Rename HGNC file to indicate version 2023-10

data/Makefile

@@ -155,7 +155,7 @@ $(TMP_DIR)/ensembl_transcript_info.txt: $(TMP_DIR)/$(SPECIES).gff3.gz
 	python ../scripts/transform_gff_to_tsv_for_exon_info_from_ensembl.py $^ $@
 
 # Add HGNC symbols, exons, UTRs, PFAM domains and Uniprot id to Ensembl Transcript
-$(TMP_DIR)/ensembl_biomart_transcripts.json.gz: $(TMP_DIR)/ensembl_biomart_transcripts.txt $(TMP_DIR)/ensembl_transcript_info.txt $(VERSION)/input/ensembl_biomart_pfam.txt $(VERSION)/input/ensembl_biomart_refseq.txt $(VERSION)/input/ensembl_biomart_ccds.txt uniprot/export/$(VERSION)_enst_to_uniprot_mapping_id.txt common_input/isoform_overrides_uniprot.txt common_input/$(MSKCC_ISOFORM_OVERRIDES_FILE_NAME) common_input/hgnc_complete_set_2023-12-26.txt
+$(TMP_DIR)/ensembl_biomart_transcripts.json.gz: $(TMP_DIR)/ensembl_biomart_transcripts.txt $(TMP_DIR)/ensembl_transcript_info.txt $(VERSION)/input/ensembl_biomart_pfam.txt $(VERSION)/input/ensembl_biomart_refseq.txt $(VERSION)/input/ensembl_biomart_ccds.txt uniprot/export/$(VERSION)_enst_to_uniprot_mapping_id.txt common_input/isoform_overrides_uniprot.txt common_input/$(MSKCC_ISOFORM_OVERRIDES_FILE_NAME) common_input/hgnc_complete_set_2023-10.txt
 	python ../scripts/add_domains_hugo_ccds_refseq_exon_info_uniprot_to_ensembl_transcript.py $^ $@
 
 # for mouse a specific recipe without overrides
@@ -165,9 +165,9 @@ $(TMP_DIR)/ensembl_biomart_transcripts_mouse.json.gz: $(TMP_DIR)/ensembl_biomart
 # give default/canonical geneid/transcript based on given hugo symbol takes
 # about 50m to run (TODO: this can be easily optimized)
 # isoform_overrides_genome_nexus.txt is made for genome nexus, others files are generated for vcf2maf
-# Please note: we should keep hgnc_complete_set_2023-12-26 in sync with https://github.com/cBioPortal/datahub-study-curation-tools/blob/master/gene-table-update/build-input-for-importer/hgnc_complete_set.txt
+# Please note: we should keep hgnc_complete_set_2023-10 in sync with https://github.com/cBioPortal/datahub-study-curation-tools/blob/master/gene-table-update/build-input-for-importer/hgnc_complete_set.txt
 # isoform_overrides_oncokb_grch3*.txt is a list of OncoKB transcripts and genes, it's generated by download_oncokb_isoform_overrides.py
-$(TMP_DIR)/ensembl_biomart_canonical_transcripts_per_hgnc.txt: $(TMP_DIR)/ensembl_canonical_data.txt common_input/hgnc_complete_set_2023-12-26.txt common_input/isoform_overrides_uniprot.txt common_input/$(MSKCC_ISOFORM_OVERRIDES_FILE_NAME) common_input/$(GENOME_NEXUS_ISOFORM_OVERRIDES_FILE_NAME) common_input/$(ONCOKB_ISOFORM_OVERRIDES_FILE_NAME) common_input/ignored_genes.txt
+$(TMP_DIR)/ensembl_biomart_canonical_transcripts_per_hgnc.txt: $(TMP_DIR)/ensembl_canonical_data.txt common_input/hgnc_complete_set_2023-10.txt common_input/isoform_overrides_uniprot.txt common_input/$(MSKCC_ISOFORM_OVERRIDES_FILE_NAME) common_input/$(GENOME_NEXUS_ISOFORM_OVERRIDES_FILE_NAME) common_input/$(ONCOKB_ISOFORM_OVERRIDES_FILE_NAME) common_input/ignored_genes.txt
 	python ../scripts/make_one_canonical_transcript_per_gene.py $^ $@
 
 # mouse version. A different script is called that set the canonicals based on Ensembl lookup.

data/common_input/version_info.txt

@@ -1,8 +1,8 @@
 name	version	type	id	genome_build	description	url
 VEP	grch37	mirrored	vep	grch37	VEP determines the effect of your variants(SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.	https://grch37.ensembl.org/info/docs/tools/vep/index.html
 VEP	grch38	mirrored	vep	grch38	VEP determines the effect of your variants(SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.	https://useast.ensembl.org/info/docs/tools/vep/index.html
-HGNC	2023-12	mirrored	hgnc	grch37	The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation	http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/
-HGNC	2023-12	mirrored	hgnc	grch38	The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation	http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/
+HGNC	2023-10	mirrored	hgnc	grch37	The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation	http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/
+HGNC	2023-10	mirrored	hgnc	grch38	The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation	http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/
 Cancer Hotspots	v2	mirrored	cancer_hotspots	grch37	A resource for statistically significant mutations in cancer 	https://www.cancerhotspots.org
 Cancer Hotspots	v2	mirrored	cancer_hotspots	grch38	A resource for statistically significant mutations in cancer 	https://www.cancerhotspots.org
 3D Hotspots	v2	mirrored	3d_hotspots	grch37	A resource for statistically significant mutations clustering in 3d protein structures in cancer	https://www.3dhotspots.org/

scripts/add_domains_hugo_ccds_refseq_exon_info_uniprot_to_ensembl_transcript.py

@@ -246,7 +246,7 @@ def main(ensembl_biomart_transcripts,
                         help="common_input/isoform_overrides_uniprot.txt")
     parser.add_argument("vcf2maf_isoform_overrides_mskcc",
                         help="common_input/isoform_overrides_at_mskcc_grch37.txt or common_input/isoform_overrides_at_mskcc_grch38.txt")
-    parser.add_argument("hgnc_symbol_set", help="common_input/hgnc_complete_set_2023-12-26.txt")
+    parser.add_argument("hgnc_symbol_set", help="common_input/hgnc_complete_set_2023-10.txt")
     parser.add_argument("ensembl_biomart_transcripts_json",
                         help="tmp/ensembl_biomart_transcripts.json.gz")
 

scripts/make_one_canonical_transcript_per_gene.py

@@ -224,7 +224,7 @@ def main(ensembl_biomart_geneids_transcript_info,
     parser.add_argument("ensembl_biomart_geneids_transcript_info",
                         help="tmp/ensembl_biomart_geneids.transcript_info.txt")
     parser.add_argument("hgnc_complete_set",
-                        help="common_input/hgnc_complete_set_2023-12-26.txt")
+                        help="common_input/hgnc_complete_set_2023-10.txt")
     parser.add_argument("isoform_overrides_uniprot",
                         help="common_input/isoform_overrides_uniprot.txt")
     parser.add_argument("isoform_overrides_at_mskcc",