Mercurial > repos > mcharles > rapsodyn
changeset 25:39376c7204be draft
Uploaded
| author | mcharles |
|---|---|
| date | Wed, 10 Sep 2014 05:12:05 -0400 |
| parents | e8e6b962c1f2 |
| children | 5c0e8f82bbbf |
| files | rapsodyn/Galaxy-Workflow-rapsosnp_v1.13.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.13_-_2x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.13_-_4x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-1x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_2x.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.15_-_4x.ga rapsodyn/ParseBlastForUniqueMatch.pl rapsodyn/ParseBlastForUniqueMatch.xml rapsodyn/mpileupfilterandstat.pl rapsodyn/mpileupfilterandstat.xml |
| diffstat | 10 files changed, 3443 insertions(+), 2928 deletions(-) [+] |
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17, + "output_name": "output_file" + }, + "input_sam_filtered_part3_file": { + "id": 18, + "output_name": "output_file" + }, + "input_sam_filtered_part4_file": { + "id": 19, + "output_name": "output_file" + }, + "input_sam_row_part1_file": { + "id": 12, + "output_name": "output" + }, + "input_sam_row_part2_file": { + "id": 13, + "output_name": "output" + }, + "input_sam_row_part3_file": { + "id": 14, + "output_name": "output" + }, + "input_sam_row_part4_file": { + "id": 15, + "output_name": "output" + }, + "input_snp_selected_file": { + "id": 42, + "output_name": "output_file" + } + }, + "inputs": [], + "name": "rapsosnp_stats4x", + "outputs": [ + { + "name": "output_file", + "type": "txt" + } + ], + "position": { + "left": 5447.5, + "top": 211 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "rapsosnp_stats4x", + "tool_state": "{\"input_blast_filtered_part2_file\": \"null\", \"input_blast_filtered_part3_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", 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\"null\"}", + "tool_version": "0.01", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/ParseBlastForUniqueMatch.pl Wed Sep 10 05:12:05 2014 -0400 @@ -0,0 +1,176 @@ +#!/usr/bin/perl +use strict; +use warnings; + + +my $input_variant_file = $ARGV[0]; +my $input_blast_file = $ARGV[1]; +my $window_length = $ARGV[2]; +my $nb_mismatch_max = $ARGV[3]; + +my %hash_name; + +open(INB, $input_blast_file) or die ("Can't open $input_blast_file\n"); +while (my $line =<INB>){ + my @fields = split (/\s+/,$line); + # print $#fields,"\n"; + # print $line; + # exit(0); + my $query_name; + my $query_start; + my $query_stop; + my $query_aln; + my $subject_aln; + my $compt_mismatch_5p=0; + my $compt_mismatch_3p=0; + + if ($#fields == 24){ + $query_name = $fields[0]; + $query_start = $fields[6]; + $query_stop = $fields[7]; + $query_aln = $fields[20]; + $subject_aln = $fields[21]; + } + elsif ($#fields == 4){ + $query_name = $fields[0]; + $query_start = $fields[1]; + $query_stop = $fields[2]; + $query_aln = $fields[3]; + $subject_aln = $fields[4]; + } + else { + print STDERR "Unrecongnized tabular format for blast result\nScript works with 25 column or 5 custom column(qseqid,qstart,qend,ssseq,sseq)\n"; + exit(0); + } + + + my @field_name = split (/\_/,$query_name); + my $name = $field_name[0]."_".$field_name[1]; + if ($query_name =~ /random/){ + $name .= "_".$field_name[2]; + # print $name."\n"; + + } + if (!$hash_name{$name}){ + $hash_name{$name}=0; + } + elsif ($hash_name{$name}>1){ + next; + } + # if ($query_name eq "chrUnn_random_8279117_1_M1_a"){ + # print "READ : $query_name\n$name\n"; + # print "HASH : ",$hash_name{$name},"\n"; + # # exit(0); + # } + + + + chomp($query_aln); + chomp($subject_aln); + + my $nb_gap_query=0; + + if (length($query_aln) == length($subject_aln)){ + if (length($query_aln)<$window_length-$nb_mismatch_max){ + } + else { + my @q = split(//,$query_aln); + my @s = split(//,$subject_aln); + 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){ + $compt_mismatch_5p++; + } + elsif ($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){ + $compt_mismatch_5p++; + } + elsif ($global_idx > $window_length){ + $compt_mismatch_3p++; + } + } + } + } + $compt_mismatch_5p += $query_start-1; + $compt_mismatch_3p += $window_length *2 + 1 - $query_stop; + + # for (my $i=0;$i<$window_length;$i++){ + # if ($tbl_q_aln[$i] eq "#"){ + # $compt_mismatch_5p++; + # } + # elsif ($tbl_q_aln[$i] ne $tbl_s_aln[$i]){ + # $compt_mismatch_5p++; + # } + # else { + # } + + # } + # for (my $i=$window_length+1;$i<=$window_length*2;$i++){ + # if ($tbl_q_aln[$i] eq "#"){ + # $compt_mismatch_3p++; + # } + # elsif ($tbl_q_aln[$i] ne $tbl_s_aln[$i]){ + # $compt_mismatch_3p++; + # } + # else { + # } + # } + if (($compt_mismatch_5p <= $nb_mismatch_max)||($compt_mismatch_3p <= $nb_mismatch_max)){ + $hash_name{$name}++; + } + + } + } + else { + print STDERR "incompatible subject and query alignement length\n $query_aln\n$subject_aln\n"; + } + + # if ($line=~/chrCnn_random_49828229/){ + # print $line; + # print $query_aln,"\n"; + # print $subject_aln,"\n"; + # print $compt_mismatch_5p,"\t",$compt_mismatch_3p,"\n"; + # print $hash_name{"chrCnn_random_49828229"},"\n"; + # print "\n"; + # } + + + +} +# exit(0); + +close (INB); + +open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); + +while (my $ligne = <INV>) { + + my @champs = split (/\s+/,$ligne); + my $header = $champs[0]."_".$champs[1]; + + if ($hash_name{$header}){ + if ($hash_name{$header}==1){ + print $ligne; + } + } + else { + #print STDERR "No blast result for ",$header,"\n"; + } + + +} + +close(INV); + + +# foreach my $key (sort keys %hash_name){ + # print $key,"\t",$hash_name{$key},"\n"; + +# }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/ParseBlastForUniqueMatch.xml Wed Sep 10 05:12:05 2014 -0400 @@ -0,0 +1,21 @@ +<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01"> +<description>Filter mpileup with blast results</description> +<command interpreter="perl"> + ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file +</command> +<inputs> +<param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> +<param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/> +<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> +<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/> +</inputs> +<outputs> + <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/mpileupfilterandstat.pl Fri Sep 05 06:12:10 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.pl Wed Sep 10 05:12:05 2014 -0400 @@ -29,19 +29,19 @@ my $ONLY_UNFILTERED_VARIANT="OFF"; my $DO_STAT="NO"; -if ($#ARGV<0){ - print "\n"; - print "perl 020_FilterPileupv6 -input_file <mpileup_file> [OPTION]\n"; - print "-input_file \tinputfile in mpileup format\n"; - print "-log_file \tlogfile containing discarded mpileup lines and the errorcode associated\n"; - print "-min_depth \tminimum depth required [1]\n"; - print "-max_depth \tmaximim depth (position with more coverage will be discarded) [100]\n"; - print "-min_frequency \tminimum variant frequency (0->1) [1] (default 1 => 100% reads show the variant at this position)\n"; - print "-min_distance \tminimum distance between variant [0]\n"; - print "-min_forward_and_reverse \tminimum number of reads in forward and reverse covering the variant required [0]\n"; - print "\n"; - exit(0); -} + +my $STAT_MIN_DEPTH_MIN = 2; +my $STAT_MIN_DEPTH_MAX = 10; +my $STAT_MIN_DEPTH_STEP = 2; +my $STAT_MAX_DEPTH_MIN = 100; +my $STAT_MAX_DEPTH_MAX = 200; +my $STAT_MAX_DEPTH_STEP = 100; +my $STAT_FREQ_MIN = 0.8; +my $STAT_FREQ_MAX = 1; +my $STAT_FREQ_STEP = 0.1; +my $STAT_DIST_MIN = 0; +my $STAT_DIST_MAX = 50; +my $STAT_DIST_STEP = 50; GetOptions ( "input_file=s" => \$inputfile, @@ -53,10 +53,21 @@ "min_forward_and_reverse=i" => \$MIN_FORWARDREVERSE, "variant_only=s" => \$ONLY_UNFILTERED_VARIANT, "v=i" => \$VERBOSE, -"do_stat=s" => \$DO_STAT +"do_stat=s" => \$DO_STAT, +"stat_min_depth_min=i" => \$STAT_MIN_DEPTH_MIN, +"stat_min_depth_max=i" => \$STAT_MIN_DEPTH_MAX, +"stat_min_depth_step=i" => \$STAT_MIN_DEPTH_STEP, +"stat_max_depth_min=i" => \$STAT_MAX_DEPTH_MIN, +"stat_max_depth_max=i" => \$STAT_MAX_DEPTH_MAX, +"stat_max_depth_step=i" => \$STAT_MAX_DEPTH_STEP, +"stat_freq_min=f" => \$STAT_FREQ_MIN, +"stat_freq_max=f" => \$STAT_FREQ_MAX, +"stat_freq_step=f" => \$STAT_FREQ_STEP, +"stat_dist_min=i" => \$STAT_DIST_MIN, +"stat_dist_max=i" => \$STAT_DIST_MAX, +"stat_dist_step=i" => \$STAT_DIST_STEP ) or die("Error in command line arguments\n"); - open(IF, $inputfile) or die("Can't open $inputfile\n"); my @tbl_line; @@ -150,22 +161,24 @@ open(LF,">$logfile") or die ("Can't open $logfile\n"); if ($DO_STAT eq "YES"){ - for (my $idx_min_depth=2;$idx_min_depth<=32;$idx_min_depth = $idx_min_depth*2){ - for (my $idx_freq = 0.5;$idx_freq<=1;$idx_freq= $idx_freq+0.1){ - for (my $idx_dist=0;$idx_dist<=50;$idx_dist = $idx_dist + 50){ - for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){ - my %stat_param; - $stat_param{"min_depth"}=$idx_min_depth; - $stat_param{"max_depth"}=250; - $stat_param{"min_freq"}=$idx_freq; - $stat_param{"min_fr"}=$idx_fr; - $stat_param{"min_dist"}=$idx_dist; + 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){ + for (my $idx_dist=$STAT_DIST_MIN;$idx_dist<=$STAT_DIST_MAX;$idx_dist = $idx_dist + $STAT_DIST_STEP){ + for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){ + my %stat_param; + $stat_param{"min_depth"}=$idx_min_depth; + $stat_param{"max_depth"}=$idx_max_depth; + $stat_param{"min_freq"}=$idx_freq; + $stat_param{"min_fr"}=$idx_fr; + $stat_param{"min_dist"}=$idx_dist; - print LF "#SNP = ",&test_check(\@tbl_line,\%stat_param),"\tdepth (min/max) = ",$stat_param{"min_depth"}," / ",$stat_param{"max_depth"},"\tmin_dist=",$stat_param{"min_dist"},"\tmin_freq=",$stat_param{"min_freq"},"\tmin_forwardreverse = ",$stat_param{"min_fr"},"\n"; - } - } + print LF "#SNP = ",&test_check(\@tbl_line,\%stat_param),"\tdepth (min/max) = ",$stat_param{"min_depth"}," / ",$stat_param{"max_depth"},"\tmin_dist=",$stat_param{"min_dist"},"\tmin_freq=",$stat_param{"min_freq"},"\tmin_forwardreverse = ",$stat_param{"min_fr"},"\n"; + } + } + } + print "\n"; } - print "\n"; } }
--- a/rapsodyn/mpileupfilterandstat.xml Fri Sep 05 06:12:10 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.xml Wed Sep 10 05:12:05 2014 -0400 @@ -1,7 +1,16 @@ -<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.07"> +<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08"> <description>Filter mpileup file entry</description> <command interpreter="perl"> - mpileupfilterandstat.pl -input_file $input_file -log_file $log_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth -do_stat $do_stat> $output_file + #if $stat.do_stat=="YES" + mpileupfilterandstat.pl -input_file $input_file -log_file $log_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth -do_stat $stat.do_stat +-stat_min_depth_min $stat.stat_min_depth_min -stat_min_depth_max $stat.stat_min_depth_max -stat_min_depth_step $stat.stat_min_depth_step +-stat_max_depth_min $stat.stat_max_depth_min -stat_max_depth_max $stat.stat_max_depth_max -stat_max_depth_step $stat.stat_max_depth_step +-stat_freq_min $stat.stat_freq_min -stat_freq_max $stat.stat_freq_max -stat_freq_step $stat.stat_freq_step +-stat_dist_min $stat.stat_dist_min -stat_dist_max $stat.stat_dist_max -stat_dist_step $stat.stat_dist_step > $output_file + #else + mpileupfilterandstat.pl -input_file $input_file -log_file $log_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth -do_stat $stat.do_stat > $output_file + #end if + </command> <inputs> <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> @@ -10,10 +19,31 @@ <param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/> <param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/> -<param name="do_stat" type="select" label="Compute stats "> - <option value="NO">NO</option> - <option value="YES">YES</option> -</param> +<conditional name="stat"> + <param name="do_stat" type="select" label="Compute stats "> + <option value="NO">NO</option> + <option value="YES">YES</option> + </param> + <when value="YES"> + <param name="stat_min_depth_min" type="integer" value = "2" label="min_depth - min" /> + <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" /> + <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" /> + <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" /> + <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" /> + <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" /> + <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" /> + <param name="stat_freq_max" type="float" value = "1" label="freq - max" /> + <param name="stat_freq_step" type="float" value = "0.1" label="freq - step" /> + <param name="stat_dist_min" type="integer" value = "0" label="dist - min" /> + <param name="stat_dist_max" type="integer" value = "50" label="dist - max" /> + <param name="stat_dist_step" type="integer" value = "50" label="dist - step" /> + </when> + <when value="NO"> + + </when> +</conditional> + + </inputs> <outputs>