fix: suffix nomenclature for SAM uncollapsing (#130)

* fix: account for additional collapsing suffixes * test: update expected output
zavolanlab · Jan 1, 2024 · 43be5ac · 43be5ac
1 parent 57c6710
commit 43be5ac
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diff --git a/scripts/sam_uncollapse.pl b/scripts/sam_uncollapse.pl
@@ -92,7 +92,7 @@ sub usage {
 Comments:
 CAUTION: Only marginal validation of the input file type/format performed!
 
-Version 1.2 (2014-08-26)
+Version 1.3 (2023-12-24)
 Written by Alexander Kanitz on 2013-11-21
 ';
 }
@@ -128,15 +128,16 @@ sub sam_uncollapse {
                         # Get QNAME
                         my ($id, $rest) = split /\t/, $line, 2;
                         # Find and remove appended copy number n
-                        $id =~ s/-(\d+)\Z//;
+                        $id =~ /^([^_-]+)-(\d+)/;
                         # Write appended copy number n to variable
-                        my $repeat = $1;
+                        my $read = $1;
+                        my $repeat = $2;
 			# If --suffix option is set...
 			if ($suffix) {
 				# Iterate over number of identical reads/alignments
 				for my $suffix (1..$repeat) {
 		                        # Recreate line with suffix
-                		        $line = join "\t", "$id.$suffix", $rest;
+                		        $line = join "\t", "$read.$suffix", $rest;
 		                        # Print line
 		                        print OUT $line;
 				}
@@ -145,7 +146,7 @@ sub sam_uncollapse {
 			# Else...
 			else {
                 	        # Recreate line
-        	                $line = join "\t", $id, $rest;
+        	                $line = join "\t", $read, $rest;
                         	# Print line n times
 	                        print OUT $line x $repeat;
 			}

diff --git a/test/expected_output.md5 b/test/expected_output.md5
@@ -1,7 +1,7 @@
 68f943f89b52d628851dd97fb1399d68  results/TABLES/all_mirna_counts.tab
 363ecee318c57ee7e2e45ca468007baa  results/TABLES/all_pri-mir_counts.tab
-0d76977b2e36046cc176112776c5fa4e  results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam.bai
-25aca3f96e7ed644067d2050393bf7a4  results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam
+a0d36054628fbe1975e142d638fbb0ff  results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam.bai
+1371823fdc7a218e1e92ad546cfac585  results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam
 cc01c7884838a597c587437cb0acf64e  results/test_lib/alignments_intersecting_mirna.sam
 b1eb81426f890d671bba8c8a815edc1e  results/test_lib/alignments_intersecting_primir.sam
 eec9be6cda61d2728290c92c1209f455  results/intermediates/TABLES/mirna_counts_test_lib
@@ -22,12 +22,12 @@ d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/oligomap_transc
 76643f87bb2e2bff77d1b1223d7720b5  results/intermediates/test_lib/segemehl_genome_mappings.sam
 d41d8cd98f00b204e9800998ecf8427e  results/intermediates/test_lib/transcriptome_mappings_to_genome.sam
 63a32839360a985b68e0685aafad5c54  results/intermediates/test_lib/fa/reads.fa
-e9e9698d9350b64b64c1f6d96019fce8  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.sam
+0a0d69662aa8190abdcd8f395802ab00  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.sam
 edcb854702519c0002d8ce89a21e54ef  results/intermediates/test_lib/reads_formatted.fasta
 1a547487b8e92ad85bb26ff9b1db1f93  results/intermediates/test_lib/intersected_extended_mirna.bed
 a287ffc43b6afbdde3e9905bc27c28a5  results/intermediates/test_lib/alignments_all_sorted_test_lib.bam
 ec0e9bcc8ea857da897035c8fca4078f  results/intermediates/test_lib/reads_trimmed_adapters.fasta
-d7a5ab720ff9c96f41f3755a05b8f9e0  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.bam
+37c74848cbbba56e29e240cc078f5249  results/intermediates/test_lib/alignments_intersecting_mirna_uncollapsed.bam
 1f1b873d05ec14ef9b16376a1c98315b  results/intermediates/test_lib/genome_mappings.sam
 f5cb65466d328036a15b66cfbd4d8419  results/intermediates/test_lib/oligomap_genome_report.txt
 6cbdb9299e09b3e39b79a50db69226b5  results/intermediates/test_lib/transcriptome_mappings_no_header.sam