Merge pull request #66 from griffithlab/gene_expr_id

Update the expression annotator to use the gene (ID) column in Kallisto files

tests/test_data/input.kallisto.gx.vcf

@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:USP18|18.4008276190378
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|18.4008276190378

tests/test_data/kallisto.genes

@@ -1,11 +1,11 @@
 gene_name	gene	abundance	counts	length
-A1BG	A1BG	9.5072780253347	253.812537262238	1113.77371499879
-A1CF	A1CF	0.170005984522626	33.3184303003113	8176.36764900294
-A2M	A2M	4.49761004558132	110	1020.35424350425
-A2ML1	A2ML1	1.78407197701224	59.8726175228087	1400.09002532749
-A2MP1	A2MP1	0.233702196740902	15	2677.74090252527
-A3GALT2	A3GALT2	0.119577011382624	2.38061461180681	830.580036203776
-A4GALT	A4GALT	0.569898611254872	15	1098.07941073092
-A4GNT	A4GNT	0.0264285588681354	1	1578.58003620378
-AAAS	AAAS	18.4008276190378	475	1076.95198457067
-USP18	USP18	18.4008276190378	475	1076.95198457067
+A1BG	ENSG00000121410	9.5072780253347	253.812537262238	1113.77371499879
+A1CF	ENSG00000148584	0.170005984522626	33.3184303003113	8176.36764900294
+A2M	ENSG00000175899	4.49761004558132	110	1020.35424350425
+A2ML1	ENSG00000166535	1.78407197701224	59.8726175228087	1400.09002532749
+A2MP1	ENSG00000291190	0.233702196740902	15	2677.74090252527
+A3GALT2	ENSG00000184389	0.119577011382624	2.38061461180681	830.580036203776
+A4GALT	ENSG00000128274	0.569898611254872	15	1098.07941073092
+A4GNT	ENSG00000118017	0.0264285588681354	1	1578.58003620378
+AAAS	ENSG00000094914	18.4008276190378	475	1076.95198457067
+USP18	ENSG00000184979	18.4008276190378	475	1076.95198457067

vatools/vcf_expression_annotator.py

@@ -12,7 +12,7 @@ def resolve_id_column(args):
         return 'tracking_id'
     elif args.format == 'kallisto':
         if args.mode == 'gene':
-            return 'gene_name'
+            return 'gene'
         elif args.mode == 'transcript':
             return 'target_id'
     elif args.format == 'stringtie':
@@ -156,7 +156,7 @@ def define_parser():
     )
     parser.add_argument(
         "-i", "--id-column",
-        help="The column header in the expression_file for the column containing gene names/transcript ids. Required when using the `custom` format."
+        help="The column header in the expression_file for the column containing gene/transcript ids. Required when using the `custom` format."
     )
     parser.add_argument(
         "-e", "--expression-column",
@@ -210,12 +210,8 @@ def main(args_input = sys.argv[1:]):
             for key, value in zip(csq_format, transcript.split('|')):
                 if key == 'Feature' and value != '' and not value.startswith('ENSR'):
                     transcript_ids.add(value)
-                if args.format == 'kallisto':
-                    if key == 'SYMBOL' and value != '':
-                        genes.add(value)
-                else:
-                    if key == 'Gene' and value != '':
-                        genes.add(value)
+                if key == 'Gene' and value != '':
+                    genes.add(value)
 
         if args.mode == 'gene':
             genes = list(genes)