Merge branch 'dev' of github.com:kbattenb/universc into dev (1079c436) · Commits · github_fork / Universc

launch_universc.sh

+1 −9

Original line number	Diff line number	Diff line
		@@ -3608,15 +3608,7 @@ fi
		#####extracting per cell data#####
		if [[ $percelldata == true ]]; then
		echo "generating basic run statistics and per cell data"
		if [[ ${barcodefile} == "default:10x" ]]; then
		barcodefile=${barcodedir}/${v3}.gz
		gunzip ${barcodefile}
		barcodefile=`echo ${barcodefile} \| sed 's/\.[^.]*$//'`
		perl ${PERCELLSTATS} ${barcodefile} ${barcodeadjust} ${id}
		gzip ${barcodefile}
		else
		perl ${PERCELLSTATS} ${barcodefile} ${barcodeadjust} ${id}
		fi
		echo "per cell data generated"
		fi
		##########

+31 −23

Original line number	Diff line number	Diff line
		@@ -43,6 +43,15 @@ elsif (! -e $feature_file \|\| ! -e $raw_barcode_file \|\| ! -e $filtered_barcode_fi
		#####MAIN#####
		#make a hash of original and adjusted barcodes
		my %adjusted2original;
		if ($barcodefile =~ m/^default\:10x$/) {
		my $originals = `zcat $filtered_barcode_file \| cut -f1 -d'-'`;
		chomp $originals;
		my @originals = split (/\n/, $originals);
		foreach my $original (@originals) {
		$adjusted2original{$original} = $original;
		}
		}
		else {
		open (ORIGINAL, "<$barcodefile") or die "cannot open $barcodefile.\n";
		while (my $line = <ORIGINAL>) {
		my $original = $line;
		@@ -60,9 +69,9 @@ while (my $line = <ORIGINAL>) {
		}

		$adjusted2original{$adjusted} = $original;
		print "Original($original) -> Adjusted($adjusted) $adjust_length\n";
		}
		close (ORIGINAL);
		}

		#gene count
		print " getting gene count.\n";
		@@ -207,10 +216,9 @@ foreach my $entry (@umicount) {
		}
		foreach my $id (keys %umicount) {
		if (exists $percell{ $barcodes{$id} }) {
		my %data = %{ $percell{ $barcodes{$id} } };
		$data{UMI} = $umicount{$id};

		$percell{ $barcodes{$id} } = \%data;
		my %barcode = %{ $percell{ $barcodes{$id} } };
		$barcode{UMI} = $umicount{$id};
		$percell{$barcodes{$id}} = \%barcode;
		}
		}
		foreach my $barcode (sort keys %percell) {