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\"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 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeFile2x.pl --- a/rapsodyn/MergeFile2x.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $in1 = $ARGV[0]; -my $in2 = $ARGV[1]; - -open(IN1, $in1) or die ("Can't open $in1\n"); -while (my $line = ){ - print $line; -} -close (IN1); - -open(IN2, $in2) or die ("Can't open $in2\n"); -while (my $line = ){ - print $line; -} -close (IN2); - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeFile2x.xml --- a/rapsodyn/MergeFile2x.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - -Merge splitted file - - MergeFile2x.pl $input_file1 $input_file2 > $output_file - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeFile4x.pl --- a/rapsodyn/MergeFile4x.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $in1 = $ARGV[0]; -my $in2 = $ARGV[1]; -my $in3 = $ARGV[2]; -my $in4 = $ARGV[3]; - -open(IN1, $in1) or die ("Can't open $in1\n"); -while (my $line = ){ - print $line; -} -close (IN1); - -open(IN2, $in2) or die ("Can't open $in2\n"); -while (my $line = ){ - print $line; -} -close (IN2); - -open(IN3, $in3) or die ("Can't open $in3\n"); -while (my $line = ){ - print $line; -} -close (IN3); - -open(IN4, $in4) or die ("Can't open $in4\n"); -while (my $line = ){ - print $line; -} -close (IN4); - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeFile4x.xml --- a/rapsodyn/MergeFile4x.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - -Merge splitted file - - MergeFile4x.pl $input_file1 $input_file2 $input_file3 $input_file4 > $output_file - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeMultiFile.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeMultiFile.pl Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,15 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; + +my @files = split(/,/,$ARGV[0]); +for (my $i=0;$i<=$#files;$i++){ + + open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n"); + while (my $line = ){ + print $line; + } + close (IN); +} + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeMultiFile.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeMultiFile.xml Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,34 @@ + +Merge multiple files + + MergeMultiFile.pl $input_files > $output_file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeSamFiles.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeSamFiles.pl Tue Oct 07 10:34:34 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 $line = ){ + if ($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); +} + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/MergeSamFiles.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeSamFiles.xml Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,18 @@ + +Merge multiple SAM files + + MergeSamFiles.pl $input_files > $output_file + + + + + + + + + + + + + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/ParseBlastForUniqueMatch.pl --- a/rapsodyn/ParseBlastForUniqueMatch.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.pl Tue Oct 07 10:34:34 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 = ) { + $nb_variant_checked++; my @champs = split (/\s+/,$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"; diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/ParseBlastForUniqueMatch.xml --- a/rapsodyn/ParseBlastForUniqueMatch.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,16 +1,17 @@ - + Filter mpileup with blast results - 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 - - - - + + + + - + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PileupVariant.pl --- a/rapsodyn/PileupVariant.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/PileupVariant.pl Tue Oct 07 10:34:34 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=){ - 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=){ + #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); diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PileupVariant.xml --- a/rapsodyn/PileupVariant.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/PileupVariant.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,13 +1,14 @@ - + Keep only mpileup line with variant - PileupVariant.pl $input_file > $output_file + PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file - + - + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PrepareFastqLight.pl --- a/rapsodyn/PrepareFastqLight.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.pl Tue Oct 07 10:34:34 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 =; 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)){ @@ -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; @@ -236,37 +265,49 @@ 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; @@ -326,7 +367,13 @@ } 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/){ @@ -343,11 +390,23 @@ # 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; - $fastq_lines .= substr($seq,$startTrim,$lengthTrim)."\n"; + my $new_seq = substr($seq,$startTrim,$lengthTrim); + $nb_base_current_t = length($new_seq); + $fastq_lines .= $new_seq."\n"; $fastq_lines .= "+\n"; - $fastq_lines .= substr($quality,$startTrim,$lengthTrim)."\n"; + my $new_q = substr($quality,$startTrim,$lengthTrim); + $fastq_lines .= $new_q."\n"; return $fastq_lines; } diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PrepareFastqLight.pl~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PrepareFastqLight.pl~ Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,457 @@ +#!/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 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PrepareFastqLight.xml --- a/rapsodyn/PrepareFastqLight.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,21 +1,22 @@ - + Fastq preparation - 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 - - - - - - - - + + + + + + + + - - + + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/PrepareFastqLight.xml~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/PrepareFastqLight.xml~ Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,27 @@ + +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 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/SplitFile10x.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile10x.pl Tue Oct 07 10:34:34 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 =){ + $current_aggregate = $line; + my $nb_line=1; + if ($NB_LINE_GROUP>1){ + while (my $add_line = ){ + $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); + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/SplitFile10x.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/SplitFile10x.xml Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,116 @@ + +Split file in 10 + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/SplitFile2x.pl --- a/rapsodyn/SplitFile2x.pl Mon Sep 29 03:02:16 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 =){ - $current_aggregate = $line; - my $nb_line=1; - if ($NB_LINE_GROUP>1){ - while (my $add_line = ){ - $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); diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/SplitFile2x.xml --- a/rapsodyn/SplitFile2x.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - -Split file in 2 - - SplitFile2x.pl $input_file $line_number $output_file1 $output_file2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/extractseq.pl --- a/rapsodyn/extractseq.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/extractseq.pl Tue Oct 07 10:34:34 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; @@ -89,7 +89,7 @@ } $variant{"desc"}=$descriptor; - print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n"; #MAJ : ajout du diese pour pas perturber blast + print ">",$variant{"ref"},"_",$descriptor,"\n",$variant{"SEQ"},"\n"; diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/extractseq.xml --- a/rapsodyn/extractseq.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/extractseq.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,4 +1,4 @@ - + Extract Sequence around variant position extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/fastaGroomerForMakeBlastdb.pl --- a/rapsodyn/fastaGroomerForMakeBlastdb.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.pl Tue Oct 07 10:34:34 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"); diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/fastaGroomerForMakeBlastdb.xml --- a/rapsodyn/fastaGroomerForMakeBlastdb.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,4 +1,4 @@ - + fasta Groomer For MakeBlastdb fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/filtersam_mapped_and_unique.pl --- a/rapsodyn/filtersam_mapped_and_unique.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.pl Tue Oct 07 10:34:34 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 $line=){ - if ($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); + + + + + + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/filtersam_mapped_and_unique.xml --- a/rapsodyn/filtersam_mapped_and_unique.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,13 +1,14 @@ - + Filter SAM file for uniq and well mapped pair-end reads - 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 - + - + + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/listfiltering.pl --- a/rapsodyn/listfiltering.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -#!/usr/bin/perl -use strict; -use Getopt::Long; - -my $inputfile; -my $headerfile; -my $nb_col=1; -my %header; - -if ($#ARGV<0){ - print "\n"; - print "perl 021_ListFiltering.pl -input_file -header_file -nb_col [1]\n"; - exit(0); -} - -GetOptions ( -"input_file=s" => \$inputfile, -"header_file=s" => \$headerfile, -"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 $line=){ - chomp($line); - 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]"; - $header{$ref}=$line; -} -close (HF); - - -open(IF, $inputfile) or die("Can't open $inputfile\n"); -while (my $line=){ - my @fields = split(/\s+/,$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}){ - # print $line; - # print $header{$ref},"\n"; - } - else { - print $line; - } - -} -close(IF); - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/listfiltering.xml --- a/rapsodyn/listfiltering.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ - -Compare listA and listB first X column and remove from listA the elements present in listB - - listfiltering.pl -input_file $input_listA -header_file $input_listB -nb_col $nb_col > $output_file - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/mpileupfilterandstat.pl --- a/rapsodyn/mpileupfilterandstat.pl Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.pl Tue Oct 07 10:34:34 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=){ + $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); diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/mpileupfilterandstat.xml --- a/rapsodyn/mpileupfilterandstat.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,4 +1,4 @@ - + Filter mpileup file entry #if $stat.do_stat=="YES" @@ -14,26 +14,26 @@ - - - + + + - + - - - - + + + + - + diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats.pl --- a/rapsodyn/rapsosnp_stats.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,215 +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 $sam_row = $ARGV[4]; -my $sam_filtered = $ARGV[5]; - -my $mpileup_variant = $ARGV[6]; - -my $list_filtered = $ARGV[7]; - -my $blast_filtered = $ARGV[8]; - -my $snp_selected = $ARGV[9]; - - -open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); -my $nbread=0; -my $nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($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=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($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=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($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=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR2T); - -print "\nSAM row\n"; -open(SAM, $sam_row) or die ("Can't open $sam_row\n"); -my %bitscore; -while (my $line=){ - if (($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 $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} - -print "bitscore\t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $key,"\t*\t"; -} -print "\n"; - -print " number \t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $bitscore{$key},"\t*\t"; -} -print "\n"; -close (SAMF); - -print "\nMPILEUP variant\n"; -open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n"); - -my $nbvariant=0; -while (my $line=){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - my $match = $fields[4]; - $match =~ s/\$//g; #the read start at this position - $match =~ s/\^.//g; #the read end at this position followed by quality char - if ($match =~/[ACGTNacgtn]+/){ - $nbvariant++; - } - } - else { - #print STDERR "Erreur : $line\n"; - } -} - -print "Variant detected :\t$nbvariant\n"; -close (MPV); - - -print "\nMPILEUP filtered without dubious position\n"; -open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} - -print "Variant selected :\t$nbvariant\n"; -close (LF); - -print "\nMPILEUP filtered without dubious position and BLAST\n"; -open(BF, $blast_filtered) or die ("Can't open $blast_filtered\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} - -print "Variant selected :\t$nbvariant\n"; -close (BF); - - -print "\nSNP selected after mpileup filtering : \t"; -open(SNP, $snp_selected) or die ("Can't open $snp_selected\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} - -print "$nbvariant\n"; -close (SNP); - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats.xml --- a/rapsodyn/rapsosnp_stats.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - -Merge best results from Blast - - rapsosnp_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_file $input_snp_selected_file > $output_file - - - - - - - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats2x.pl --- a/rapsodyn/rapsosnp_stats2x.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,307 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $read1_row = $ARGV[0]; -my $read2_row = $ARGV[1]; - -my $read1_trimmed_part1 = $ARGV[2]; -my $read1_trimmed_part2 = $ARGV[3]; -my $read2_trimmed_part1 = $ARGV[4]; -my $read2_trimmed_part2 = $ARGV[5]; - -my $sam_row_part1 = $ARGV[6]; -my $sam_row_part2 = $ARGV[7]; -my $sam_filtered_part1 = $ARGV[8]; -my $sam_filtered_part2 = $ARGV[9]; - -my $mpileup_variant = $ARGV[10]; - -my $list_filtered = $ARGV[11]; - -my $blast_filtered_part1 = $ARGV[12]; -my $blast_filtered_part2 = $ARGV[13]; - -my $snp_selected = $ARGV[14]; - - -open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); -my $nbread=0; -my $nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($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=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - } -} -print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR2R); - - - - - -open(INR1TP1, $read1_trimmed_part1) or die ("Can't open $read1_trimmed_part1\n"); -$nbread=0; -$nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP1); -open(INR1TP2, $read1_trimmed_part2) or die ("Can't open $read1_trimmed_part2\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP2); -print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; - - - - -open(INR2TP1, $read2_trimmed_part1) or die ("Can't open $read2_trimmed_part1\n"); -$nbread=0; -$nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP2); -open(INR2TP2, $read2_trimmed_part2) or die ("Can't open $read2_trimmed_part2\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP2); -print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; - - - - -print "\nSAM row\n"; -open(SAMP1, $sam_row_part1) or die ("Can't open $sam_row_part1\n"); -my %bitscore; -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP1); -open(SAMP2, $sam_row_part2) or die ("Can't open $sam_row_part2\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP2); -print "bitscore\t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $key,"\t*\t"; -} -print "\n"; -print " number \t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $bitscore{$key},"\t*\t"; -} -print "\n"; - - - - -print "\nSAM filtered\n"; -open(SAMFP1, $sam_filtered_part1) or die ("Can't open $sam_filtered_part1\n"); -undef %bitscore; -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP1); -open(SAMFP2, $sam_filtered_part2) or die ("Can't open $sam_filtered_part2\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP2); -print "bitscore\t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $key,"\t*\t"; -} -print "\n"; -print " number \t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $bitscore{$key},"\t*\t"; -} -print "\n"; - - - - -print "\nMPILEUP variant\n"; -open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n"); -my $nbvariant=0; -while (my $line=){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - my $match = $fields[4]; - $match =~ s/\$//g; #the read start at this position - $match =~ s/\^.//g; #the read end at this position followed by quality char - if ($match =~/[ACGTNacgtn]+/){ - $nbvariant++; - } - } - else { - #print STDERR "Erreur : $line\n"; - } -} -print "Variant detected :\t$nbvariant\n"; -close (MPV); - - - - - - -print "\nMPILEUP filtered without dubious position\n"; -open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} -print "Variant selected :\t$nbvariant\n"; -close (LF); - - - - - -print "\nMPILEUP filtered without dubious position and BLAST\n"; -open(BFP1, $blast_filtered_part1) or die ("Can't open $blast_filtered_part1\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} -close (BFP1); -open(BFP2, $blast_filtered_part2) or die ("Can't open $blast_filtered_part2\n"); -while (my $line=){ - $nbvariant++; -} -close (BFP2); -print "Variant selected :\t$nbvariant\n"; - - - - - -print "\nSNP selected after mpileup filtering : \t"; -open(SNP, $snp_selected) or die ("Can't open $snp_selected\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} - -print "$nbvariant\n"; -close (SNP); - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats2x.xml --- a/rapsodyn/rapsosnp_stats2x.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ - -Stats for rapsosnp workflow - - rapsosnp_stats2x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_snp_selected_file > $output_file - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats4x.pl --- a/rapsodyn/rapsosnp_stats4x.pl Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,447 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -my $read1_row = $ARGV[0]; -my $read2_row = $ARGV[1]; - -my $read1_trimmed_part1 = $ARGV[2]; -my $read1_trimmed_part2 = $ARGV[3]; -my $read1_trimmed_part3 = $ARGV[4]; -my $read1_trimmed_part4 = $ARGV[5]; -my $read2_trimmed_part1 = $ARGV[6]; -my $read2_trimmed_part2 = $ARGV[7]; -my $read2_trimmed_part3 = $ARGV[8]; -my $read2_trimmed_part4 = $ARGV[9]; - -my $sam_row_part1 = $ARGV[10]; -my $sam_row_part2 = $ARGV[11]; -my $sam_row_part3 = $ARGV[12]; -my $sam_row_part4 = $ARGV[13]; -my $sam_filtered_part1 = $ARGV[14]; -my $sam_filtered_part2 = $ARGV[15]; -my $sam_filtered_part3 = $ARGV[16]; -my $sam_filtered_part4 = $ARGV[17]; - -my $mpileup_variant = $ARGV[18]; - -my $list_filtered = $ARGV[19]; - -my $blast_filtered_part1 = $ARGV[20]; -my $blast_filtered_part2 = $ARGV[21]; -my $blast_filtered_part3 = $ARGV[22]; -my $blast_filtered_part4 = $ARGV[23]; - -my $snp_selected = $ARGV[24]; - - -open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); -my $nbread=0; -my $nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($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=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - } -} -print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; -close (INR2R); - - - - - -open(INR1TP1, $read1_trimmed_part1) or die ("Can't open $read1_trimmed_part1\n"); -$nbread=0; -$nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP1); -open(INR1TP2, $read1_trimmed_part2) or die ("Can't open $read1_trimmed_part2\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP2); -open(INR1TP3, $read1_trimmed_part3) or die ("Can't open $read1_trimmed_part3\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP3); -open(INR1TP4, $read1_trimmed_part4) or die ("Can't open $read1_trimmed_part4\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR1TP4); -print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; - - - - -open(INR2TP1, $read2_trimmed_part1) or die ("Can't open $read2_trimmed_part1\n"); -$nbread=0; -$nbbase =0; -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP2); -open(INR2TP2, $read2_trimmed_part2) or die ("Can't open $read2_trimmed_part2\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP2); -open(INR2TP3, $read2_trimmed_part3) or die ("Can't open $read2_trimmed_part3\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP3); -open(INR2TP4, $read2_trimmed_part4) or die ("Can't open $read2_trimmed_part4\n"); -while (my $line1=){ - my $line2 = ; - my $line3 = ; - my $line4 = ; - if ($line1 =~ /^@/){ - $nbread++; - if ($line2=~/([ATGCNX]+)/i){ - $nbbase += length($1); - } - else { - print STDERR "$line1\n$line2\n"; - } - } -} -close (INR2TP4); -print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; - - - - -print "\nSAM row\n"; -open(SAMP1, $sam_row_part1) or die ("Can't open $sam_row_part1\n"); -my %bitscore; -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP1); -open(SAMP2, $sam_row_part2) or die ("Can't open $sam_row_part2\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP2); -open(SAMP3, $sam_row_part3) or die ("Can't open $sam_row_part3\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP3); -open(SAMP4, $sam_row_part4) or die ("Can't open $sam_row_part4\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMP4); -print "bitscore\t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $key,"\t*\t"; -} -print "\n"; -print " number \t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $bitscore{$key},"\t*\t"; -} -print "\n"; - - - - -print "\nSAM filtered\n"; -open(SAMFP1, $sam_filtered_part1) or die ("Can't open $sam_filtered_part1\n"); -undef %bitscore; -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP1); -open(SAMFP2, $sam_filtered_part2) or die ("Can't open $sam_filtered_part2\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP2); -open(SAMFP3, $sam_filtered_part3) or die ("Can't open $sam_filtered_part3\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP3); -open(SAMFP4, $sam_filtered_part4) or die ("Can't open $sam_filtered_part4\n"); -while (my $line=){ - if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ - my @fields = split(/\s+/,$line); - my $bit = $fields[1]; - if ($bitscore{$bit}){ - $bitscore{$bit}++; - } - else { - $bitscore{$bit}=1; - } - } -} -close (SAMFP4); -print "bitscore\t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $key,"\t*\t"; -} -print "\n"; -print " number \t"; -foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { - print $bitscore{$key},"\t*\t"; -} -print "\n"; - - - - -print "\nMPILEUP variant\n"; -open(MPV, $mpileup_variant) or die ("Can't open $mpileup_variant\n"); -my $nbvariant=0; -while (my $line=){ - my @fields = split(/\s+/,$line); - if ($#fields >= 4){ - my $match = $fields[4]; - $match =~ s/\$//g; #the read start at this position - $match =~ s/\^.//g; #the read end at this position followed by quality char - if ($match =~/[ACGTNacgtn]+/){ - $nbvariant++; - } - } - else { - #print STDERR "Erreur : $line\n"; - } -} -print "Variant detected :\t$nbvariant\n"; -close (MPV); - - - - - - -print "\nMPILEUP filtered without dubious position\n"; -open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} -print "Variant selected :\t$nbvariant\n"; -close (LF); - - - - - -print "\nMPILEUP filtered without dubious position and BLAST\n"; -open(BFP1, $blast_filtered_part1) or die ("Can't open $blast_filtered_part1\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} -close (BFP1); -open(BFP2, $blast_filtered_part2) or die ("Can't open $blast_filtered_part2\n"); -while (my $line=){ - $nbvariant++; -} -close (BFP2); -open(BFP3, $blast_filtered_part3) or die ("Can't open $blast_filtered_part3\n"); -while (my $line=){ - $nbvariant++; -} -close (BFP3); -open(BFP4, $blast_filtered_part4) or die ("Can't open $blast_filtered_part4\n"); -while (my $line=){ - $nbvariant++; -} -close (BFP4); -print "Variant selected :\t$nbvariant\n"; - - - - - -print "\nSNP selected after mpileup filtering : \t"; -open(SNP, $snp_selected) or die ("Can't open $snp_selected\n"); -$nbvariant=0; -while (my $line=){ - $nbvariant++; -} - -print "$nbvariant\n"; -close (SNP); - - - - - - - - diff -r 1776b8ddd87e -r 3f7b0788a1c4 rapsodyn/rapsosnp_stats4x.xml --- a/rapsodyn/rapsosnp_stats4x.xml Mon Sep 29 03:02:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - -Stats for rapsosnp workflow - - rapsosnp_stats4x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read1_part3_trimmed_file $input_read1_part4_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_read2_part3_trimmed_file $input_read2_part4_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_row_part3_file $input_sam_row_part4_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_sam_filtered_part3_file $input_sam_filtered_part4_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_blast_filtered_part3_file $input_blast_filtered_part4_file $input_snp_selected_file > $output_file - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -