Mercurial > repos > mcharles > rapsodyn
changeset 24:e8e6b962c1f2 draft
Uploaded
| author | mcharles |
|---|---|
| date | Fri, 05 Sep 2014 06:12:10 -0400 |
| parents | edddaa8ab855 |
| children | 39376c7204be |
| files | rapsodyn/Galaxy-Workflow-Rapsodyn_v1.34.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.34_-_Filtering.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.34_-_Preparation___Mapping.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.13.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.13_-_2x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.13_-_4x.ga rapsodyn/PileupVariant.pl rapsodyn/PileupVariant.xml rapsodyn/PrepareFastqLight.pl rapsodyn/PrepareFastqLight.xml rapsodyn/SplitFile2x.pl rapsodyn/SplitFile2x.xml rapsodyn/SplitFile4x.pl rapsodyn/SplitFile4x.xml rapsodyn/mpileupfilter.pl rapsodyn/mpileupfilter.xml rapsodyn/mpileupfilterandstat.pl rapsodyn/mpileupfilterandstat.xml rapsodyn/rapsodyn_stats.pl rapsodyn/rapsodyn_stats.xml rapsodyn/rapsodyn_stats_filtering.pl rapsodyn/rapsodyn_stats_filtering.xml rapsodyn/rapsodyn_stats_mapping.pl rapsodyn/rapsodyn_stats_mapping.xml rapsodyn/repository_dependencies.xml |
| diffstat | 25 files changed, 4109 insertions(+), 2515 deletions(-) [+] |
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\"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": "0.07", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PileupVariant.pl Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,19 @@ +#!/usr/bin/perl +use strict; + +my $inputfile = $ARGV[0]; +open(IF, $inputfile) or die("Can't open $inputfile\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); + + if ($field[4]=~/[ATGCN]/i){ + print $line; + } +} +close(IF);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PileupVariant.xml Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,18 @@ +<tool id="PileupVariant" name="PileupVariant" version="0.01"> +<description>Keep only mpileup line with variant</description> +<command interpreter="perl"> + PileupVariant.pl $input_file > $output_file +</command> +<inputs> +<param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PrepareFastqLight.pl Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,420 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $read1 = $ARGV[0]; +my $read2 = $ARGV[1]; + +my $output1 = $ARGV[2]; +my $output2 = $ARGV[3]; + +my $TYPE = $ARGV[4]; +my $MIN_LENGTH = $ARGV[5]; +my $MIN_QUALITY = $ARGV[6]; + +my $VERBOSE = $ARGV[7]; + +if (!$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 $error1=0; +my $error2=0; +my $error3=0; +my $error4=0; +my $error5=0; +my $error6=0; +my $error7=0; +my $error8=0; +my $error9=0; +my $error10=0; + +while (my $ligne1_r1 =<READ1>){ + my $ligne2_r1 =<READ1>; + my $ligne3_r1 =<READ1>; + my $ligne4_r1 =<READ1>; + my $ligne1_r2 =<READ2>; + my $ligne2_r2 =<READ2>; + my $ligne3_r2 =<READ2>; + my $ligne4_r2 =<READ2>; + +#@ 1 sec + if ((!$ligne1_r1)||(!$ligne2_r1)||(!$ligne3_r1)||(!$ligne4_r1)||(!$ligne1_r2)||(!$ligne2_r2)||(!$ligne3_r2)||(!$ligne4_r2)){ + if ($VERBOSE eq "ON"){ + print "Error in file format"; + if ($ligne1_r1){print $ligne1_r1;} + if ($ligne2_r1){print $ligne2_r1;} + if ($ligne3_r1){print $ligne3_r1;} + if ($ligne4_r1){print $ligne4_r1;} + if ($ligne1_r2){print $ligne1_r2;} + if ($ligne2_r2){print $ligne2_r2;} + if ($ligne3_r2){print $ligne3_r2;} + if ($ligne4_r2){print $ligne4_r2;} + print "\n"; + } + $error1++; + } + elsif(($ligne1_r1 !~/^\@/)||($ligne1_r2 !~/^\@/)||($ligne3_r1 !~/^\+/)||($ligne3_r2 !~/^\+/)){ + if ($VERBOSE eq "ON"){ + print "Error in header : format\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error2++; + } +#@ 1 - 2 sec + else { + + my $length_seq1 = length($ligne2_r1); + my $length_qual1 =length($ligne4_r1); + my $seq1; + my $qual1; + + my $length_seq2 = length($ligne2_r2); + my $length_qual2 =length($ligne4_r2); + my $seq2; + my $qual2; + my $header1=""; + my $header2=""; + my $repheader1=""; + my $repheader2=""; + + if ($ligne1_r1 =~/^\@(.*?)\#/){ + $header1 = $1; + } + + if ($ligne3_r1 =~/^\+(.*?)\#/){ + $repheader1 = $1; + } + + if ($ligne1_r2 =~/^\@(.*?)\#/){ + $header2 = $1; + } + + if ($ligne3_r2 =~/^\+(.*?)\#/){ + $repheader2 = $1; + } +#@ 2 sec + + ### Verification de la coherence sequence /qualité @ 1 sec + if (($TYPE eq "illumina")&&((!$header1)||(!$header2)||(!$repheader1)||(!$repheader2))){ + if ($VERBOSE eq "ON"){ + print "Error in header : empty\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error3++; + } + elsif (($TYPE eq "sanger")&&((!$header1)||(!$header2))){ + if ($VERBOSE eq "ON"){ + print "Error in header refgsd : empty\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error3++; + } + elsif (($TYPE eq "illumina")&&(($header1 ne $repheader1)||($header2 ne $repheader2)||($header1 ne $header2))){ + if ($VERBOSE eq "ON"){ + print "Error in header : different\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error4++; + } + elsif (($TYPE eq "sanger")&&($header1 ne $header2)){ + if ($VERBOSE eq "ON"){ + print "Error in header : different\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error4++; + } + elsif (($length_seq1 != $length_qual1)||($length_seq2 != $length_qual2)){ + if ($VERBOSE eq "ON"){ + print "Error in seq/qual length\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error5++; + } +#@ 1 - 2 sec + else { + ### Parsing sequence & qualité + if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){ + $seq1 = $1; + } + if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){ + $seq2 = $1; + } + if ($ligne4_r1 =~ /^(.*)\s*$/i){ + $qual1 = $1; + } + if ($ligne4_r2 =~ /^(.*)\s*$/i){ + $qual2 = $1; + } +#@ 2 sec + ### Verification du parsing et de la coherence sequence /qualité (n°2) + if ((!$seq1)||(!$seq2)||(!$qual1)||(!$qual2)){ + if ($VERBOSE eq "ON"){ + print "Error parsing seq / quality \n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error6++; + } + elsif ((length($seq1) != length($qual1))||(length($seq2) != length($qual2))){ + if ($VERBOSE eq "ON"){ + print "Error in seq/qual length after parsing\n"; + print $ligne1_r1; + print $ligne2_r1; + print $ligne3_r1; + print $ligne4_r1; + print $ligne1_r2; + print $ligne2_r2; + print $ligne3_r2; + print $ligne4_r2; + print "\n"; + } + $error7++; + } +#@ <1 sec + else { + my $fastq_lines_r1=""; + my $fastq_lines_r2=""; + $fastq_lines_r1 = &grooming_and_trimming($ligne1_r1,$seq1,$qual1); + if ($fastq_lines_r1){ + $fastq_lines_r2 = &grooming_and_trimming($ligne1_r2,$seq2,$qual2); + } + if ($fastq_lines_r2){ + print OUT1 $fastq_lines_r1; + print OUT2 $fastq_lines_r2; + } + } + } + + # 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); + + + + +sub grooming_and_trimming{ + my $header = shift; + my $seq = shift; + my $quality = shift; + my $quality_converted=""; + + my $startnoN = 0; + my $stopnoN = length($quality)-1; + + #print "SEQ :\n$seq\n"; + + my $chercheN = $seq; + my @bad_position; + my $current_index = index($chercheN,"N"); + my $abs_index = $current_index; + while ($current_index >=0){ + push (@bad_position,$abs_index); + + if ($current_index<length($seq)){ + $chercheN = substr($chercheN,$current_index+1); + $current_index = index($chercheN,"N"); + $abs_index = $current_index + $bad_position[$#bad_position]+1; + } + else { + last; + } + } + + + 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 $quality_converted=""; + my @bad_position; + + my @q = split(//,$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 $fastq_lines; + } + else { + return ""; + } + + + + } + else { + return ""; + } + + + # my @s = split(//,$seq); + # my $sanger_quality=""; + + + + + # return $sanger_quality; +} + +sub extract_longer_string_coordinates_from_bad_position{ + my $start=shift; + my $stop =shift; + my $refbad = shift; + my @bad_position = @$refbad; + my %coord; + + my $current_start = $start; + my $current_stop = $bad_position[0]-1; + if ($current_stop < $start){$current_stop = $start;} + + + #debut -> premier N + my $current_length = $current_stop - $current_start +1; + my $test_length; + + #entre les N + for (my $i=1;$i<=$#bad_position;$i++){ + $test_length = $bad_position[$i]+1-$bad_position[$i-1]-1; + if ( $test_length > $current_length){ + $current_start = $bad_position[$i-1]+1; + $current_stop = $bad_position[$i]-1; + $current_length = $current_stop - $current_start +1; + } + } + + #dernier N -> fin + $test_length = $stop-$bad_position[$#bad_position]+1; + if ( $test_length > $current_length){ + $current_start = $bad_position[$#bad_position]+1; + if ($current_start > $stop){$current_start=$stop;} + $current_stop = $stop; + } + $coord{"start"}=$current_start; + $coord{"stop"}= $current_stop; + $coord{"lenght"}=$current_stop-$current_start+1; + + return \%coord; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PrepareFastqLight.xml Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,26 @@ +<tool id="PrepareFastqLight" name="PrepareFastqLight" version="0.01"> +<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 $min_length +</command> +<inputs> +<param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> +<param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> +<param name="quality_type" type="select" label="Select input quality format"> + <option value="sanger">Sanger</option> + <option value="illumina">Illumina 1.3-1.7</option> + </param> +<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> +<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> +</inputs> +<outputs> +<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> +<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile2x.pl Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,54 @@ +#!/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);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile2x.xml Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,44 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile4x.pl Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,70 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $in = $ARGV[0]; +my $NB_LINE_GROUP = $ARGV[1]; +my $NB_FILE = 4; +my $out1 = $ARGV[2]; +my $out2 = $ARGV[3]; +my $out3 = $ARGV[4]; +my $out4 = $ARGV[5]; + +if (!$NB_LINE_GROUP){ + $NB_LINE_GROUP=4; +} + +if (!$NB_FILE){ + $NB_FILE=4; +} + +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"); + + +for (my $i=0;$i<=$#in;$i++){ + if ($i <= $#in/4){ + print OUT1 $in[$i]; + } + elsif ($i <= $#in/2){ + print OUT2 $in[$i]; + } + elsif ($i <= $#in*3/4){ + print OUT3 $in[$i]; + } + elsif ($i <= $#in){ + print OUT4 $in[$i]; + } + else { + + } + + +} +close (OUT1); +close (OUT2); +close (OUT3); +close (OUT4);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile4x.xml Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,62 @@ +<tool id="SplitFile4x" name="SplitFile4x" version="0.01"> +<description>Split file in 4</description> +<command interpreter="perl"> + SplitFile4x.pl $input_file $line_number $output_file1 $output_file2 $output_file3 $output_file4 +</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> + +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/mpileupfilter.pl Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,394 +0,0 @@ -#!/usr/bin/perl -use strict; -use Getopt::Long; - -# -# Filter a pileup file on forward/reverse presence and %read having the variant -# The error code -# 1 : multiple variant type detected insertion/deletion/mutation -# 1i : inconsistency in insertion -# 1d : inconsistency in deletion -# 1m : inconsistency in mutation -# 2 : insufficient depth -# 3 : insufficient variant frequency -# 4 : variant position not covered by forward and reverse reads -# 5 : variant with other variant in neighbourhood -# 6 : too much depth -# 8 : parsing error (couldn't parse the mpileup line correctly) -# 9 : parsing error (couldn't parse the readbase string correctly) - - -my $inputfile; -my $logfile; -my $MIN_DISTANCE=0; -my $MIN_VARIANTFREQUENCY=0; -my $MIN_FORWARDREVERSE=0; -my $MIN_DEPTH=0; -my $MAX_DEPTH=500; -my $VERBOSE=0; -my $ONLY_UNFILTERED_VARIANT="OFF"; - -if ($#ARGV<0){ - print "\n"; - print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n"; - print "-input_file \tinputfile in mpileup format\n"; - print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n"; - print "-min_depth \tminimum depth required [1]\n"; - print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n"; - print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n"; - print "-min_distance \tminimum distance between variant [0]\n"; - print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n"; - print "\n"; - exit(0); -} - -GetOptions ( -"input_file=s" => \$inputfile, -"log_file=s" => \$logfile, -"min_depth=i" => \$MIN_DEPTH, -"max_depth=i" => \$MAX_DEPTH, -"min_frequency=f" => \$MIN_VARIANTFREQUENCY, -"min_distance=i" => \$MIN_DISTANCE, -"min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE, -"variant_only=s" => \$ONLY_UNFILTERED_VARIANT, -"v=i" => \$VERBOSE -) or die("Error in command line arguments\n"); - - -open(IF, $inputfile) or die("Can't open $inputfile\n"); - -my @tbl_line; -my @tbl_variant_position; -my @tbl_variant_chr; -my @tbl_variant_refbase; -my @tbl_variant_coverage; -my @tbl_variant_readbase_string; -my @tbl_variant_quality_string; - -#Extraction des variants -my $nb_line=0; -while (my $line=<IF>){ - $nb_line++; - if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){ - print "$nb_line\n"; - } - my $error_code=0; - if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){ - my $current_chromosome = $1; - my $current_position = $2; - my $current_refbase = $3; - my $current_coverage = $4; - my $current_readbase_string = $5; - my $current_quality_string = $6; - - #Suppression of mPileUp special character - $current_readbase_string =~ s/\$//g; #the read start at this position - $current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char - - if ($current_readbase_string =~ /[ATGCNatgcn\d]/){ - push(@tbl_line,$line); - push(@tbl_variant_chr,$current_chromosome); - push(@tbl_variant_position,$current_position); - push(@tbl_variant_refbase,$current_refbase); - push(@tbl_variant_coverage,$current_coverage); - push(@tbl_variant_readbase_string,$current_readbase_string); - push(@tbl_variant_quality_string,$current_quality_string); - if ($ONLY_UNFILTERED_VARIANT eq "ON"){ - print $line; - } - - } - else { - #Position with no variant - } - - } - else { - #Error Parsing - print STDERR "$line #8"; - } -} -close(IF); - -if ($ONLY_UNFILTERED_VARIANT eq "ON"){ - exit(0); -} - -####Checking the distance between variant and other filter - -if ($logfile){ - open(LF,">$logfile") or die ("Cant't open $logfile\n"); -} - -for (my $i=0;$i<=$#tbl_line;$i++){ - # print "ligne : $tbl_line[$i]\n"; - - my $error_code=0; - if ($i==0){ - #Comparing $i and $i+1 for neighbourhood filter; - if ($#tbl_line>0){ - if (($tbl_variant_chr[$i+1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i]+$MIN_DISTANCE>=$tbl_variant_position[$i+1])){ - $error_code=5; - chomp($tbl_line[$i]); - if ($logfile){ - print LF "$tbl_line[$i]\tcode:$error_code\n"; - } - next; - } - } - - #Additionnal filters - $error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]); - - } - else { - #Compairing $i and $i-1 for neighbourhood filter - if (($tbl_variant_chr[$i-1] eq $tbl_variant_chr[$i])&&($tbl_variant_position[$i-1]+$MIN_DISTANCE>=$tbl_variant_position[$i])){ - $error_code=5; - chomp($tbl_line[$i]); - if ($logfile){ - print LF "$tbl_line[$i]\tcode:$error_code\n"; - } - next; - } - else { - #Additionnal filters - $error_code = check_error($tbl_variant_chr[$i],$tbl_variant_position[$i],$tbl_variant_refbase[$i],$tbl_variant_coverage[$i],$tbl_variant_readbase_string[$i]); - } - } - if ($error_code == 0){ - print $tbl_line[$i]; - } - else { - chomp($tbl_line[$i]); - if ($logfile){ - print LF "$tbl_line[$i]\tcode:$error_code\n"; - } - } -} - -if ($logfile){ - close (LF); -} - -sub check_error{ - my $current_chromosome = shift; - my $current_position = shift; - my $current_refbase = shift; - my $current_coverage = shift; - my $current_readbase_string = shift; - - # print "test : $current_readbase_string\n"; - - - - #Extraction of insertions - - ################################################################## - # my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g; - # my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g; - # print "IN : @IN\n"; - # print "DEL :@DEL\n"; - #$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g; - ################################################################## - #!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct - ################################################################## - - # => parcours de boucle - my @readbase = split(//,$current_readbase_string); - my $cleaned_readbase_string=""; - my @IN; - my @DEL; - my $current_IN=""; - my $current_DEL=""; - my $current_size=0; - - for (my $i=0;$i<=$#readbase;$i++){ - if ($readbase[$i] eq "+"){ - #Ouverture de IN - $current_IN="+"; - - #Recuperation de la taille - my $sub = substr $current_readbase_string,$i; - if ($sub=~/^\+(\d+)/){ - $current_size = $1; - } - my $remaining_size = $current_size; - while (($remaining_size>0)&&($i<=$#readbase)){ - $i++; - $current_IN.=$readbase[$i]; - if ($readbase[$i]=~ /[ATGCNatgcn]/){ - $remaining_size--; - } - } - push(@IN,$current_IN); - } - elsif ($readbase[$i] eq "-"){ - #Ouverture de DEL - $current_DEL="-"; - - #Recuperation de la taille - my $sub = substr $current_readbase_string,$i; - if ($sub=~/^\-(\d+)/){ - $current_size = $1; - } - my $remaining_size = $current_size; - while (($remaining_size>0)&&($i<=$#readbase)){ - $i++; - $current_DEL.=$readbase[$i]; - if ($readbase[$i]=~ /[ATGCNatgcn]/){ - $remaining_size--; - } - } - push(@DEL,$current_DEL); - - } - else { - #Ajout a la string - $cleaned_readbase_string .= $readbase[$i]; - } - } - - - # print "IN : @IN\n"; - # print "DEL :@DEL\n"; - # print "$cleaned_readbase_string\n"; - - my @current_readbase_array = split(//,$cleaned_readbase_string); - - #Filtering : error detection - - if ($#current_readbase_array+1 != $current_coverage){ - return 9; - #parsing error (couldn't parse the readbase string correctly) - } - elsif ($current_coverage<$MIN_DEPTH){ - return 2; - # 2 : insufficient depth - } - elsif ($current_coverage>$MAX_DEPTH){ - return 6; - # 6 : too much depth - } - else { - if ($#IN>=0){ - if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){ - return 1; - # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation) - } - else { - ########## TEST de coherence des insertions ################ - # for (my $i=0;$i<=$#IN;$i++){ - # if (uc($IN[0]) ne uc($IN[$i])){ - # print uc($IN[0]),"\n"; - # print uc($IN[$i]),"\n"; - # return "1i"; - # } - # } - ########################################################### - - if($#IN+1 < $current_coverage*$MIN_VARIANTFREQUENCY){ - return 3; - # 3 : insufficient variant frequency - } - } - } - elsif ($#DEL>=0){ - if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){ - return 1; - # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation) - } - else { - ########## TEST de coherence des deletions ################ - # for (my $i=0;$i<=$#DEL;$i++){ - # if (uc($DEL[0]) ne uc($DEL[$i])){ - # print uc($DEL[0]),"\n"; - # print uc($DEL[$i]),"\n"; - # return "1d"; - # } - # } - ########################################################### - - if($#DEL+1 < $current_coverage*$MIN_VARIANTFREQUENCY){ - return 3; - # 3 : insufficient variant frequency - } - } - } - else { - my $nbA=0; - $nbA++ while ($current_readbase_string =~ m/A/g); - my $nbC=0; - $nbC++ while ($current_readbase_string =~ m/C/g); - my $nbT=0; - $nbT++ while ($current_readbase_string =~ m/T/g); - my $nbG=0; - $nbG++ while ($current_readbase_string =~ m/G/g); - my $nbN=0; - $nbN++ while ($current_readbase_string =~ m/N/g); - my $nba=0; - $nba++ while ($current_readbase_string =~ m/a/g); - my $nbc=0; - $nbc++ while ($current_readbase_string =~ m/c/g); - my $nbt=0; - $nbt++ while ($current_readbase_string =~ m/t/g); - my $nbg=0; - $nbg++ while ($current_readbase_string =~ m/g/g); - my $nbn=0; - $nbn++ while ($current_readbase_string =~ m/n/g); - - if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){ - return "1m"; - } - if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){ - return "1m"; - } - if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){ - return "1m"; - } - if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){ - return "1m"; - } - if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){ - return "1m"; - } - - if ($nbA+$nba >= $current_coverage*$MIN_VARIANTFREQUENCY){ - if (($nbA<$MIN_FORWARDREVERSE)||($nba<$MIN_FORWARDREVERSE)){ - return 4; - # 4 : variant position not covered by forward and reverse reads - } - } - elsif ($nbT+$nbt >= $current_coverage*$MIN_VARIANTFREQUENCY){ - if (($nbT<$MIN_FORWARDREVERSE)||($nbt<$MIN_FORWARDREVERSE)){ - return 4; - # 4 : variant position not covered by forward and reverse reads - } - } - elsif ($nbG+$nbg >= $current_coverage*$MIN_VARIANTFREQUENCY){ - if (($nbG<$MIN_FORWARDREVERSE)||($nbg<$MIN_FORWARDREVERSE)){ - return 4; - # 4 : variant position not covered by forward and reverse reads - } - } - elsif ($nbC+$nbc >= $current_coverage*$MIN_VARIANTFREQUENCY){ - if (($nbC<$MIN_FORWARDREVERSE)||($nbc<$MIN_FORWARDREVERSE)){ - return 4; - # 4 : variant position not covered by forward and reverse reads - } - } - elsif ($nbN+$nbn >= $current_coverage*$MIN_VARIANTFREQUENCY){ - if (($nbN<$MIN_FORWARDREVERSE)||($nbn<$MIN_FORWARDREVERSE)){ - return 4; - # 4 : variant position not covered by forward and reverse reads - } - } - else { - return 3; - # 3 : insufficient variant frequency - } - } - } - - return 0; -}
--- a/rapsodyn/mpileupfilter.xml Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -<tool id="mpileupfilter" name="mpileupfilter" version="0.05"> -<description>Filter mpileup file entry</description> -<command interpreter="perl"> - mpileupfilter.pl -input_file $input_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth > $output_file -</command> -<inputs> -<param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> -<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/> -<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/> -<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> -<param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/> -<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/> -</inputs> -<outputs> - <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> -</outputs> - -<help> - - - -</help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/mpileupfilterandstat.pl Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,469 @@ +#!/usr/bin/perl +use strict; +use Getopt::Long; + +# +# Filter a pileup file on forward/reverse presence and %read having the variant +# The error code +# 1 : multiple variant type detected insertion/deletion/mutation +# 1i : inconsistency in insertion +# 1d : inconsistency in deletion +# 1m : inconsistency in mutation +# 2 : insufficient depth +# 3 : insufficient variant frequency +# 4 : variant position not covered by forward and reverse reads +# 5 : variant with other variant in neighbourhood +# 6 : too much depth +# 8 : parsing error (couldn't parse the mpileup line correctly) +# 9 : parsing error (couldn't parse the readbase string correctly) + + +my $inputfile; +my $logfile; +my $MIN_DISTANCE=0; +my $MIN_VARIANTFREQUENCY=0; +my $MIN_FORWARDREVERSE=0; +my $MIN_DEPTH=0; +my $MAX_DEPTH=500; +my $VERBOSE=0; +my $ONLY_UNFILTERED_VARIANT="OFF"; +my $DO_STAT="NO"; + +if ($#ARGV<0){ + print "\n"; + print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n"; + print "-input_file \tinputfile in mpileup format\n"; + print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n"; + print "-min_depth \tminimum depth required [1]\n"; + print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n"; + print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n"; + print "-min_distance \tminimum distance between variant [0]\n"; + print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n"; + print "\n"; + exit(0); +} + +GetOptions ( +"input_file=s" => \$inputfile, +"log_file=s" => \$logfile, +"min_depth=i" => \$MIN_DEPTH, +"max_depth=i" => \$MAX_DEPTH, +"min_frequency=f" => \$MIN_VARIANTFREQUENCY, +"min_distance=i" => \$MIN_DISTANCE, +"min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE, +"variant_only=s" => \$ONLY_UNFILTERED_VARIANT, +"v=i" => \$VERBOSE, +"do_stat=s" => \$DO_STAT +) or die("Error in command line arguments\n"); + + +open(IF, $inputfile) or die("Can't open $inputfile\n"); + +my @tbl_line; +my %USR_PARAM; +$USR_PARAM{"min_depth"} = $MIN_DEPTH; +$USR_PARAM{"max_depth"} = $MAX_DEPTH; +$USR_PARAM{"min_freq"} = $MIN_VARIANTFREQUENCY; +$USR_PARAM{"min_dist"} = $MIN_DISTANCE; +$USR_PARAM{"min_fr"} = $MIN_FORWARDREVERSE; + + + +#Extraction des variants +my $nb_line=0; +while (my $line=<IF>){ + $nb_line++; + if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){ + print "$nb_line\n"; + } + my $error_code=0; + if ($line=~/(.*?)\s+(\d+)\s+([ATGCN])\s+(\d+)\s+(.*?)\s+(.*?)$/){ + my $current_chromosome = $1; + my $current_position = $2; + my $current_refbase = $3; + my $current_coverage = $4; + my $current_readbase_string = $5; + my $current_quality_string = $6; + + #Suppression of mPileUp special character + $current_readbase_string =~ s/\$//g; #the read start at this position + $current_readbase_string =~ s/\^.//g; #the read end at this position followed by quality char + + if ($current_readbase_string =~ /[ATGCNatgcn\d]/){ + my %variant; + $variant{"line"} = $line; + $variant{"chr"} = $current_chromosome; + $variant{"pos"} = $current_position; + $variant{"refbase"} = $current_refbase; + $variant{"coverage"} = $current_coverage; + $variant{"readbase"} = $current_readbase_string; + $variant{"quality"} = $current_quality_string; + push(@tbl_line,\%variant); + + if ($ONLY_UNFILTERED_VARIANT eq "ON"){ + print $line; + } + + } + else { + #Position with no variant + } + + } + else { + #Error Parsing + print STDERR "$line #8"; + } +} +close(IF); + +if ($ONLY_UNFILTERED_VARIANT eq "ON"){ + exit(0); +} + +####Checking the distance between variant and other filter + + +my @error; +for (my $i=0;$i<=$#tbl_line;$i++){ + # print "ligne : $tbl_line[$i]\n"; + my $before=""; + my $after=""; + my %line = %{$tbl_line[$i]}; + + if ($tbl_line[$i-1]){ + $before = $tbl_line[$i-1]; + } + if ($tbl_line[$i+1]){ + $after = $tbl_line[$i+1]; + } + my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM); + if ($error_code == 0){ + print $line{"line"}; + } + else { + push(@error,$error_code,"\t",$line{"line"}); + } +} + +### LOG +open(LF,">$logfile") or die ("Can't open $logfile\n"); + +if ($DO_STAT eq "YES"){ + for (my $idx_min_depth=2;$idx_min_depth<=32;$idx_min_depth = $idx_min_depth*2){ + for (my $idx_freq = 0.5;$idx_freq<=1;$idx_freq= $idx_freq+0.1){ + for (my $idx_dist=0;$idx_dist<=50;$idx_dist = $idx_dist + 50){ + for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){ + my %stat_param; + $stat_param{"min_depth"}=$idx_min_depth; + $stat_param{"max_depth"}=250; + $stat_param{"min_freq"}=$idx_freq; + $stat_param{"min_fr"}=$idx_fr; + $stat_param{"min_dist"}=$idx_dist; + + print LF "#SNP = ",&test_check(\@tbl_line,\%stat_param),"\tdepth (min/max) = ",$stat_param{"min_depth"}," / ",$stat_param{"max_depth"},"\tmin_dist=",$stat_param{"min_dist"},"\tmin_freq=",$stat_param{"min_freq"},"\tmin_forwardreverse = ",$stat_param{"min_fr"},"\n"; + } + } + } + print "\n"; + } +} + + +for (my $i=0;$i<=$#error;$i++){ + print LF $error[$i]; +} +close (LF); + + + + +sub test_check{ + my $ref_tbl_line = shift; + my $ref_param = shift; + my @tbl_line = @$ref_tbl_line; + my %param = %$ref_param; + my $nb=0; + + for (my $i=0;$i<=$#tbl_line;$i++){ + my $before=""; + my $after=""; + my %line = %{$tbl_line[$i]}; + + if ($tbl_line[$i-1]){ + $before = $tbl_line[$i-1]; + } + if ($tbl_line[$i+1]){ + $after = $tbl_line[$i+1]; + } + my $error_code = check_error($tbl_line[$i],$before,$after,\%param); + if ($error_code == 0){ + $nb++; + } + } + + return $nb; +} + +sub check_error{ + my $refline = shift; + my %line = %$refline; + my $refbefore = shift; + my $refafter = shift; + my $refparam = shift; + my %param = %$refparam; + + + my $current_chromosome = $line{"chr"}; + my $current_position = $line{"pos"}; + my $current_refbase = $line{"refbase"}; + my $current_coverage = $line{"coverage"}; + my $current_readbase_string = $line{"readbase"}; + + + my $min_depth = $param{"min_depth"}; + my $max_depth = $param{"max_depth"}; + my $min_variant_frequency = $param{"min_freq"}; + my $min_forward_reverse = $param{"min_fr"}; + my $min_dist = $param{"min_dist"}; + + #Verification of neightbourhood + if ($refbefore){ + my %compareline = %$refbefore; + my $compare_chromosome = $compareline{"chr"}; + my $compare_position = $compareline{"pos"}; + my $compare_refbase = $compareline{"refbase"}; + my $compare_coverage = $compareline{"coverage"}; + my $compare_readbase_string = $compareline{"readbase"}; + + if (($current_chromosome eq $compare_chromosome )&&($compare_position + $min_dist >= $current_position)){ + return 5; + } + } + + if ($refafter){ + my %compareline = %$refafter; + my $compare_chromosome = $compareline{"chr"}; + my $compare_position = $compareline{"pos"}; + my $compare_refbase = $compareline{"refbase"}; + my $compare_coverage = $compareline{"coverage"}; + my $compare_readbase_string = $compareline{"readbase"}; + + if (($current_chromosome eq $compare_chromosome )&&($current_position + $min_dist >= $compare_position)){ + return 5; + } + } + + + + + #Extraction of insertions + + ################################################################## + # my @IN = $current_readbase_string =~ m/\+[0-9]+[ACGTNacgtn]+/g; + # my @DEL = $current_readbase_string =~ m/\-[0-9]+[ACGTNacgtn]+/g; + # print "IN : @IN\n"; + # print "DEL :@DEL\n"; + #$current_readbase_string=~s/[\+\-][0-9]+[ACGTNacgtn]+//g; + ################################################################## + #!!! marche pas : exemple .+1Ct. correspond a . / +1C / t /. mais le match de l'expression vire +1Ct + ################################################################## + + # => parcours de boucle + my @readbase = split(//,$current_readbase_string); + my $cleaned_readbase_string=""; + my @IN; + my @DEL; + my $current_IN=""; + my $current_DEL=""; + my $current_size=0; + + for (my $i=0;$i<=$#readbase;$i++){ + if ($readbase[$i] eq "+"){ + #Ouverture de IN + $current_IN="+"; + + #Recuperation de la taille + my $sub = substr $current_readbase_string,$i; + if ($sub=~/^\+(\d+)/){ + $current_size = $1; + } + my $remaining_size = $current_size; + while (($remaining_size>0)&&($i<=$#readbase)){ + $i++; + $current_IN.=$readbase[$i]; + if ($readbase[$i]=~ /[ATGCNatgcn]/){ + $remaining_size--; + } + } + push(@IN,$current_IN); + } + elsif ($readbase[$i] eq "-"){ + #Ouverture de DEL + $current_DEL="-"; + + #Recuperation de la taille + my $sub = substr $current_readbase_string,$i; + if ($sub=~/^\-(\d+)/){ + $current_size = $1; + } + my $remaining_size = $current_size; + while (($remaining_size>0)&&($i<=$#readbase)){ + $i++; + $current_DEL.=$readbase[$i]; + if ($readbase[$i]=~ /[ATGCNatgcn]/){ + $remaining_size--; + } + } + push(@DEL,$current_DEL); + + } + else { + #Ajout a la string + $cleaned_readbase_string .= $readbase[$i]; + } + } + + + # print "IN : @IN\n"; + # print "DEL :@DEL\n"; + # print "$cleaned_readbase_string\n"; + + my @current_readbase_array = split(//,$cleaned_readbase_string); + + #Filtering : error detection + + if ($#current_readbase_array+1 != $current_coverage){ + return 9; + #parsing error (couldn't parse the readbase string correctly) + } + elsif ($current_coverage<$min_depth){ + return 2; + # 2 : insufficient depth + } + elsif ($current_coverage>$max_depth){ + return 6; + # 6 : too much depth + } + else { + if ($#IN>=0){ + if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){ + return 1; + # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation) + } + else { + ########## TEST de coherence des insertions ################ + # for (my $i=0;$i<=$#IN;$i++){ + # if (uc($IN[0]) ne uc($IN[$i])){ + # print uc($IN[0]),"\n"; + # print uc($IN[$i]),"\n"; + # return "1i"; + # } + # } + ########################################################### + + if($#IN+1 < $current_coverage*$min_variant_frequency ){ + return 3; + # 3 : insufficient variant frequency + } + } + } + elsif ($#DEL>=0){ + if (($cleaned_readbase_string=~/[ACGTNacgtn]/)){ + return 1; + # 1 : variant type overload (multiple variant type detected insertion/deletion/mutation) + } + else { + ########## TEST de coherence des deletions ################ + # for (my $i=0;$i<=$#DEL;$i++){ + # if (uc($DEL[0]) ne uc($DEL[$i])){ + # print uc($DEL[0]),"\n"; + # print uc($DEL[$i]),"\n"; + # return "1d"; + # } + # } + ########################################################### + + if($#DEL+1 < $current_coverage*$min_variant_frequency){ + return 3; + # 3 : insufficient variant frequency + } + } + } + else { + my $nbA=0; + $nbA++ while ($current_readbase_string =~ m/A/g); + my $nbC=0; + $nbC++ while ($current_readbase_string =~ m/C/g); + my $nbT=0; + $nbT++ while ($current_readbase_string =~ m/T/g); + my $nbG=0; + $nbG++ while ($current_readbase_string =~ m/G/g); + my $nbN=0; + $nbN++ while ($current_readbase_string =~ m/N/g); + my $nba=0; + $nba++ while ($current_readbase_string =~ m/a/g); + my $nbc=0; + $nbc++ while ($current_readbase_string =~ m/c/g); + my $nbt=0; + $nbt++ while ($current_readbase_string =~ m/t/g); + my $nbg=0; + $nbg++ while ($current_readbase_string =~ m/g/g); + my $nbn=0; + $nbn++ while ($current_readbase_string =~ m/n/g); + + if (($nbA+$nba>0)&&($nbT+$nbt+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){ + return "1m"; + } + if (($nbT+$nbt>0)&&($nbA+$nba+$nbG+$nbg+$nbC+$nbc+$nbN+$nbn>0)){ + return "1m"; + } + if (($nbG+$nbg>0)&&($nbA+$nba+$nbT+$nbt+$nbC+$nbc+$nbN+$nbn>0)){ + return "1m"; + } + if (($nbC+$nbc>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbN+$nbn>0)){ + return "1m"; + } + if (($nbN+$nbn>0)&&($nbA+$nba+$nbT+$nbt+$nbG+$nbg+$nbC+$nbc>0)){ + return "1m"; + } + + if ($nbA+$nba >= $current_coverage*$min_variant_frequency){ + if (($nbA<$min_forward_reverse)||($nba<$min_forward_reverse)){ + return 4; + # 4 : variant position not covered by forward and reverse reads + } + } + elsif ($nbT+$nbt >= $current_coverage*$min_variant_frequency){ + if (($nbT<$min_forward_reverse)||($nbt<$min_forward_reverse)){ + return 4; + # 4 : variant position not covered by forward and reverse reads + } + } + elsif ($nbG+$nbg >= $current_coverage*$min_variant_frequency){ + if (($nbG<$min_forward_reverse)||($nbg<$min_forward_reverse)){ + return 4; + # 4 : variant position not covered by forward and reverse reads + } + } + elsif ($nbC+$nbc >= $current_coverage*$min_variant_frequency){ + if (($nbC<$min_forward_reverse)||($nbc<$min_forward_reverse)){ + return 4; + # 4 : variant position not covered by forward and reverse reads + } + } + elsif ($nbN+$nbn >= $current_coverage*$min_variant_frequency){ + if (($nbN<$min_forward_reverse)||($nbn<$min_forward_reverse)){ + return 4; + # 4 : variant position not covered by forward and reverse reads + } + } + else { + return 3; + # 3 : insufficient variant frequency + } + } + } + + return 0; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/mpileupfilterandstat.xml Fri Sep 05 06:12:10 2014 -0400 @@ -0,0 +1,29 @@ +<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.07"> +<description>Filter mpileup file entry</description> +<command interpreter="perl"> + mpileupfilterandstat.pl -input_file $input_file -log_file $log_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth -do_stat $do_stat> $output_file +</command> +<inputs> +<param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> +<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/> +<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/> +<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> +<param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/> +<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/> +<param name="do_stat" type="select" label="Compute stats "> + <option value="NO">NO</option> + <option value="YES">YES</option> +</param> + +</inputs> +<outputs> + <data name="output_file" format="pileup" label="${tool.name} MPILEUP on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/rapsodyn_stats.pl Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,277 +0,0 @@ -#!/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 $read1_trimmed_noN = $ARGV[4]; -my $read2_trimmed_noN = $ARGV[5]; - -my $sam_row = $ARGV[6]; - -my $sam_filtered = $ARGV[7]; - -my $mpileup_row = $ARGV[8]; - -my $mpileup_filtered = $ARGV[9]; - -my $list_filtered = $ARGV[10]; - -my $blast_filtered = $ARGV[11]; - - - - -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); - -open(INR1N, $read1_trimmed_noN) or die ("Can't open $read1_trimmed_noN\n"); -$nbread=0; -$nbbase =0; -while (my $line1=<INR1N>){ - my $line2 = <INR1N>; - my $line3 = <INR1N>; - my $line4 = <INR1N>; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -print "Trimmed (no N) Reads 1\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR1N); - -open(INR2N, $read2_trimmed_noN) or die ("Can't open $read2_trimmed_noN\n"); -$nbread=0; -$nbbase =0; -while (my $line1=<INR2N>){ - my $line2 = <INR2N>; - my $line3 = <INR2N>; - my $line4 = <INR2N>; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -print "Trimmed (no N) Reads 2\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR2N); - -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 row\n"; -open(MPR, $mpileup_row) or die ("Can't open $mpileup_row\n"); -my $basecovered=0; -my $nbvariant=0; -while (my $line=<MPR>){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - $basecovered++; - 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 : $line\n"; - } -} - -print "Base covered :\t$basecovered\n"; -print "Variant detected :\t$nbvariant\n"; -close (MPR); - -print "\nMPILEUP filered\n"; -open(MPF, $mpileup_filtered) or die ("Can't open $mpileup_filtered\n"); - -$basecovered=0; -$nbvariant=0; -while (my $line=<MPF>){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - $basecovered++; - 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 : $line\n"; - } -} - -print "Variant selected :\t$nbvariant\n"; -close (MPF); - -print "\nMPILEUP filered 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 filered 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); - - - - - - - - - -
--- a/rapsodyn/rapsodyn_stats.xml Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -<tool id="rapsodyn_stats" name="rapsodyn_stats" version="0.01"> -<description>Merge best results from Blast</description> -<command interpreter="perl"> - rapsodyn_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_read1_trimmednoN_file $input_read2_trimmednoN_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_row_file $input_mpileup_filtered_file $input_list_filtered_file $input_blast_filtered_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_read1_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED noN file from your history"/> -<param name="input_read2_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED noN 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_row_file" type="data" format="pileup" label="Select a suitable input MPILEUP file from your history"/> -<param name="input_mpileup_filtered_file" type="data" format="pileup" label="Select a suitable input MPILEUP FILTERED 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"/> -</inputs> -<outputs> - <data name="output_file" format="txt" label="STATS"/> -</outputs> - - -<help> - -</help> -</tool>
--- a/rapsodyn/rapsodyn_stats_filtering.pl Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $mpileup_row = $ARGV[0]; - -my $mpileup_filtered = $ARGV[1]; - -my $list_filtered = $ARGV[2]; - -my $blast_filtered = $ARGV[3]; - - -print "\nMPILEUP row\n"; -open(MPR, $mpileup_row) or die ("Can't open $mpileup_row\n"); -my $basecovered=0; -my $nbvariant=0; -while (my $line=<MPR>){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - $basecovered++; - 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 : $line\n"; - } -} - -print "Base covered :\t$basecovered\n"; -print "Variant detected :\t$nbvariant\n"; -close (MPR); - -print "\nMPILEUP filered\n"; -open(MPF, $mpileup_filtered) or die ("Can't open $mpileup_filtered\n"); - -$basecovered=0; -$nbvariant=0; -while (my $line=<MPF>){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - $basecovered++; - 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 : $line\n"; - } -} - -print "Variant selected :\t$nbvariant\n"; -close (MPF); - -print "\nMPILEUP filered 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 filered 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); - - - - - - - - - -
--- a/rapsodyn/rapsodyn_stats_filtering.xml Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -<tool id="rapsodyn_stats_filtering" name="rapsodyn_stats_filtering" version="0.01"> -<description>Merge best results from Blast</description> -<command interpreter="perl"> - rapsodyn_stats_filtering.pl $input_mpileup_row_file $input_mpileup_filtered_file $input_list_filtered_file $input_blast_filtered_file > $output_file -</command> -<inputs> -<param name="input_mpileup_row_file" type="data" format="pileup" label="Select a suitable input MPILEUP file from your history"/> -<param name="input_mpileup_filtered_file" type="data" format="pileup" label="Select a suitable input MPILEUP FILTERED 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"/> -</inputs> -<outputs> - <data name="output_file" format="txt" label="STATS"/> -</outputs> - - -<help> - -</help> -</tool>
--- a/rapsodyn/rapsodyn_stats_mapping.pl Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ -#!/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 $read1_trimmed_noN = $ARGV[4]; -my $read2_trimmed_noN = $ARGV[5]; - -my $sam_row = $ARGV[6]; - -my $sam_filtered = $ARGV[7]; - - - - - -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); - -open(INR1N, $read1_trimmed_noN) or die ("Can't open $read1_trimmed_noN\n"); -$nbread=0; -$nbbase =0; -while (my $line1=<INR1N>){ - my $line2 = <INR1N>; - my $line3 = <INR1N>; - my $line4 = <INR1N>; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -print "Trimmed (no N) Reads 1\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR1N); - -open(INR2N, $read2_trimmed_noN) or die ("Can't open $read2_trimmed_noN\n"); -$nbread=0; -$nbbase =0; -while (my $line1=<INR2N>){ - my $line2 = <INR2N>; - my $line3 = <INR2N>; - my $line4 = <INR2N>; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -print "Trimmed (no N) Reads 2\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR2N); - -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); -
--- a/rapsodyn/rapsodyn_stats_mapping.xml Thu Aug 21 08:39:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -<tool id="rapsodyn_stats_mapping" name="rapsodyn_stats_mapping" version="0.01"> -<description>Stats on the mapping</description> -<command interpreter="perl"> - rapsodyn_stats_mapping.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_read1_trimmednoN_file $input_read2_trimmednoN_file $input_sam_row_file $input_sam_filtered_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_read1_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED noN file from your history"/> -<param name="input_read2_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED noN 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"/> -</inputs> -<outputs> - <data name="output_file" format="txt" label="STATS"/> -</outputs> - - -<help> - -</help> -</tool>
--- a/rapsodyn/repository_dependencies.xml Thu Aug 21 08:39:15 2014 -0400 +++ b/rapsodyn/repository_dependencies.xml Fri Sep 05 06:12:10 2014 -0400 @@ -1,10 +1,8 @@ <?xml version="1.0"?> <repositories description="Rapsodyn worflow needed repository"> - <repository changeset_revision="c70137414dcd" name="sickle" owner="nikhil-joshi" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="1298445c852b" name="fastq_groomer" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="b4427dbb6ced" name="bwa_wrappers" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="9710e9bcc5f3" name="samtools_filter" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b4427dbb6ced" name="bwa_wrappers" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a7a49d31c5cf" name="sam_merge" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>