temporary commit to test multithreading (3b5b0f80) · Commits · github_fork / ZUMIs

ExampleData/tiny.BCstats.txt

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ExampleData/tiny.BCstats.txt.gz

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barcodeIDFUN.R

+3 −1

Original line number	Diff line number	Diff line
		@@ -101,6 +101,7 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){
		return(bccount[keep==TRUE,XC])
		}
		.cellBarcode_known <- function( bccount, bcfile ){

		bc<-read.table(bcfile,header = F,stringsAsFactors = F)$V1
		if( any( bc %in% bccount$XC ) ){
		bccount[XC %in% bc,keep:=TRUE]
		@@ -122,6 +123,7 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){
		cellBC<-function(bcfile, bcnum, bccount_file, outfilename=NULL){
		bccount<-data.table::fread( bccount_file )
		names(bccount)<-c("XC","n")
		bccount <- bccount[,list(n=sum(n)),by=XC]
		bccount<-bccount[n>=opt$barcodes$nReadsperCell][order(-n)][,cellindex:=1:(.N)][,keep:=FALSE]

		if(is.null(bcfile)==FALSE){

fqfilter_v2.pl

+27 −27

Original line number	Diff line number	Diff line
		@@ -2,35 +2,24 @@
		# LMU Munich. AG Enard
		# A script to filter reads based on Barcode base quality.

		if(@ARGV != 5)
		if(@ARGV != 6)
		{
		print
		"\n#####################################################################################
		Usage: perl $0 <yaml> <samtools-executable> <rscript-executable> <pigz-executable> <zUMIs-dir>\n
		Usage: perl $0 <yaml> <samtools-executable> <rscript-executable> <pigz-executable> <zUMIs-dir> <tmpPrefix>\n
		Please drop your suggestions and clarifications to <sparekh\@age.mpg.de>\n
		######################################################################################\n\n";
		exit;
		}

		BEGIN{
		$yml=$ARGV[0];
		$samtoolsexc=$ARGV[1];
		$rscriptexc=$ARGV[2];
		$pigz=$ARGV[3];
		$zumisdir=$ARGV[4];
		=begin
		chomp($zumisdir);
		print $zumisdir;
		print $yml;
		print $samtoolsexc;
		print $pigz;
		print $rscriptexc;
		=cut
		BEGIN{
		# print $zumisdir;
		#print "@INC";
		unshift @INC, '/data/share/htp/zUMIs2/zUMIs';
		# print "@INC";
		$tmpPrefix=$ARGV[5];
		}
		use lib "$zumisdir";
		use distilReads;

		open(YL,"Rscript $zumisdir/readYaml4fqfilter.R $yml \|");
		@@ -61,8 +50,8 @@ chomp($num_threads);
		chomp($BCfilter);
		chomp($UMIfilter);

		$outbcstats = "$outdir/$StudyName.BCstats.txt";
		$outbam = "$outdir/$StudyName.filtered.tagged.bam";
		$outbcstats = "$outdir/zUMIs_output/.tmpMerge/$StudyName.$tmpPrefix.BCstats.txt";
		$outbam = "$outdir/zUMIs_output/.tmpMerge/$StudyName.$tmpPrefix.filtered.tagged.bam";

		# Make and open all the file handles
		%file_handles = distilReads::makeFileHandles($f,$st);
		@@ -77,9 +66,21 @@ for($i=0;$i<=$#keys;$i++){
		@fp = split(":",$file_handles{$fh});

		if ($fp[0] =~ /\.gz$/) {
		open $fh, '-\|', $pigz, '-dc', $fp[0] \|\| die "Couldn't open file ".$fp[0].". Check permissions!\n Check if it is differently zipped then .gz\n\n";
		$oriF = $fp[0];
		$oriBase = `basename $oriF .gz`;
		chomp($oriBase);

		#change the file name to temporary prefix for its chunk
		$chunk = "$outdir/zUMIs_output/.tmpMerge/$oriBase$tmpPrefix.gz";
		open $fh, '-\|', $pigz, '-dc', $chunk \|\| die "Couldn't open file ".$chunk.". Check permissions!\n Check if it is differently zipped then .gz\n\n";
		}else {
		open $fh, "<", $fp[0] \|\| die "Couldn't open file ".$fp[0].". Check permissions!\n Check if it is differently zipped then .gz\n\n";

		$oriF = $fp[0];
		$oriBase = `basename $oriF'`;
		#change the file name to temporary prefix for its chunk
		$chunk = "$outdir/zUMIs_output/.tmpMerge/$oriBase$tmpPrefix.gz";

		open $fh, "<", $chunk \|\| die "Couldn't open file ".$chunk.". Check permissions!\n Check if it is differently zipped then .gz\n\n";
		}
		}

		@@ -149,10 +150,10 @@ while(<$fh1>){
		$bclist{$bcseq}++;
		#print $lay,"\n";
		if($lay eq "SE"){
		print BCBAM $1,"\t4\t\t0\t0\t\t*\t0\t0\t",$cseqr1,"\t",$cqseqr1,"\tRG:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		print BCBAM $1,"\t4\t\t0\t0\t\t*\t0\t0\t",$cseqr1,"\t",$cqseqr1,"\tBC:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		}else{
		print BCBAM $1,"\t77\t\t0\t0\t\t*\t0\t0\t",$cseqr1,"\t",$cqseqr1,"\tRG:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		print BCBAM $1,"\t141\t\t0\t0\t\t*\t0\t0\t",$cseqr2,"\t",$cqseqr2,"\tRG:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		print BCBAM $1,"\t77\t\t0\t0\t\t*\t0\t0\t",$cseqr1,"\t",$cqseqr1,"\tBC:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		print BCBAM $1,"\t141\t\t0\t0\t\t*\t0\t0\t",$cseqr2,"\t",$cqseqr2,"\tBC:Z:",$bcseq,"\tUB:Z:",$ubseq,"\n";
		}
		}
		}
		@@ -167,7 +168,6 @@ close BCOUT;

		print "Raw reads: $total \nFiltered reads: $filtered \n\n";

		open YAML, '>>', $yml \|\| die "Couldn't open file ".$yml.". Check permissions!\n";
		print YAML "read_layout: ",$lay,"\n";
		close YAML;
		=cut
		#open YAML, '>>', $yml \|\| die "Couldn't open file ".$yml.". Check permissions!\n";
		#print YAML "read_layout: ",$lay,"\n";
		#close YAML;

listPrefix.sh

0 → 100644

+18 −0

Original line number	Diff line number	Diff line
		#!/bin/bash
		# LMU Munich. AG Enard
		# getting list of prefix from tmpMerge
		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

		zumisdir=$1
		tmpMerge=$2
		f=$3
		project=$4

		if [[ $f =~ \.gz$ ]]; then
		pref=`basename $f .gz`
		ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" \| sed 's/.gz//' > $tmpMerge/$project.listPrefix.txt
		else
		pref=`basename $f`
		ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" > $tmpMerge/$project.listPrefix.txt
		fi

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