Modify the barcode list in the output gene barcode matrix to recover the original state (7d66ebd8) · Commits · github_fork / Universc

BarcodeRecovery.pl

0 → 100644

+73 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/perl

		#########################################
		# #
		# Written by Kai Battenberg #
		# Plant Symbiosis Research Team #
		# #
		#########################################

		use strict;
		use warnings;

		#####Options#####
		my $barcodefile = $ARGV[0];
		my $adjust_length = $ARGV[1];
		my $cellranger_dir = $ARGV[2];
		##########



		#####Main#####
		#make a hash of original and adjusted barcodes
		my %barcodes;
		open (ORIGINAL, "<$barcodefile") or die "cannot open $barcodefile.\n";
		while (my $line = <ORIGINAL>) {
		my $original = $line;
		$original =~ s/\r//sig;
		$original =~ s/\n//sig;

		my $adjusted = $original;
		if ($adjust_length >= 0) {
		my $length = $adjust_length;
		$adjusted = substr ($length, 0, $adjusted);
		}
		else {
		my $length = abs ($adjust_length);
		my $As = "A" x $length;
		$adjusted = $As.$adjusted;
		}

		$barcodes{$adjusted} = $original;
		}
		close (ORIGINAL);

		#get modified barcode list (raw)
		my $raw_file = $cellranger_dir."/outs/raw_feature_bc_matrix/barcodes.tsv.gz";
		my $modified_barcodes_raw = `zcat $raw_file \| cut -f1 -d'-'`;
		$modified_barcodes_raw =~ s/\n$//;
		my @modified_barcodes_raw = split (/\n/, $modified_barcodes_raw);

		#get modified barcode list (filtered)
		my $filtered_file = $cellranger_dir."/outs/filtered_feature_bc_matrix/barcodes.tsv.gz";
		my $modified_barcodes_filtered = `zcat $filtered_file \| cut -f1 -d'-'`;
		$modified_barcodes_filtered =~ s/\n$//;
		my @modified_barcodes_filtered = split (/\n/, $modified_barcodes_filtered);

		#replace barcodes
		my $temp = "barcodes.txt";
		open (TEMP, ">$temp") or die "cannot open $temp.\n";
		foreach my $barcode (@modified_barcodes_raw) {
		print TEMP "$barcodes{$barcode}-1\n";
		}
		close (TEMP);
		system "gzip -c $temp > $raw_file";

		open (TEMP, ">$temp") or die "cannot open $temp.\n";
		foreach my $barcode (@modified_barcodes_filtered) {
		print TEMP "$barcodes{$barcode}-1\n";
		}
		close (TEMP);
		system "gzip -c $temp > $filtered_file";
		unlink ($temp);
		##########

ExtractBasicStats.pl

+42 −17

Original line number	Diff line number	Diff line
		@@ -12,7 +12,9 @@ use warnings;
		use List::Util qw( min max sum);

		#####Options#####
		my $indir = $ARGV[0];
		my $barcodefile=$ARGV[0];
		my $adjust_length=$ARGV[1];
		my $indir = $ARGV[2];
		##########


		@@ -38,6 +40,29 @@ elsif (! -e $feature_file \|\| ! -e $raw_barcode_file \|\| ! -e $filtered_barcode_fi


		#####MAIN#####
		#make a hash of original and adjusted barcodes
		my %adjusted2original;
		open (ORIGINAL, "<$barcodefile") or die "cannot open $barcodefile.\n";
		while (my $line = <ORIGINAL>) {
		my $original = $line;
		$original =~ s/\r//sig;
		$original =~ s/\n//sig;

		my $adjusted = $original;
		if ($adjust_length >= 0) {
		my $length = $adjust_length;
		$adjusted = substr ($length, 0, $adjusted);
		}
		else {
		my $length = abs ($adjust_length);
		my $As = "A" x $length;
		$adjusted = $As.$adjusted;
		}

		$adjusted2original{$adjusted} = $original;
		}
		close (ORIGINAL);

		#gene count
		print " getting gene count.\n";

		@@ -110,10 +135,10 @@ foreach my $barcode (@assigned_reads_percell) {
		$count =~ s/ $//;
		my @count = split (/ /, $count);

		if (exists $percell{$count[1]}) {
		if (exists $percell{ $adjusted2original{$count[1]} }) {
		my %count;
		$count{ASSIGNED} = $count[0];
		$percell{$count[1]} = \%count;
		$percell{ $adjusted2original{$count[1]} } = \%count;
		}
		}
		foreach my $barcode (sort keys %percell) {
		@@ -138,10 +163,10 @@ foreach my $barcode (@mapped_reads_percell) {
		$count =~ s/ $//;
		my @count = split (/ /, $count);

		if (exists $percell{$count[1]}) {
		my %count = %{ $percell{$count[1]} };
		if (exists $percell{ $adjusted2original{$count[1]} }) {
		my %count = %{ $percell{ $adjusted2original{$count[1]} } };
		$count{MAPPED} = $count[0];
		$percell{$count[1]} = \%count;
		$percell{ $adjusted2original{$count[1]} } = \%count;
		}
		}
		foreach my $barcode (sort keys %percell) {

launch_universc.sh

+17 −5

Original line number	Diff line number	Diff line
		@@ -3,11 +3,12 @@
		install=false

		######convert version#####
		convertversion="0.3.0.90005"
		convertversion="0.3.0.90007"
		##########


		####cellrenger version#####

		#####cellrenger version#####
		cellrangerpath=`which cellranger` #location of cellranger
		if [[ -z $cellrangerpath ]]; then
		echo "cellranger command is not found."
		@@ -42,6 +43,7 @@ if [[ $RDIR != $SDIR ]]; then
		fi
		echo "Running launch_universc.sh in '$SDIR'"

		BARCODERECOVER=${SDIR}/BarcodeRecovery.pl
		PERCELLSTATS=${SDIR}/ExtractBasicStats.pl
		##########

		@@ -67,7 +69,7 @@ Mandatory arguments to long options are mandatory for short options too.
		-R2, --read2 FILE Read 2 FASTQ file to pass to cellranger
		-f, --file NAME Path and the name of FASTQ files to pass to cellranger (prefix before R1 or R2)
		e.g. /path/to/files/Example_S1_L001
		--trim run adapter and quality trimming on R2 files prior to running cellranger
		--trim run adapter and quality trimming on R2 files prior to running cellranger (underconstruction)

		-i, --id ID A unique run id, used to name output folder
		-d, --description TEXT Sample description to embed in output files.
		@@ -1137,10 +1139,20 @@ fi



		#####Readjusting the barcodes in the cellranger output back to its original state#####
		if [[ ${barcodefile} != "default" ]]; then
		echo "replacing modified barcodes with the original in the output gene barcode matrix"
		perl ${BARCODERECOVER} ${barcodefile} ${barcodeadjust} ${id}
		echo "barcodes recovered"
		fi
		##########



		#####extracting per cell data#####
		if [[ $percelldata == true ]]; then
		echo "generating basic run statistics and per cell data"
		perl ${PERCELLSTATS} ${id}
		perl ${PERCELLSTATS} ${barcodefile} ${barcodeadjust} ${id}
		echo "per cell data generated"
		fi
		##########

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