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"output_paired2" + }, + "input_read2_trimmednoN_file": { + "id": 7, + "output_name": "output_paired2" + }, + "input_sam_filtered_file": { + "id": 9, + "output_name": "output_file" + }, + "input_sam_row_file": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "name": "rapsodyn_stats", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 4964.0001220703125, + "top": 427.5 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "rapsodyn_stats", + "tool_state": "{\"input_read1_trimmed_file\": \"null\", \"input_read2_trimmednoN_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_read2_trimmed_file\": \"null\", \"__page__\": 0, \"input_sam_row_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_mpileup_filtered_file\": \"null\", \"input_read1_trimmednoN_file\": \"null\", \"input_assembly_file\": \"null\", \"input_sam_filtered_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_mpileup_row_file\": \"null\", \"input_list_filtered_file\": \"null\", \"input_blast_filtered_file\": \"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file diff -r 658acc3202dc -r f487491e1091 rapsodyn/filtersam_mapped_and_unique.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/filtersam_mapped_and_unique.pl Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,23 @@ +#!/usr/bin/perl +use strict; +use warnings; + +open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); +while (my $line=){ + if ($line =~ /^\@/){ + #Header conservation + print $line; + } + else { + #Optionnal flag verification + if (($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)){ + print $line; + } + } + } +} + + +close (IN); \ No newline at end of file diff -r 658acc3202dc -r f487491e1091 rapsodyn/filtersam_mapped_and_unique.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/filtersam_mapped_and_unique.xml Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,18 @@ + +Filter SAM file for uniq and well mapped pair-end reads + + filtersam_mapped_and_unique.pl $input_sam_file > $output_file + + + + + + + + + + + + + + diff -r 658acc3202dc -r f487491e1091 rapsodyn/filtersamunique.pl --- a/rapsodyn/filtersamunique.pl Tue Aug 19 13:00:53 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; - -open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); -while (my $line=){ - if ($line =~ /^\@/){ - #Header conservation - print $line; - } - else { - #Optionnal flag verification - if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ - print $line; - } - } -} - - -close (IN); \ No newline at end of file diff -r 658acc3202dc -r f487491e1091 rapsodyn/filtersamunique.xml --- a/rapsodyn/filtersamunique.xml Tue Aug 19 13:00:53 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - -Filter SAM file for uniquelly match reads - - filtersamunique.pl $input_sam_file > $output_file - - - - - - - - - - - - - - diff -r 658acc3202dc -r f487491e1091 rapsodyn/rapsodyn_stats.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats.pl Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,277 @@ +#!/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=){ + 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); + +open(INR1N, $read1_trimmed_noN) or die ("Can't open $read1_trimmed_noN\n"); +$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$line2\n"; + } + } +} +print "Trimmed (no N) Reads 1\tNumber of reads : ",$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=){ + my $line2 = ; + my $line3 = ; + my $line4 = ; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed (no N) Reads 2\tNumber of reads : ",$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 $line=){ + if (($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 row\n"; +open(MPR, $mpileup_row) or die ("Can't open $mpileup_row\n"); +my $basecovered=0; +my $nbvariant=0; +while (my $line=){ + my @fields = split(/\s+/,$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 $line=){ + my @fields = split(/\s+/,$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=){ + $nbvariant++; +} + +print "Variant selected :\t$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=){ + $nbvariant++; +} + +print "Variant selected :\t$nbvariant\n"; +close (BF); + + + + + + + + + + diff -r 658acc3202dc -r f487491e1091 rapsodyn/rapsodyn_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats.xml Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,28 @@ + +Merge best results from Blast + + 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 + + + + + + + + + + + + + + + + + + + + + + + + diff -r 658acc3202dc -r f487491e1091 rapsodyn/sickle.xml --- a/rapsodyn/sickle.xml Tue Aug 19 13:00:53 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ - - Windowed Adaptive Trimming of FastQ data - - sickle - - - sickle $readtype.single_or_paired --quiet - - #if str($readtype.single_or_paired) == "se": - -f $input_single -o $output_single - - #if $input_single.ext == "fastq": - -t sanger - #else if $input_single.ext == "fastqsanger": - -t sanger - #else if $input_single.ext == "fastqillumina": - -t illumina - #else if $input_single.ext == "fastqsolexa": - -t solexa - #end if - - #end if - - #if str($readtype.single_or_paired) == "pe": - -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single - - #if $input_paired1.ext == "fastq": - -t sanger - #else if $input_paired1.ext == "fastqsanger": - -t sanger - #else if $input_paired1.ext == "fastqillumina": - -t illumina - #else if $input_paired1.ext == "fastqsolexa": - -t solexa - #end if - - #end if - - #if str($qual_threshold) != "": - -q $qual_threshold - #end if - - #if str($length_threshold) != "": - -l $length_threshold - #end if - - #if $no_five_prime: - -x - #end if - - #if $discard_n: - -n - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (readtype['single_or_paired'] == 'se') - - - - (readtype['single_or_paired'] == 'pe') - - - - (readtype['single_or_paired'] == 'pe') - - - - (readtype['single_or_paired'] == 'pe') - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses. - -Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely. 5'-end trimming can be disabled. - -Sickle also has an option to discard reads with any Ns in them. - -Sickle supports three types of quality values: Illumina, Solexa, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sanger encoded. Sickle will get the quality type from the datatype of the file. - -Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it with simply a "+". This is the default format for CASAVA >= 1.8. - -Sickle also supports gzipped file inputs. - - - diff -r 658acc3202dc -r f487491e1091 rapsodyn/tempo2.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/tempo2.pl Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,28 @@ +#!/usr/bin/perl +#V1.10 + +use strict; +use warnings; +use Getopt::Long; + +my $input1 = $ARGV[0]; +my $output1 = $ARGV[1]; +my $input2 = $ARGV[2]; +my $output2 = $ARGV[3]; + +open(IN1, $input1) or die ("Can't open $input1\n"); +open(OUT1, ">$output1") or die ("Can't open $output1\n"); +while (my $ligne = ){ + print OUT1 $ligne; +} +close (IN1); +close (OUT1); + +open(IN2, $input2) or die ("Can't open $input2\n"); +open(OUT2, ">$output2") or die ("Can't open $output2\n"); +while (my $ligne = ){ + print OUT2 $ligne; +} +close (IN2); +close (OUT2); + diff -r 658acc3202dc -r f487491e1091 rapsodyn/tempo2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/tempo2.xml Wed Aug 20 12:11:09 2014 -0400 @@ -0,0 +1,66 @@ + +Temporisation with 2 inputs + + tempo2.pl $input1 $output1 $input2 $output2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 658acc3202dc -r f487491e1091 rapsodyn/test.pl --- a/rapsodyn/test.pl Tue Aug 19 13:00:53 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -#!/usr/bin/perl -#V1.10 - -use strict; -use warnings; -use Getopt::Long; - -my $input_read1_file = $ARGV[0]; -my $input_read2_file = $ARGV[1]; -my $input_assembly_file = $ARGV[2]; -my $output_read1_file = $ARGV[3]; -my $output_read2_file = $ARGV[4]; -my $output_assembly_file = $ARGV[5]; - -#$output_read1_file = $input_read1_file.".tmp"; -#$output_read2_file = $input_read2_file.".tmp"; -#$output_assembly_file = $input_assembly_file.".tmp"; - - - -open(INR1, $input_read1_file) or die ("Can't open $input_read1_file\n"); -open(INR2, $input_read2_file) or die ("Can't open $input_read2_file\n"); -open(INAF, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); - - -open(OUTR1, ">$output_read1_file") or die ("Can't open $output_read1_file\n"); -open(OUTR2, ">$output_read2_file") or die ("Can't open $output_read2_file\n"); -open(OUTAF, ">$output_assembly_file") or die ("Can't open $output_assembly_file\n"); - - - -while (my $ligne = ){ - print OUTR1 $ligne; -} - -close (INR1); -close (OUTR1); - -while (my $ligne = ){ - print OUTR2 $ligne; -} - -close (INR2); -close (OUTR2); - -while (my $ligne = ){ - print OUTAF $ligne; -} - -close (INAF); -close (OUTAF); - -print "Filler\n"; -print "$output_read1_file\n"; - diff -r 658acc3202dc -r f487491e1091 rapsodyn/test.xml --- a/rapsodyn/test.xml Tue Aug 19 13:00:53 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - -Merge best results from Blast - - test.pl $input_read1_file $input_read2_file $input_assembly_file $output_read1_file $output_read2_file $output_assembly_file > $output_stat_file - - - - - - - - - - - - - - - - -