Mercurial > repos > priti > vdt_sequence
changeset 17:9efb80df2560 draft
Deleted selected files
| author | priti |
|---|---|
| date | Sat, 07 Jun 2014 07:50:48 -0400 |
| parents | 53692027fb02 |
| children | df141814fe8c |
| files | SoftSearch.pl softsearch_wrapper.xml tool-data/fasta_indexes.loc.sample tool-data/tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 5 files changed, 0 insertions(+), 1365 deletions(-) [+] |
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--- a/SoftSearch.pl Sat Jun 07 07:42:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1192 +0,0 @@ -#!/usr/bin/perl - -#### -#### Usage: SoftSearch.pl [-lqrmsd] -b <BAM> -f <Genome.fa> -sam <samtools path> -bed <bedtools path> -#### Created 1-30-2012 by Steven Hart, PhD -#### hart.steven@mayo.edu -#### Required bedtools & samtools to be in path - - -use lib "/home/plus91/galaxy-dist/tool_dependency_dir/softsearch/0.6/priti/vdt_dependency/e184c650a023/lib" ; - -use Getopt::Long; -use strict; -use warnings; -#use Data::Dumper; -use LevD; -use File::Basename; - -my ($INPUT_BAM,$INPUT_FASTA,$OUTPUT_FILE,$minSoft,$minSoftReads,$dist_To_Soft,$bedtools,$samtools); -my ($minRP, $temp_output, $num_sd, $MapQ, $chrom, $unmated_pairs, $minBQ, $pair_only, $disable_RP_only); -my ($levD_local_threshold, $levD_distl_threshold,$pe_upper_limit,$high_qual,$sv_only,$blacklist,$genome_file,$verbose); - -my $cmd = ""; - -#Declare variables -GetOptions( - 'b=s' => \$INPUT_BAM, - 'f=s' => \$INPUT_FASTA, - 'o:s' => \$OUTPUT_FILE, - 'm:i' => \$minRP, - 'l:i' => \$minSoft, - 'r:i' => \$minSoftReads, - 't:i' => \$temp_output, - 's:s' => \$num_sd, - 'd:i' => \$dist_To_Soft, - 'q:i' => \$MapQ, - 'c:s' => \$chrom, - 'u:s' => \$unmated_pairs, - 'x:s' => \$minBQ, - 'p' => \$pair_only, - 'g' => \$disable_RP_only, - 'j:s' => \$levD_local_threshold, - 'k:s' => \$levD_distl_threshold, - 'a:s' => \$pe_upper_limit, - 'e:s' => \$high_qual, - 'L' => \$sv_only, - 'v' => \$verbose, - 'blacklist:s' => \$blacklist, - 'genome_file:s' => \$genome_file, - "help|h|?" => \&usage); - -unless($sv_only){$sv_only=""}; -if(defined($INPUT_BAM)){$INPUT_BAM=$INPUT_BAM} else {print usage();die "Where is the BAM file?\n\n"} -if(defined($INPUT_FASTA)){$INPUT_FASTA=$INPUT_FASTA} else {print usage();die "Where is the fasta file?\n\n"} -my ($fn,$pathname) = fileparse($INPUT_BAM,".bam"); -my $index=`ls $pathname/$fn*bai|head -1`; -#my $index =`ls \${INPUT_BAM%.bam}*bai`; -#print "INDEX=$index\n"; -if(!$index){die "\n\nERROR: you need index your BAM file\n\n"} - -### get current time -print "Start Time : " . &spGetCurDateTime() . "\n"; -my $now = time; - -#if(defined($OUTPUT_FILE)){$OUTPUT_FILE=$OUTPUT_FILE} else {$OUTPUT_FILE="output.vcf"; print "\nNo outfile specified. Using output.vcf as default\n\n"} -if(defined($minSoft)){$minSoft=$minSoft} else {$minSoft=5} -if(defined($minRP)){$minRP=$minRP} else {$minRP=5} -if(defined($minSoftReads)){$minSoftReads=$minSoftReads} else {$minSoftReads=5} -if(defined($dist_To_Soft)){$dist_To_Soft=$dist_To_Soft} else {$dist_To_Soft=300} -if(defined($num_sd)){$num_sd=$num_sd} else {$num_sd=6} -if(defined($MapQ)){$MapQ=$MapQ} else {$MapQ=20} - -unless (defined $pe_upper_limit) { $pe_upper_limit = 10000; } -unless (defined $levD_local_threshold) { $levD_local_threshold = 0.05; } -unless (defined $levD_distl_threshold) { $levD_distl_threshold = 0.05; } -#Get sample name if available -my $SAMPLE_NAME=""; -my $OUTNAME =""; -$SAMPLE_NAME=`samtools view -f2 -H $INPUT_BAM|awk '{if(\$1~/^\@RG/){sub("ID:","",\$2);name=\$2;print name}}'|head -1`; -$SAMPLE_NAME=~s/\n//g; -if (!$OUTPUT_FILE){ - if($SAMPLE_NAME ne ""){$OUTNAME=$SAMPLE_NAME.".vcf"} - else {$OUTNAME="output.vcf"} -} -else{$OUTNAME=$OUTPUT_FILE} - -print "Writing results to $OUTNAME\n"; - - -##Make sure if submitting on SGE, to prepned the "chr". Not all referecne FAST files require "chr", so we shouldn't force the issue. -if(!defined($chrom)){$chrom=""} -if(!defined($unmated_pairs)){$unmated_pairs=0} - -my $badQualValue=chr($MapQ); -if(defined($minBQ)){ $badQualValue=chr($minBQ); } - -if($badQualValue eq "#"){$badQualValue="\#"} - -# adding and cheking for samtools and bedtools in the PATh -## check for bedtools and samtools in the path -$bedtools=`which intersectBed` ; -if(!defined($bedtools)){die "\nError:\n\tno bedtools. Please install bedtools and add to the path\n";} -#$samtools=`samtools 2>&1`; -$samtools=`which samtools`; -if($samtools !~ /(samtools)/i){die "\nError:\n\tno samtools. Please install samtools and add to the path\n";} - -print "Usage = SoftSearch.pl -l $minSoft -q $MapQ -r $minSoftReads -d $dist_To_Soft -m $minRP -s $num_sd -c $chrom -b $INPUT_BAM -f $INPUT_FASTA -o $OUTNAME \n\n"; -sub usage { - print "\nusage: SoftSearch.pl [-cqlrmsd] -b <BAM> -f <Genome.fa> \n"; - print "\t-q\t\tMinimum mapping quality [20]\n"; - print "\t-l\t\tMinimum length of soft-clipped segment [5]\n"; - print "\t-r\t\tMinimum depth of soft-clipped reads at position [5]\n"; - print "\t-m\t\tMinimum number of discordant read pairs [5]\n"; - print "\t-s\t\tNumber of sd away from mean to be considered discordant [6]\n"; - print "\t-u\t\tNumber of unmated pairs [0]\n"; - print "\t-d\t\tMax distance between soft-clipped segments and discordant read pairs [300]\n"; - print "\t-o\t\tOutput file name [output.vcf]\n"; - print "\t-t\t\tPrint temp files for debugging [no|yes]\n"; - print "\t-c\t\tuse only this chrom or chr:pos1-pos2\n"; - print "\t-p\t\tuse paired-end mode only. In other words, don't try to find soft-clipping events!\n"; - print "\t-g\t\tEnable paired-only seach. This will look for discordant read pairs even without soft clips.\n"; - print "\t-a\t\tset the minimum distance for a discordant read pair without soft-clipping info [10000]\n"; - print "\t-L\t\tFlag to print out even small deletions (low quality)\n"; - print "\t-e\t\tdisable strict quality filtering of base qualities in soft-clipped reads [no]\n"; - print "\t-blacklist\tareas of the genome to skip calling. Requires -genome_file\n"; - print "\t-genome_file\ttab seperated value of chromosome name and length. Only used with -blacklist option\n\n"; - - exit 1; - } - - -############################################################# -# create temporary variable name -############################################################# -srand (time ^ $$ ^ unpack "%L*", `ps axww | gzip -f`); -our $random_name=join "", map { ("a".."z")[rand 26] } 1..8; - -############################################################# -## create green list -############################################################## -# -my $new_blacklist=""; -if($blacklist){ - if(!$genome_file){die "if using a blacklist, you must also specify the location of a genome_file - The format of the genome_file should be - chrom size - chr1 249250621 - chr2 243199373 - ... - - If using hg19, you can ge the genome file by - mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg19.chromInfo\" > hg19.genome";} - - $cmd=join("","complementBed -i $blacklist -g $genome_file >",$random_name,".bed") ; - system ($cmd); - $new_blacklist=join(""," -L ",$random_name,".bed "); - } - -if($verbose){print "CMD=$cmd\nBlacklist is $new_blacklist\n";} - - - - - -############################################################# -# Calcualte insert size distribution of properly mated reads -############################################################# - -#Change for compatability with other operating systems -#my $metrics=`samtools view -q $MapQ -f2 $INPUT_BAM $chrom|cut -f9|head -10000|awk '{if (\$1<0){\$1=-\$1}else{\$1=\$1} sum+=\$1; sumsq+=\$1*\$1} END {print sum/NR, sqrt(sumsq/NR - (sum/NR)**2)}'`; - -my $metrics=`samtools view -q $MapQ -f2 $INPUT_BAM $chrom|head -10000|cut -f9|awk '{if (\$1<0){\$1=-\$1}else{\$1=\$1} sum+=\$1; sumsq+=\$1*\$1} END {print sum/NR, sqrt(sumsq/NR - (sum/NR)^2)}'`; -#my ($mean,$stdev)=split(/ /,$metrics); -my ($mean,$stdev)=split(/\s/,$metrics); -$stdev=~s/\n//; -my $upper_limit=int($mean+($num_sd*$stdev)); -my $lower_limit=int($mean-($num_sd*$stdev)); -die if (!$mean); -print qq{The mean insert size is $mean +/- $stdev (sd) -The upper limit = $upper_limit -The lower limit = $lower_limit\n -}; -if($lower_limit<0){ - print "Warning!! Given this insert size distribution, we can not call small indels. No other data will be affected\n"; - $lower_limit=1; -} -my $tmp_name=join ("",$random_name,".tmp.bam"); -my $random_file_sc = ""; -my $command = ""; - -############################################################# -# Make sam file that has soft clipped reads -############################################################# -#give file a name -if(!defined($pair_only)){ - $random_file_sc=join ("",$random_name,".sc.sam"); - $command=join ("","samtools view -q $MapQ -F 1024 $INPUT_BAM $chrom $new_blacklist| awk '{OFS=\"\\t\"}{c=0;if(\$6~/S/){++c};if(c == 1){print}}' | perl -ane '\$TR=(\@F[10]=~tr/\#//);if(\$TR<2){print}' > ", $random_file_sc); - - print "Making SAM file of soft-clipped reads\n"; -if($verbose){ print "$command\n";} - system("$command"); - - ############################################################# - # Find areas that have deep enough soft-clip coverage - print "Identifying soft-clipped regions that are at least $minSoft bp long \n"; - open (FILE,"$random_file_sc")||die "Can't open soft-clipped sam file $random_file_sc\n"; - - my $tmpfile=join("",$random_file_sc,".sc.passfilter"); - open (OUT,">$tmpfile")||die "Can't write files here!\n"; - - while(<FILE>){ - @_ = split(/\t/, $_); - #### parse CIGAR string and create a hash of array of each operation - my @CIGAR = split(/([0-9]+[SMIDNHXP])/, $_[5]); - my $hash; - map { push(@{$hash->{$2}}, $1) if (/(\d+)([SMIDNHXP])/) } @CIGAR; - - #for ($i=0; $i<=$#softclip_pos; $i++) { - foreach my $softclip (@{$hash->{S}}) { - #if ($CIGAR[$softclip_pos[$i]] > $minSoft){ - if ($softclip > $minSoft){ - ###############Make sure base qualities don't have more than 2 bad marks - my $qual=$_[10]; - my $TR=($qual=~tr/$badQualValue//); - if($badQualValue eq "#"){ $TR=($qual=~tr/\#//); } - #Skip the soft clip if there is more than 2 bad qual values - #next if($TR > 2); -# if (!$high_qual){next if($TR > 2);} - print OUT; - last; - } - } - } - close FILE; - close OUT; - - $command=join(" ","mv",$tmpfile,$random_file_sc); -if($verbose){ print "$command\n";} - system("$command"); -} - -######################################################### -#Stack up SoftClips -######################################################### -my $random_file=join("",$random_name,".sc.direction.bed"); -if(!defined($pair_only)){ - open (FILE,"$random_file_sc")|| die "Can't open sam file\n"; - #$random_file=join("",$random_name,".sc.direction"); - - print "Calling sides of soft-clips\n"; - #\nTMPOUT=$random_file\tINPUT=$random_file_sc\n\n"; - open (TMPOUT,">$random_file")|| die "Can't create tmp file\n"; - - while (<FILE>){ - @_ = split(/\t/, $_); - #### parse CIGAR string and create a hash of array of each operation - my @CIGAR = split(/([0-9]+[SMIDNHXP])/, $_[5]); - my $hash; - map { push(@{$hash->{$2}}, $1) if (/(\d+)([SMIDNHXP])/) } @CIGAR; - - #### next if softclips on each end - next if ($_[5] =~ /^[0-9]+S.*S$/); - - #### next softclip occurs in the middle - next if ($_[5] =~ /^[0-9]+[^S][0-9].*S.+$/); - - my $softclip = $hash->{S}[0]; - - my $end1 = 0; - my $end2 = 0; - my $softBases = ""; - my $right_corrected="";my $left_corrected=""; - - if ($softclip > $minSoft) { - - ####If the soft clip occurs at end of read and its on the minus strand, then it's a right clip - if ($_[5] =~ /^.*S$/) { - $end1=$_[3]+length($_[9])-$softclip-1; - $end2=$end1+1; -next if ($end1<0); - #RIGHT clip on Minus - $softBases=substr($_[9], length($_[9])-$softclip, length($_[9])); - #Right clips don't always get clipped correctly, so fix that - # Check to see if sc base matches ref - $right_corrected=baseCheck($_[2],$end2,"right",$softBases); - print TMPOUT "$right_corrected\n" - - } else { - #### Begins with S (left clip) - $end1=$_[3]-$softclip; -next if ($end1<0); - - $softBases=substr($_[9], 0,$softclip);#print "TMP=$softBases\n"; - $left_corrected=baseCheck($_[2],$end1,"left",$softBases); -if(!$left_corrected){print "baseCheck($_[2],$end1,left,$softBases)\n";next} - print TMPOUT "$left_corrected\n"; -#print "\nSEQ=$_[9]\t\n"; - - } - } - } -close FILE; -close TMPOUT; -} -sub baseCheck{ - my ($chrom,$pos,$direction,$softBases)=@_; - #skip if position is less than 0, which is caused by MT DNA - return if ($pos<0); - my $exit=""; - - while(!$exit){ - if($direction=~/right/){ - my $refBase=getSeq($chrom,$pos,$INPUT_FASTA); - my $softBase=substr($softBases,0,1); - if ($softBase !~ /$refBase/){ - my $value=join("\t",$chrom,$pos,$pos+1,join("|",$softBases,$direction)); - $exit="STOP"; - return $value; - } - else{ - $pos=$pos+1; - $softBases=substr($softBases, 1,length($softBases)); - } - } - else{ - my $refBase=getSeq($chrom,$pos+1,$INPUT_FASTA); - my $softBase=substr($softBases,-1,1); - if ($softBase !~ /$refBase/){ - $pos=$pos-1+length($softBases); - my $value=join("\t",$chrom,$pos-1,$pos,join("|",$softBases,$direction)); - $exit="STOP"; - return $value; - } - else{ - $pos=$pos-1; - $softBases=substr($softBases, 0, -1); - #print "Trying again $softBases\n"; - } - - } - -} -} -#Remove SAM files to conserve space -unlink($random_file_sc); - - -my $random_file_disc="$INPUT_BAM"; -### -# -###################################################### -# Transform Read pair groups into softclip equivalents -###################################################### -# -# -# -my $v=""; -#if($disable_RP_only){ -print "Running Bam2pair.pl\n"; -print "Looking for discordant read pairs without requiring soft-clipping information\n"; - use FindBin qw($Bin); - my $path=$Bin; -# print"\n\nPATH=$path\n\n"; -if($verbose){$v="-v"} - my $tmp_out=join("",$random_name,"RP.out"); - $command=join("","perl ",$path,"/Bam2pair.pl -b $random_file_disc -o $tmp_out -isize $pe_upper_limit -winsize $dist_To_Soft -min $minRP -chrom $chrom -prefix $random_name -q $MapQ -blacklist $random_name.bed $v"); -if($verbose){ print "$command\n"}; - system("$command"); - $command=join("","perl -ane '\$end1=\@F[1];\$end2=\@F[3];print join(\"\\t\",\@F[0..1],\$end1,\"unknown|left\");print \"\\n\";print join(\"\\t\",\@F[2..3],\$end2,\"unknown|left\");print \"\\n\"' ", $tmp_out," >> ",$random_file); -if($verbose){print "$command\n"}; - system($command); - unlink($tmp_out); -#} -# - - -###################################################### -unlink("$random_file","$tmp_name","$random_file","$index","$random_name","$new_blacklist") if (-z $random_file || ! -e $random_file ) ; -if (-z $random_file || ! -e $random_file){ - print "Softclipped file is empty($random_file).\nNo soft clipping found using desired paramters\n\n"; - open (OUT,">$OUTNAME")||die "Can't write files here!\n"; - &print_header(); - close OUT; - exit; - } - - -############################################################# -# Make sure there are enough soft-clippped supporting reads -############################################################# -my $outfile=join("",$random_file,".sc.merge.bed"); -#sortbed -i .sc.direction | mergeBed -nms -d 25 -i stdin > .sc.merge.bed -$command=join(" ","sortBed -i",$random_file," | mergeBed -nms -i stdin","|egrep \";|,\"","|awk '{OFS=\"\t\"}(NF==4)'",">",$outfile); - -print "$command\n" if ($verbose); -system("$command"); - -if (-z $outfile || ! -e $outfile){ - unlink("$tmp_name","$random_file","$outfile","$index","$random_name","$new_blacklist"); - print "mergeBed file is empty.\nNo strucutral variants found\n\n" ; - open (OUT,">$OUTNAME")||die "Can't write files here!\n"; - &print_header(); - close OUT; - exit; -} - -print "completed mergeBed\n"; - -############################################################### -# If left and right are on the same line, make into 2 lines -############################################################### -open (INFILE,$outfile)||die "couldn't open temp file : $. \n\n"; -my $tmp2=join("",$random_name,".sc.fixed.merge.bed"); -#print "INFILE=$outfile\tOUTFILE=$tmp2\n\n"; -#INPUT FORMAT=chr9\t131467\t131473\tATGCTTATTAAAA|left;TTATTAAAAGCATA|left -open (OUTFILE,">$tmp2")||die "couldn't create temp file : $. \n\n"; -while(<INFILE>){ - chomp $_; - my $l = $_; - - my @a = split(/\t/, $l); - my $info = $a[3]; - my @info_arr = split(/\;/, $info); - my @left_arr=(); - my @right_arr=(); - @left_arr = grep(/left/, @info_arr); - @right_arr = grep(/right/, @info_arr); - - #New - my $left = join(";", @left_arr); - my $right = join(";", @right_arr); - $info = join(";", @info_arr); - - if((@left_arr) && (@right_arr)){ - print OUTFILE "$a[0]\t$a[1]\t$a[2]\t$left\n$a[0]\t$a[1]\t$a[2]\t$right\n"; - } else{ - my $all=join("\t",@a[0..2],$info); - print OUTFILE "$all\n"; - } -} - -# make sure output file name is $outfile -$command=join(" ","sed -e '/ /s//\t/g'", $tmp2,"|awk 'BEGIN{OFS=\"\\t\"}(NF==4)'", "|perl -pne 's/ /\t/g'>",$outfile); -system("$command"); -if($verbose){print "$command\n"}; -unlink("$tmp_name","$random_file","$tmp2","$outfile","$index","random_name","$new_blacklist") if (-z $outfile || ! -e $outfile) ; - if (-z $outfile || ! -e $outfile){ - print "Fixed mergeBed file is empty($outfile).\nNo strucutral variants found\n\n"; - open (OUT,">$OUTNAME")||die "Can't write files here!\n"; - &print_header(); - close OUT; - exit; -} - -print "completed fixing mergeBed\n\n"; - -############################################################### -# Seperate directions of soft clips -############################################################### -my $left_sc = join("", "left", $tmp2); -my $right_sc = join("", "right", $tmp2); -use FindBin qw($Bin); -#my $path=$Bin; - -$command=join("","grep left ", $tmp2, " |sed -e '/left /s//left\;/g' | sed -e '/ /s//\t/g'|perl ".$path."/direction_filter.pl - >",$left_sc); -system("$command"); -#print "$command\n"; -$command=join("","grep right ", $tmp2, " |sed -e '/right /s//right\;/g' | sed -e '/ /s//\t/g'|perl ".$path."/direction_filter.pl - >",$right_sc); -#$command=join(" ","grep right ", $tmp2, " |sed -e '/right /s//right\;/g' | sed -e '/ /s//\t/g' >",$right_sc); -system("$command"); -#print "$command\n"; -#die "CHECK $right_sc\n"; - -############################################################### -# Count the number and identify directions of soft clips -############################################################### -print "Count the number and identify directions of soft clips\n"; -#print "looking in $outfile\n"; -$outfile=join("",$random_name,".sc.fixed.merge.bed"); - -open (INFILE,$outfile)||die "couldn't open temp file\n\n"; -my $tmp3 = join("", $random_file, "predSV"); -open (OUTFILE, ">$tmp3")||die "couldn't create temp file\n\n"; -while(<INFILE>){ -chomp; - @_=split(/\t/,$_); - my $count=tr/\;//;$count+=tr/\,//; - $count=$count+1; - my $left=0; - my $right=0; - - while ($_ =~ /left/g) { $left++ } # count number of right clips - while ($_ =~ /right/g) { $right++ } # count number of left clips - - ############################################################### - if ($count >= $minSoftReads){ - ####get longets soft-clipped read - my @clips=split(/\;|,|\|/,$_[3]); - - my ($max, $temp, $temp2, $temp3, $dir, $maxSclip) = (0) x 6; - for (my $i=0; $i<$count; $i++) { - my $plus1=$i+1; - $temp=length($clips[$i]); - $temp2=$clips[$plus1]; - $temp3=$clips[$i]; - - if ($temp > $max){ - $maxSclip=$temp3; - $max =$temp; - $dir=$temp2; - } else { - $max=$max; - $dir=$dir; - $maxSclip=$maxSclip; - } - $i++; - } - my $order2 = join("|", $left, $right); - #print join ("\t",@_[0..2],$maxSclip,$max,$dir,$count,$order2) . "\n"; - print OUTFILE join ("\t",@_[0..2],$maxSclip,$max,$dir,$count,$order2) . "\n"; - } elsif($_=~/unknown/){ - print OUTFILE join ("\t",@_[0..2],"NA","NA","left","NA","NA|NA") . "\n"; - print OUTFILE join ("\t",@_[0..2],"NA","NA","right","NA","NA|NA") . "\n"; - } - ####Format is Chrom,start, end,longest Soft-clip,length of longest Soft-clip, direction of longest soft-clip,#supporting softclips,#right Sclips|#left Sclips -} -close INFILE; -close OUTFILE; - -unlink("$tmp2","$tmp_name","$random_file","$tmp3","$outfile","$index","$random_name","$right_sc","$left_sc","$new_blacklist") if (-z $tmp3 || !-e $tmp3) ; - - if (-z $tmp3 || !-e $tmp3){ - print "No structural variants found while Counting the number and identify directions of soft clips.\n" ; - - open (OUT,">$OUTNAME")||die "Can't write files here!\n"; - &print_header(); - close OUT; - exit; - -} - -print "Done counting Softclipped reads\n"; -############################################################### -#### Print header information -############################################################### -open (OUT,">$OUTNAME")||die "Can't write files here!\n"; -&print_header(); -close OUT; - -############################################################### -############################################################### -#### DO the bulk of the work -############################################################### -use List::Util qw(min max); -open (FILE,"$tmp3")|| die "Can't open file\n"; -open (OUT,">>$OUTNAME")|| die "Can't open file\n"; - -#print "\nusing $tmp3 and writing to $OUTPUT_FILE \n"; -while (<FILE>){ - #If left clip {+- or -- or -+ }{+- are uninformative b/c they go upstream} - #If right clip {++ or -- or +-} - chomp $_; - my $line = $_; - my @info = split(/\t/, $_); - - if($info[5] eq "left") { - bulk_work("left", $line, $random_file_disc); - - } elsif ($info[5] eq "right") { - bulk_work("right", $line, $random_file_disc); - } -#if($. ==6){print "THIS IS LINE 6\n$_\n";die} -print "Completed line $.\n" if ($verbose); -} -close FILE; -close OUT; - -############################################################################### -############################################################################### -#### Delete temp files -my $meregedBed=join("",$random_name,".sc.direction.bed.sc.merge.bed"); - -if(defined($temp_output)){$temp_output=$temp_output} else {$temp_output="no"} - -if ($temp_output eq "no"){ - unlink("$tmp_name","$random_file","$tmp2",,"$tmp3","$outfile","$index","$random_name","$right_sc","$left_sc","$meregedBed","$random_name.bed"); -} -####Sort VCF -my $tmp=join(".",$random_name,"tmp"); -#Get header -$cmd="grep \"#\" $OUTNAME > $tmp"; -system($cmd); -#sort results -$cmd="grep -v \"#\" $OUTNAME|perl -pne 's/chr//'|sort -k1,1n -k2,2n|perl -ne 'print \"chr\".\$_' >>$tmp"; -system($cmd); -$cmd="mv $tmp $OUTNAME"; -system($cmd); -#remove entries next to each other - - - - -############################################################# -##May not need this anymore since filtering on left and right -############################################################# -#my $tmpout=$OUTNAME; -#$tmpout.=".tmp"; -#use FindBin qw($Bin); -##my $path=$Bin; -#$command="perl ".$path."/Extract_nSC.pl $OUTNAME -q nSC > $tmpout"; -##print "Command=$command\n"; -#system($command); -#$command="perl ".$path."/reduce_redundancy.pl $tmpout $upper_limit |cut -f1-10 > $OUTNAME"; -##print "$command\n"; -#system($command); -#system("rm $tmpout"); -######################################################## - - - - -print "Analysis Completed\n\nYou did it!!!\n"; -print "Finish Time : " . &spGetCurDateTime() . "\n"; -$now = time - $now; -printf("\n\nTotal running time: %02d:%02d:%02d\n\n", int($now / 3600), int(($now % 3600) / 60), -int($now % 60)); - -exit; - -############################################################################### -sub rev_comp { - my $dna = shift; - my $revcomp = reverse($dna); - $revcomp =~ tr/ACGTacgt/TGCAtgca/; - - return $revcomp; -} - - -############################################################################### -#### to get reference base -sub getSeq{ - my ($chr,$pos,$fasta)=@_; - #don't require chr - #if($chr !~ /^chr/){die "$chr is not correct\n";} -# die "$pos is not a number\n" if ($pos <0); -my @result=(); - if ($pos <0){print "$pos is not a valid position (likely caused by circular MT chromosome)\n";return;} - - @result = `samtools faidx $fasta $chr:$pos-$pos`; - if($result[1]){chomp($result[1]); - return uc($result[1]); - } - return("NA"); - #### after return will not be printed - ####print "RESULTS=@result\n"; -} - -sub getBases{ - my ($chr,$pos1,$pos2,$fasta)=@_; - #don't require chr - #if($chr !~ /^chr/){die "$chr is not correct\n";} -my @result=(); - if ($pos1 <0){print "$pos1 is not a valid position (likely caused by circular MT chromosome)\n";return;}; - - @result = `samtools faidx $fasta $chr:$pos1-$pos2`; - if(!$result[1]){$result[1]="NA"}; - chomp($result[1]); - return uc($result[1]); - - #### after return will not be printed - ####print "RESULTS=@result\n"; -} -############################################################################### -#### to get time -sub spGetCurDateTime { - my ($sec, $min, $hour, $mday, $mon, $year) = localtime(); - my $curDateTime = sprintf "%4d-%02d-%02d %02d:%02d:%02d", - $year+1900, $mon+1, $mday, $hour, $min, $sec; - return ($curDateTime); -} - - -############################################################################### -#### print header -sub print_header { - my $date=&spGetCurDateTime(); - my $header = qq{##fileformat=VCFv4.1 -##fileDate=$date -##source=SoftSearch.pl -##reference=$INPUT_FASTA -##Usage= SoftSearch.pl -l $minSoft -q $MapQ -r $minSoftReads -d $dist_To_Soft -m $minRP -u $unmated_pairs -s $num_sd -b $INPUT_BAM -f $INPUT_FASTA -o $OUTNAME -##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> -##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> -##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> -##INFO=<ID=ISIZE,Number=.,Type=String,Description="Size of the SV"> -##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> -##FORMAT=<ID=lSC,Number=1,Type=Integer,Description="Length of the longest soft clips supporting the BND"> -##FORMAT=<ID=nSC,Number=1,Type=Integer,Description="Number of supporting soft-clips\"> -##FORMAT=<ID=uRP,Number=1,Type=Integer,Description="Number of unmated read pairs nearby Soft-Clips"> -##FORMAT=<ID=levD_local,Number=1,Type=Float,Description="Levenstein distance between soft-clipped bases and the area around the original soft-clipped site"> -##FORMAT=<ID=levD_distl,Number=1,Type=Float,Description="Levenstein distance between the soft-clipped bases and mate location"> -##FORMAT=<ID=CTX,Number=1,Type=Integer,Description="Number of chromosomal translocations"> -##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="Number of reads supporting Large Deletions"> -##FORMAT=<ID=INS,Number=1,Type=Integer,Description="Number of reads supporting Large insertions"> -##FORMAT=<ID=NOV_INS,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion"> -##FORMAT=<ID=TDUP,Number=1,Type=Integer,Description="Number of reads supporting a tandem duplication"> -##FORMAT=<ID=INV,Number=1,Type=Integer,Description="Number of reads supporting inversions"> -##FORMAT=<ID=sDEL,Number=1,Type=Integer,Description="Number of reads supporting novel sequence insertion"> -##INFO=<ID=NO_MATE_SC,Number=1,Type=Flag,Description="When there is no softclipping of the mate read location, an appromiate position is used"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Dummy value for maintaining VCF-Spec"> -#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$SAMPLE_NAME\n}; - - print OUT $header; -} - - -############################################################################### -sub bulk_work { -print "#####################################@_\n" if ($verbose); - my ($side, $line, $file) = @_; - my $local_levD = 0; - my $distl_levD = 0; - - #my @info = split(/\t/, $line); - my @plus_Reads = split(/\t/, $line); - $plus_Reads[7] =~ s/\n//g; - - #### softclip length and softclip size. - my $lSC = $plus_Reads[4]; - my $nSC = $plus_Reads[6]; - - - #Get all types of compatible reads - #Get improperly paired reads (@ max distance) - - #### default value for left SIDE. - #If left-clip, then look downstream for match of softclipped reads to define a deletion, but look for DRPs upstream - my $sv_type = "SVTYPE=BND"; - my $start_local=0; my $end_local=0;my $target_local="";my $target_drp="";my $start_drp="";my $end_drp=""; - if ($side =~ /left/) { - $start_local = $plus_Reads[1]-$dist_To_Soft; - $end_local = $plus_Reads[2]; - $start_drp = $plus_Reads[1]; - $end_drp = $plus_Reads[1]+$dist_To_Soft; - - } - else{ - $start_local = $plus_Reads[1]; - $end_local = $plus_Reads[1]+$dist_To_Soft; - $start_drp = $plus_Reads[1]-$dist_To_Soft; - $end_drp = $plus_Reads[1]; - } - - $target_local=join("", $plus_Reads[0], ":", $start_local, "-", $end_local); - $target_drp=join("", $plus_Reads[0], ":", $start_drp, "-", $end_drp); - my $num_unmapped_pairs=""; - if ($side =~ /right/) { - $num_unmapped_pairs=`samtools view $new_blacklist -q $MapQ -f8 -F 1536 -c $INPUT_BAM $target_drp`; - } else { - $num_unmapped_pairs=`samtools view $new_blacklist -q $MapQ -f24 -F 1536 -c $INPUT_BAM $target_drp`; - } -if($verbose){print "samtools view $new_blacklist -q $MapQ -f24 -F 1536 -c $INPUT_BAM $target_drp\n";} - - $num_unmapped_pairs=~s/\n//; -if($verbose){print "NUM UNMAPPED PAIRS= $num_unmapped_pairs\n";} - my $REF1_base = ""; - my $REF2_base = ""; - my $INFO_1 = ""; - my $INFO_2 = ""; - my $ALT_1 = ""; - my $ALT_2 = ""; - my $isize = 0; - my $QUAL = ""; - my $FORMAT = "GT:"; - - #### get 8 bit rand id - my $BND1_name = join "", map { ("a".."z")[rand 26] } 1..8; - my $BND2_name = join "", map { ("a".."z")[rand 26] } 1..8; - $BND1_name=join "_","BND",$BND1_name; - $BND2_name=join "_","BND",$BND2_name; - - my $counts = {CTX => 0, DEL => 0, INS => 0, INV => 0, TDUP => 0, NOV_INS => 0 }; - my $event_mate_info = {CTX => "", DEL => "", INS => "", INV => "", TDUP => "", NOV_INS => "" }; - - #### get mate pair info and counts per event - foreach my $e (sort keys %{$counts}) { - my $h = get_counts_n_info($e, $side, $MapQ, $file, $dist_To_Soft, $target_drp, $upper_limit, $lower_limit); - - $counts->{$e} = $h->{count}; - $event_mate_info->{$e} = $h->{info}; - } -#print Dumper($counts); - - my $max = 0; - my $type = "UNKNOWN"; - my $nRP = 0; - my $mate_info = "NA\tNA\tNA\tNA"; - my $summary = "GT:"; - - #### find max count of events and set type, nRP and info to corresponding - #### max count event. - #### also create a summary string of all counts to be added to VCF file. - foreach my $e (sort keys %{$counts}){ -# if ($counts->{$e} >=i $max){ - if ($counts->{$e} > $max){ - $type = $e .",". $counts->{$e}; - $nRP = $counts->{$e}; - - $max = $counts->{$e}; - - if (length($event_mate_info->{$e})) { - $mate_info = $event_mate_info->{$e}; - } - } - - $summary .= $e .",". $counts->{$e} .":"; - } -# print "done with Summary\n"; - #### remove last colon ":" from - $summary =~ s/:$//; - if (($minRP > $max)&&(!$disable_RP_only )){if ($verbose){print "FAILED BECAUSE ($minRP > $max)&&(!$disable_RP_only )"};return}; - - #### Run Levenstein distance on softclip in target region to find out if its a small deletion/insetion - #### passing 1: clip_seq, 2: chr, 3: start, 4: end, 5: ref file. - my $levD = new LevD; -######################################################## -######################################################## -######################################################## - - #### redefine start and end location for LevD calc. -# $start = $plus_Reads[1]-$dist_To_Soft; -# $end = $plus_Reads[2]; - my $num_bases_to_loc=0; - my $new_start=0; - my $new_end=0; - my $del_seq=""; - my $start = $start_local; - my $end = $end_local; - if ($lSC=~/NA/){$lSC=0} - - if ($side =~ /right/) { - $levD->search($plus_Reads[3], $plus_Reads[0], $start, $end, $INPUT_FASTA); - $local_levD = sprintf("%.2f", $levD->{relative_edit_dist}); - $num_bases_to_loc=$levD->{index}; - $new_start = $plus_Reads[2]; - if ($plus_Reads[2]=~/^[0-9]/){$new_end=$plus_Reads[2]+$lSC}; - } - else{ - $levD->search($plus_Reads[3], $plus_Reads[0], $start, $end, $INPUT_FASTA); - $local_levD = sprintf("%.2f", $levD->{relative_edit_dist}); - $num_bases_to_loc=$levD->{index}; - if ($plus_Reads[2]=~/^[0-9]/){$new_start=$plus_Reads[2]-$lSC}; - $new_end = $plus_Reads[2]; - } - if((!$new_start)||(!$new_end)||($new_start<0)){print "FAILED AT ((!$new_start)||(!$new_end)||($new_start<0))\n";return}; - - $del_seq=getBases($plus_Reads[0], $new_start,$new_end,$INPUT_FASTA); -############################################################################## -# #If there is a match, where is the start position of the match? -# -############################################################################## - - - #if $plus_Reads[3] eq "NA", then it was found without soft-clipped reads - if($plus_Reads[3] !~ /NA/){ - if (($local_levD < $levD_local_threshold)) { - return if (!$sv_only); - #### add value to summary to be written to vcf file. - $summary = "GT:sDel," . $plus_Reads[6]; - $type = "sDEL"; - ########################################################################### - ##### Printing output - - ######################################### - ##### Get DNA info - ######################################### - #$REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA); - $REF1_base = substr($del_seq, 0, 1); - - #### this is alt ref. for softclip its $plus_Reads[3] - $REF2_base = $del_seq; - $QUAL = 1/($local_levD + 0.001); - $QUAL = sprintf("%.2f",$QUAL); - $isize = length($del_seq); - - #### svtype = none for sDEL - #### isize = length($info[3]); - #### nRP = NA - #### mate_id = NA - #### CTX,:DEL,:....sDEL,## - $INFO_1=join(";", "SVTYPE=NA", "EVENT=$type", "ISIZE=$isize"); - - #Add Sample infomration - my $FORMAT="GT:sDEL"; - $FORMAT .= ":lSC:nSC:uRP:levD_local"; - my $SAMPLE= "0/1:"; - $SAMPLE .= "$plus_Reads[6]:$lSC:$nSC:$num_unmapped_pairs:$local_levD"; - - #### remove any white spaces. - $INFO_1=~s/\s//g; - $INFO_2=~s/\s//g; - - $BND1_name =~ s/^BND/LEVD/; - # If left, then the start position is plus_Reads[1]-isize - my $start_pos=0; - #Make sure Ref1 and Ref2 bases are different - if($REF2_base eq $REF1_base){$REF1_base="NA"} - if($side=~/left/){$start_pos=$plus_Reads[1]-$isize}else{$start_pos=$plus_Reads[1]}; - print OUT join ("\t", $plus_Reads[0], $start_pos, $BND1_name, $REF2_base, $REF1_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n"); - if ($verbose){print "No Softclipped reads here!\n"} - return; - } - } - - #### Otherwise, look for DRP mate info - #if($nRP=~/NA/){print "MATE_INFO=$mate_info\tSide=$side\tline=$line\n";} - my @mate_info_arr = split(/\t/, $mate_info); - $nRP = $mate_info_arr[3]; - my $mate_chr=$mate_info_arr[0]; - - if((! defined $nRP) || ($nRP =~ /na/i) || ($mate_chr =~ /NA/) ){ - #PRINT UNKNOWN - if ($nRP =~ /na/i){print "Can't find SC reads\n" if ($verbose);return}; - if ($verbose){print "There is an unknown\nNRP=$nRP Mate_CHR=$mate_chr minRP=$minRP\n"} - $summary .= ":unknown," . $plus_Reads[6]; - $type = "unknown"; - $REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA); - $REF2_base = $plus_Reads[3]; - $BND1_name =~ s/^BND/UNKNOWN/; - $QUAL = 1/($local_levD + 0.001); - $QUAL = sprintf("%.2f",$QUAL); - $INFO_1=join(";", "SVTYPE=unknown", "EVENT=unknown", "ISIZE=unknown"); - #Add Sample infomration - my $FORMAT="GT:sDEL"; - $FORMAT .= ":lSC:nSC:uRP:levD_local"; - my $SAMPLE = "0/1:"; - $SAMPLE .= "$plus_Reads[6]:$lSC:$nSC:$num_unmapped_pairs:$local_levD"; - $SAMPLE=~s/NA/0/g; - #### remove any white spaces. - $INFO_1=~s/\s//g; - #print join ("\t", $plus_Reads[0], $plus_Reads[1], $REF2_base, $REF1_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n"); - - print OUT join ("\t", $plus_Reads[0], $plus_Reads[1], $BND1_name, $REF1_base, $REF2_base, $QUAL, "PASS", $INFO_1,$FORMAT,$SAMPLE, "\n"); - return; - - } - #### end if there is no mate info or nRP+uRP<minRP - if (($nRP<$minRP)&&($unmated_pairs > ($num_unmapped_pairs+$nRP))){ - print "Something failed here\nif (($nRP<$minRP)&&($unmated_pairs > ($num_unmapped_pairs+$nRP)))\n"; - return} - - ################################################################################## - # Find out if mates have nearby soft-clips (to refine the breakpoints) - ################################################################################## - #Look for evidence of soft-clipping near mate - my @mate_soft_arr = (); - my $mate_start = 0; - my $mate_soft = ""; - - @mate_info_arr = split(/\t/, $mate_info); - - #### mate start and end locations. - my $filename = $right_sc; - - $start = $mate_info_arr[1] - $dist_To_Soft; - $end = $mate_info_arr[1]; - - if ($side =~ /right/) { - $start = $mate_info_arr[2]; - $end = $mate_info_arr[2] + $dist_To_Soft; - - $filename = $left_sc; - } - - #### add levenstein distance to Summary - #print "Calc distal Levd\n"; - $levD->search(rev_comp($plus_Reads[3]), $mate_info_arr[0], $start, $end, $INPUT_FASTA); - $distl_levD = sprintf("%.2f", $levD->{relative_edit_dist}); - $distl_levD = "NA" if($plus_Reads[3] =~ /NA/); - #If there is no softclips to string match, then give 0 as quality value - if ($plus_Reads[3] !~ /NA/){ - $QUAL=1/($distl_levD + 0.001); - } - else { - $QUAL=0; - }; - $QUAL=sprintf("%.2f",$QUAL); - #### looking for softclips to refine break point - #### if left look in right and vice-versa. - $cmd = qq{echo -e "$mate_info_arr[0]\t$start\t$end"}; - $cmd .= qq{ | awk -F'\t' 'NF==3' | intersectBed -a stdin -b $filename | head -1}; -print "$cmd\n" if $verbose; - $mate_soft = `$cmd`; - - $mate_soft =~ s/\n//g; - @mate_soft_arr = split(/\s/, $mate_soft); -my $NO_MATE_SC=""; - if(@mate_soft_arr){ - $mate_chr = $mate_soft_arr[0]; - $mate_start = $mate_soft_arr[1]; - $NO_MATE_SC="APPROXIMATE"; - - } else{ - @mate_info_arr = split(/\s/,$mate_info); - $mate_chr = $mate_info_arr[0]; - $mate_start = $mate_info_arr[1]; - } - - #end if there is no mate info - return if ($mate_chr eq ""); - #end if there is no mate info and !disable_RP_only - return if (($lSC =~/NA/)&&(!$disable_RP_only)); - - - ########################################################################### - ##### Printing output - - ######################################### - # Get DNA info - ######################################### - #print "PLUS_READS=$plus_Reads[0],$plus_Reads[1]\nMATE=$mate_chr,$mate_start,$INPUT_FASTA\n"; - $REF1_base = getSeq($plus_Reads[0], $plus_Reads[1], $INPUT_FASTA); - - ### this is alt ref. for softclip its $plus_Reads[3] - $REF2_base = getSeq($mate_chr, $mate_start, $INPUT_FASTA); - - ######################################### - # print in VCF format - ######################################### - - #### abs value to account for left and right reads. - $isize = abs($plus_Reads[1]-$mate_start); - - my $event_type=$type; - $event_type=~ s/,|[0-9]//g; - $INFO_1=join(";", "$sv_type", "EVENT=$event_type","END=$mate_start", "ISIZE=$isize","MATEID=$BND2_name"); - $INFO_2=join(";", "$sv_type", "EVENT=$event_type","END=$plus_Reads[1]", "ISIZE=$isize","MATEID=$BND1_name"); - - #### remove any white spaces. - #### ask: did you mean to remove space from ends? eg. trim() - $INFO_1=~s/\s//g; - $INFO_2=~s/\s//g; - - $FORMAT=$summary; - $FORMAT=~ s/,|[0-9]//g; - $FORMAT .= ":lSC:nSC:uRP:distl_levD"; - if($NO_MATE_SC){$INFO_2 .= ":NO_MATE_SC"} - my $SAMPLE="0/1:"; - $SAMPLE .=$summary; -# if($NO_MATE_SC){$SAMPLE.= ":$NO_MATE_SC"} - - $SAMPLE=~s/[A-Z|,|_]//g; - my $MATE_SAMPLE=$SAMPLE; - $SAMPLE .= ":$lSC:$nSC:$num_unmapped_pairs:$distl_levD"; - $MATE_SAMPLE .=":NA:NA:NA:NA"; - $SAMPLE=~s/::/:/g; - $MATE_SAMPLE=~s/::/:/g; - $MATE_SAMPLE=~s/NA/0/g; - $SAMPLE=~s/NA/0/g; - - if($type !~ /INV/){ - $ALT_1 = join("","]",$mate_chr,":",$mate_start,"]",$REF1_base); - $ALT_2 = join("",$REF2_base,"[",$plus_Reads[0],":",$plus_Reads[1],"["); - # 2 321682 bnd_V T ]13:123456]T 6 PASS SVTYPE=BND - # 13 123456 bnd_U C C[2:321682[ 6 PASS SVTYPE=BND - } else { - $ALT_1 = join("", "]", $plus_Reads[0], ":", $plus_Reads[1], "]", $REF2_base); - $ALT_2 = join("", $REF1_base, "[", $mate_chr, ":", $mate_start, "["); - } - - if(($mate_chr) && ($plus_Reads[0])){ - print OUT join ("\t", $plus_Reads[0], $plus_Reads[1], $BND1_name, $REF1_base, $ALT_1, $QUAL,"PASS", $INFO_1, $FORMAT,$SAMPLE,"\n"); - print OUT join ("\t", $mate_chr, $mate_start, $BND2_name, $REF2_base, $ALT_2, $QUAL, "PASS", $INFO_2, $FORMAT,$MATE_SAMPLE,"\n"); - } -} - -############################################################################### -############################################################################### -sub get_counts_n_info { - my ($event, $side, $mapQ, $file, $dist, $target, $upL, $lwL) = @_; - - my $mate_info = ""; - my $cmd = ""; - - if ($event =~ /^CTX$/i) { - #print "CTX side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1536 $file $target}; - $cmd .= qq{ | perl -ane 'if(\$F[6] ne "="){\$end=\$F[7]+1; print join ("\\t",\$F[6],\$F[7],\$end,"\\n")}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info=`$cmd`; - } else { - $cmd = qq{ samtools view $new_blacklist -q $mapQ -f 16 -F 1536 $file $target}; - $cmd .= qq{ | perl -ane 'if(\$F[6] ne "="){\$end=\$F[7]+1; print join ("\\t",\$F[6],\$F[7],\$end,"\\n")}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info=`$cmd`; - } - } elsif ($event =~ /^DEL$/i) { - #print "DEL side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1552 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info=`$cmd`; - } else { - $cmd = qq{samtools view $new_blacklist -q $mapQ -F 1568 -f 16 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"} {if((\$7 ~ /=/)&&(\$9<-$upL)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist_To_Soft -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - - $mate_info=`$cmd`; - } - } elsif ($event =~ /^INS$/i) { - #print "INS side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1552 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9<$lwL && \$9 > 0 )){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } else { - $cmd = qq {samtools view $new_blacklist -q $mapQ -f 16 -F 1568 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>-$lwL && \$9 < 0 )){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } - } elsif ($event =~ /^INV$/i) { - #print "INV side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -F 1596 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist_To_Soft -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } else { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 48 -F 1548 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } - } elsif ($event =~ /^TDUP$/i) { - #print "TDUP side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 32 -F 1552 $file $target}; -# $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$4>\$8)&&(\$9<0)&& (\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } else { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 16 -F 1568 $file $target}; -# $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$9<-$upL )){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | awk '{OFS="\\t"}{if((\$7 ~ /=/)&&(\$4<\$8)&&(\$9>0)&&(\$9>$upL)){end=\$8+1;print \$3,\$8,end}}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } - } elsif ($event =~ /^NOV_INS$/i) { - #print "NOV_INS side $side\n"; - if ($side =~ /right/i) { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 8 -F 1552 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{end=\$8+1;print \$3,\$8,end}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } else { - $cmd = qq{samtools view $new_blacklist -q $mapQ -f 24 -F 1536 $file $target}; - $cmd .= qq{ | awk '{OFS="\\t"}{end=\$8+1;print \$3,\$8,end}'}; - $cmd .= qq{ | sortBed | mergeBed -d $dist -n | sort -k4nr | head -1}; -#if($verbose){print "$cmd\n"} - $mate_info = `$cmd`; - } - } - - $mate_info=~s/\n//g; - my @tmp=split(/\t/, $mate_info); - - my $counts = 0; - - if (defined $tmp[3]) { - $tmp[3] =~ s/\n//g; - - $counts = $tmp[3] if (length($tmp[3])); - } - return ({count=>$counts, info=>$mate_info}); -}
--- a/softsearch_wrapper.xml Sat Jun 07 07:42:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -<?xml version="1.0"?> -<tool id="Softsearch" name="softsearch" version="0.6"> - <requirements> - <requirement type="package" version="0.6">softsearch</requirement> - </requirements> - <description>for structure variation</description> - <command interpreter="perl">#if $source.index_source=="history" - samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1 - #else - samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1 - #end if - </command> - <inputs> - <param name="bam_file" type="data" format="bam" label="BAM Files" /> - <conditional name="source"> - <param name="index_source" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="history"> - <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/> - </when> - <when value="cached"> - <param name="ref_fasta" type="select" > - <options from_data_table="fasta_indexes"> - <validator type="no_options" message="No Fasta file is available" /> - </options> - </param> - </when> - </conditional> - <param name="inc" type="hidden" value="n=$RANDOM" /> - <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> - <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> - <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> - <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> - <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" /> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <help> - </help> -</tool> - - - - - - - - - - - - -
--- a/tool-data/fasta_indexes.loc.sample Sat Jun 07 07:42:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a fasta_indexes.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The fasta_indexes.loc -#file has this format (white space characters are TAB characters): -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg19 Canonical indexed stored in -# -# /depot/data2/galaxy/hg19/sam/, -# -#then the fasta_indexes.loc entry would look like this: -# -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -# -#and your /depot/data2/galaxy/hg19/sam/ directory -#would contain hg19canon.fa and hg19canon.fa.fai files. -# -#Your fasta_indexes.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa -#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- a/tool-data/tool_data_table_conf.xml.sample Sat Jun 07 07:42:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> - <!-- Locations of indexes in the BFAST mapper format --> - <table name="bfast_indexes" comment_char="#"> - <columns>value, dbkey, formats, name, path</columns> - <file path="tool-data/bfast_indexes.loc" /> - </table> - <!-- Locations of nucleotide (mega)blast databases --> - <table name="blastdb" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/blastdb.loc" /> - </table> - <!-- Locations of protein (mega)blast databases --> - <table name="blastdb_p" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/blastdb_p.loc" /> - </table> - <!-- Locations of indexes in the BWA mapper format --> - <table name="bwa_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index.loc" /> - </table> - <!-- Locations of indexes in the BWA color-space mapper format --> - <table name="bwa_indexes_color" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index_color.loc" /> - </table> - <!-- Locations of MAF files that have been indexed with bx-python --> - <table name="indexed_maf_files"> - <columns>name, value, dbkey, species</columns> - <file path="tool-data/maf_index.loc" /> - </table> - <!-- Locations of fasta files appropriate for NGS simulation --> - <table name="ngs_sim_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/ngs_sim_fasta.loc" /> - </table> - <!-- Locations of PerM base index files --> - <table name="perm_base_indexes" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/perm_base_index.loc" /> - </table> - <!-- Locations of PerM color-space index files --> - <table name="perm_color_indexes" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/perm_color_index.loc" /> - </table> - <!-- Location of Picard dict file and other files --> - <table name="picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/picard_index.loc" /> - </table> - <!-- Location of Picard dict files valid for GATK --> - <table name="gatk_picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/gatk_sorted_picard_index.loc" /> - </table> - <!-- Available of GATK references --> - <table name="gatk_annotations" comment_char="#"> - <columns>value, name, gatk_value, tools_valid_for</columns> - <file path="tool-data/gatk_annotations.txt" /> - </table> - <!-- Location of SRMA dict file and other files --> - <table name="srma_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/picard_index.loc" /> - </table> - <!-- Location of Mosaik files --> - <table name="mosaik_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/mosaik_index.loc" /> - </table> - <table name="fasta_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/fasta_indexes.loc" /> - </table> -</tables>
--- a/tool_dependencies.xml Sat Jun 07 07:42:51 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="softsearch" version="0.6"> - <repository changeset_revision="e184c650a023" name="vdt_dependency" owner="priti" toolshed="http://toolshed.g2.bx.psu.edu"/> - </package> -</tool_dependency>