -<param name="input_listA" type="data" format="pileup" label="Select a suitable input file from your history"/> -<param name="input_listB" type="data" format="txt" label="Select a suitable input file from your history"/> +<param name="input_list1" type="data" format="txt,pileup" label="Select list1 file from your history"/> +<param name="input_list2" type="data" format="txt,pileup" label="Select list2 file from your history"/> +<param name="type" type="select" label="Select type of filtering"> + <option value="specific">Only in list1</option> + <option value="common">Common</option> +</param> <param name="nb_col" type="integer" value="2" label="Number of column to compare"/> </inputs> <outputs> - <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> </outputs> <help>
--- a/rapsodyn/mpileupfilterandstat.pl Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.pl Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,5 @@ #!/usr/bin/perl +#V1.0.0 use strict; use Getopt::Long; @@ -29,6 +30,9 @@ my $ONLY_UNFILTERED_VARIANT="OFF"; my $DO_STAT="NO"; +my $nb_variant_checked=0; +my $nb_variant_selected=0; + my $STAT_MIN_DEPTH_MIN = 2; my $STAT_MIN_DEPTH_MAX = 10; @@ -83,6 +87,7 @@ #Extraction des variants my $nb_line=0; while (my $line=<IF>){ + $nb_variant_checked++; $nb_line++; if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){ print "$nb_line\n"; @@ -151,6 +156,7 @@ my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM); if ($error_code == 0){ print $line{"line"}; + $nb_variant_selected++; } else { push(@error,$error_code,"\t",$line{"line"}); @@ -159,8 +165,12 @@ ### LOG open(LF,">$logfile") or die ("Can't open $logfile\n"); - -if ($DO_STAT eq "YES"){ +print LF "\n####\t MPileup filtering \n"; +print LF "Variant checked :\t$nb_variant_checked\n"; +if ($DO_STAT eq "NO"){ + print LF "Variant selected :\t$nb_variant_selected\n"; +} +elsif ($DO_STAT eq "YES"){ for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){ for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){ for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ @@ -183,9 +193,9 @@ } -for (my $i=0;$i<=$#error;$i++){ - print LF $error[$i]; -} +#for (my $i=0;$i<=$#error;$i++){ +# print LF $error[$i]; +#} close (LF);
--- a/rapsodyn/mpileupfilterandstat.xml Wed Sep 10 08:10:38 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.xml Wed Oct 08 09:06:53 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08"> +<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00"> <description>Filter mpileup file entry</description> <command interpreter="perl"> #if $stat.do_stat=="YES" @@ -14,26 +14,26 @@ </command> <inputs> <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> -<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/> -<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/> -<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> +<param name="min_depth" type="integer" value="1" label="Minimum depth at variant position "/> +<param name="max_depth" type="integer" value="500" label="Maximum depth at variant position "/> +<param name="min_frequency" type="float" value="0" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/> -<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/> +<param name="min_distance" type="integer" value="0" label="Minimum physical distance between variant"/> <conditional name="stat"> <param name="do_stat" type="select" label="Compute stats "> <option value="NO">NO</option> <option value="YES">YES</option> </param> <when value="YES"> - <param name="stat_min_depth_min" type="integer" value = "2" label="min_depth - min" /> - <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" /> - <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" /> - <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" /> + <param name="stat_min_depth_min" type="integer" value = "4" label="min_depth - min" /> + <param name="stat_min_depth_max" type="integer" value = "20" label="min_depth - max" /> + <param name="stat_min_depth_step" type="integer" value = "4" label="min_depth - step" /> + <param name="stat_max_depth_min" type="integer" value = "200" label="max_depth - min" /> <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" /> <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" /> <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" /> <param name="stat_freq_max" type="float" value = "1" label="freq - max" /> - <param name="stat_freq_step" type="float" value = "0.1" label="freq - step" /> + <param name="stat_freq_step" type="float" value = "0.2" label="freq - step" /> <param name="stat_dist_min" type="integer" value = "0" label="dist - min" /> <param name="stat_dist_max" type="integer" value = "50" label="dist - max" /> <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />