Add the cell_id information to the smartseq output.

README.md

@@ -42,12 +42,12 @@ TRUST4 is also available form [Bioconda](https://anaconda.org/bioconda/trust4).
 			-t INT: number of threads (default: 1)
 			-k INT: the starting k-mer size for indexing contigs (default: 9)
 			--barcode STRING: if -b, bam field for barcode; if -1 -2/-u, file containing barcodes (defaul: not used)
+			--barcodeLevel STRING: barcode is for cell or molecule (default: cell)
 			--barcodeWhitelist STRING: path to the barcode whitelist (default: not used)
 			--barcodeTranslate STRING: path to the barcode translate file (default: not used)
 			--UMI STRING: if -b, bam field for 10x Genomics-like UMI; if -1 -2/-u, file containing 10x Genomics-like UMIs (default: not used)
 			--readFormat STRING: format for read, barcode and UMI files (example: r1:0:-1,r2:0:-1,bc:0:15,um:16:-1 for paired-end files with barcode and UMI)
 			--repseq: the data is from TCR-seq or BCR-seq (default: not set)
-			--barcodeLevel STRING: barcode is for cell or molecule (default: cell)
 			--minHitLen INT: the minimal hit length for a valid overlap (default: auto)
 			--mateIdSuffixLen INT: the suffix length in read id for mate. (default: not used)
 			--skipMateExtension: do not extend assemblies with mate information, useful for SMART-seq (default: not used)

run-trust4

@@ -7,7 +7,7 @@ use Cwd qw(cwd abs_path) ;
 use File::Basename ;
 use File::Path qw(make_path) ;
 
-die "TRUST4 v1.1.0-r499 usage: ./run-trust4 [OPTIONS]:\n".
+die "TRUST4 v1.1.0-r500 usage: ./run-trust4 [OPTIONS]:\n".
     "Required:\n".
     #"\t[Input]:\n".
     "\t-b STRING: path to bam file\n".
@@ -22,6 +22,7 @@ die "TRUST4 v1.1.0-r499 usage: ./run-trust4 [OPTIONS]:\n".
 		"\t-k INT: the starting k-mer size for indexing contigs (default: 9)\n".
     #"\t-h: print help message and exit.\n"
     "\t--barcode STRING: if -b, bam field for barcode; if -1 -2/-u, file containing barcodes (default: not used)\n".
+		"\t--barcodeLevel STRING: barcode is for cell or molecule (default: cell)\n".
 		#"\t--barcodeRange INT INT CHAR: start, end(-1 for length-1), strand in a barcode is the true barcode (default: 0 -1 +)\n".
     "\t--barcodeWhitelist STRING: path to the barcode whitelist (default: not used)\n".
 		"\t--barcodeTranslate STRING: path to the barcode translate file (default: not used)\n".
@@ -31,7 +32,6 @@ die "TRUST4 v1.1.0-r499 usage: ./run-trust4 [OPTIONS]:\n".
 		#"\t--umiRange INT INT CHAR: start, end(-1 for lenght-1), strand in a UMI is the true UMI (default: 0 -1 +)\n".
 		"\t--readFormat STRING: format for read, barcode and UMI files (example: r1:0:-1,r2:0:-1,bc:0:15,um:16:-1 for paired-end files with barcode and UMI)\n".
     "\t--repseq: the data is from TCR-seq or BCR-seq (default: not set)\n".
-		"\t--barcodeLevel STRING: barcode is for cell or molecule (default: cell)\n".
 		"\t--minHitLen INT: the minimal hit length for a valid overlap (default: auto)\n".
     "\t--mateIdSuffixLen INT: the suffix length in read id for mate. (default: not used)\n".
     "\t--skipMateExtension: do not extend assemblies with mate information, useful for SMART-seq (default: not used)\n".

trust-smartseq.pl

@@ -232,13 +232,22 @@ sub GetPairChainType
 	# Process the AIRR file
 	open FPairr, "tmp_smartseq_airr.tsv" ;
 	my $lineCnt = 0 ;
+	my %airrNameToCol ;
 	while (<FPairr>)
 	{
 		chomp ;
 		if ($cellProcessed == 0 && $lineCnt == 0)
 		{
 			print FPfinalairr $_,"\n" ;
+
+			chomp ;
+			my @cols = split /\t/ ;
+			for ($i = 0 ; $i < scalar(@cols) ; ++$i)
+			{
+				$airrNameToCol{ $cols[$i] } = $i ;
+			}
 		}
+
 		if ($lineCnt == 0)
 		{
 			++$lineCnt ;
@@ -254,6 +263,10 @@ sub GetPairChainType
 		if ($matchedCols[2] eq $cols[13])
 		{
 			$cols[0] = ${cellPrefix}."_".$cols[0] ;
+
+			# Add the cell id
+			$cols[ $airrNameToCol{"cell_id"} ] = $cellPrefix ;
+
 			print FPfinalairr join("\t", @cols), "\n" ;
 		}
 	}