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"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 diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/PrepareFastqLight.pl --- a/rapsodyn/PrepareFastqLight.pl Tue Oct 07 10:34:34 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.pl Fri Oct 10 07:05:36 2014 -0400 @@ -1,4 +1,6 @@ #!/usr/bin/perl +#v1.0.3 support rapsodyn header (.... 1:... / .... 2:...) +#V1.0.2 added auto type detection #V1.0.1 added log, option parameters use strict; use warnings; @@ -41,11 +43,12 @@ 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 $output2_file\n"); +open (LF,">$log_file") or die("Can't open $log_file\n"); + my $error1=0; my $error2=0; @@ -58,6 +61,59 @@ my $error9=0; my $error10=0; +my $auto_type=""; +my %qual; +if ($TYPE eq "auto"){ + my $compt=0; + open(DETECT, $read1_file) or die ("Can't open $read1_file\n"); + while (my $ligne1_r1 =){ + my $ligne2_r1 =; + my $ligne3_r1 =; + my $ligne4_r1 =; + $compt++; + if ($ligne4_r1 =~ /^(.*)\s*$/i){ + my $qual = $1; + my @q = split(//,$qual); + for (my $i=0;$i<=$#q;$i++){ + my $num = ord($q[$i]); + if ($qual{$num}){ + $qual{$num}++; + } + else { + $qual{$num} = 1; + } + #range sanger / illumina 1.8+ : 33->94 + #range illumina 1.3->1.7 : 64->105 + if ($num > 94){$auto_type = "illumina";last;} + if ($num < 64){$auto_type = "sanger";last;} + } + } + else { + print STDERR "Error in format detection : quality not recognized\n$ligne4_r1"; + exit(0); + } + + if ($auto_type ne ""){ + last; + } + + } + close (DETECT); + if ($auto_type eq ""){ + print STDERR "Error in format detection : type not recognized parsing read1\n"; + foreach my $key (sort {$a <=> $b} keys %qual){ + print "$key\t:\t",$qual{$key},"\n"; + } + exit(0); + } + else { + $TYPE = $auto_type; + } +} + + + + while (my $ligne1_r1 =){ my $ligne2_r1 =; my $ligne3_r1 =; @@ -119,19 +175,19 @@ my $repheader2=""; - if ($ligne1_r1 =~/^\@(.*?)\#/){ + if ($ligne1_r1 =~/^\@(.*?)[\s\/]/){ $header1 = $1; } - if ($ligne3_r1 =~/^\+(.*?)\#/){ + if ($ligne3_r1 =~/^\+(.*?)[\s\/]/){ $repheader1 = $1; } - if ($ligne1_r2 =~/^\@(.*?)\#/){ + if ($ligne1_r2 =~/^\@(.*?)[\s\/]/){ $header2 = $1; } - if ($ligne3_r2 =~/^\+(.*?)\#/){ + if ($ligne3_r2 =~/^\+(.*?)[\s\/]/){ $repheader2 = $1; } #@ 2 sec @@ -298,8 +354,8 @@ close (OUT1); close (OUT2); -open (LF,">$log_file") or die("Can't open $log_file\n"); print LF "\n####\t Fastq preparation \n"; +print LF "Fastq format : $TYPE\n"; print LF "## Before preparation\n"; print LF "#Read1 :\t$nb_read1\t#Base :\t$nb_base_read1\n"; print LF "#Read2 :\t$nb_read2\t#Base :\t$nb_base_read2\n"; diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/PrepareFastqLight.pl~ --- a/rapsodyn/PrepareFastqLight.pl~ Tue Oct 07 10:34:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,457 +0,0 @@ -#!/usr/bin/perl -#V1.0.1 added log, option parameters -use strict; -use warnings; -use Getopt::Long; - -my $read1_file; -my $read2_file; -my $log_file; -my $output1_file; -my $output2_file; - -my $TYPE="sanger"; -my $MIN_LENGTH=30; -my $MIN_QUALITY=30; - -my $VERBOSE = "OFF"; - -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"); - - -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; -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 =){ - my $ligne2_r1 =; - my $ligne3_r1 =; - my $ligne4_r1 =; - my $ligne1_r2 =; - my $ligne2_r2 =; - my $ligne3_r2 =; - my $ligne4_r2 =; - - $nb_read1++; - $nb_read2++; - -#@ 1 sec - if ((!$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; - $nb_base_read1 += length($seq1); - } - if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){ - $seq2 = $1; - $nb_base_read2 += length($seq2); - } - if ($ligne4_r1 =~ /^(.*)\s*$/i){ - $qual1 = $1; - } - if ($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=""; - 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 += $nb_base_current_read2_t; - - - } - } - } - - -#@ 7 sec - } -} - -close (READ1); -close (READ2); -close (OUT1); -close (OUT2); - -open (LF,">$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 $lengthseq = length($seq); - my $startTrim = 0; - my $stopTrim = length($quality)-1; - my $startnoN = $startTrim; - my $stopnoN = $stopTrim; - - - my $chercheN = $seq; - 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_N,$abs_index); - - if ($current_index 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){ - @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 $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 ""; - } -} - -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; -} diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/PrepareFastqLight.xml --- a/rapsodyn/PrepareFastqLight.xml Tue Oct 07 10:34:34 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.xml Fri Oct 10 07:05:36 2014 -0400 @@ -1,4 +1,4 @@ - + Fastq preparation 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 @@ -7,6 +7,7 @@ + diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/PrepareFastqLight.xml~ --- a/rapsodyn/PrepareFastqLight.xml~ Tue Oct 07 10:34:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ - -Fastq preparation - - 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 - - - - - - - - - - - - - - - - - - - - - - - diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/listfiltering.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/listfiltering.pl Fri Oct 10 07:05:36 2014 -0400 @@ -0,0 +1,86 @@ +#!/usr/bin/perl +# v1.0.1 added log, and two different type of filtering (common / specific) +use strict; +use Getopt::Long; + +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; + + +GetOptions ( +"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(L2, $list2_file) or die("Can't open $list2_file\n"); +while (my $line=){ + $nb_list2++; + chomp($line); + my @fields = split(/\s+/,$line); + my $ref=""; + my $compt=0; + while ($compt<$NB_COL){ + if ($ref){$ref.="\t";} + $ref.=$fields[$compt]; + $compt++; + } + $header{$ref}=$line; +} +close (L2); + + +open(L1, $list1_file) or die("Can't open $list1_file\n"); +while (my $line=){ + $nb_list1++; + my @fields = split(/\s+/,$line); + my $ref=""; + my $compt=0; + while ($compt<$NB_COL){ + if ($ref){$ref.="\t";} + $ref.=$fields[$compt]; + $compt++; + } + # my $ref = "$fields[0]\t$fields[1]"; + + if ($header{$ref}){ + $nb_common++; + if ($TYPE eq "common"){ + print $line; + } + elsif ($TYPE eq "specific") { + } + else { + } + } + else { + if ($TYPE eq "common"){ + } + elsif ($TYPE eq "specific") { + print $line; + } + else { + } + } + +} +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); + diff -r 3f7b0788a1c4 -r d857538d9fea rapsodyn/listfiltering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/listfiltering.xml Fri Oct 10 07:05:36 2014 -0400 @@ -0,0 +1,25 @@ + +Compare list1 and list2 + + listfiltering.pl -list1_file $input_list1 -list2_file $input_list2 -nb_col $nb_col -type $type -log_file $log_file > $output_file + + + + + + + + + + + + + + + + + + + + +