diff --git a/speos/tests/files/dummy_graph/dummy_other_label.tsv b/speos/tests/files/dummy_graph/dummy_other_label.tsv index ebd134b..af5ac89 100644 --- a/speos/tests/files/dummy_graph/dummy_other_label.tsv +++ b/speos/tests/files/dummy_graph/dummy_other_label.tsv @@ -1,4 +1,3 @@ -HGNC BEND7 POTEF AADAC \ No newline at end of file diff --git a/speos/tests/files/dummy_graph/dummy_translation_table.tsv b/speos/tests/files/dummy_graph/dummy_translation_table.tsv index 0d68255..f78b682 100644 --- a/speos/tests/files/dummy_graph/dummy_translation_table.tsv +++ b/speos/tests/files/dummy_graph/dummy_translation_table.tsv @@ -1,8 +1,4 @@ hgnc_id symbol name locus_group locus_type status location location_sortable alias_symbol alias_name prev_symbol prev_name gene_group gene_group_id date_approved_reserved date_symbol_changed date_name_changed date_modified entrez_id ensembl_gene_id vega_id ucsc_id ena refseq_accession ccds_id uniprot_ids pubmed_id mgd_id rgd_id lsdb cosmic omim_id mirbase homeodb snornabase bioparadigms_slc orphanet pseudogene.org horde_id merops imgt iuphar kznf_gene_catalog mamit-trnadb cd lncrnadb enzyme_id intermediate_filament_db rna_central_ids lncipedia gtrnadb agr mane_select gencc -HGNC:17 AADAC arylacetamide deacetylase protein-coding gene gene with protein product Approved 3q25.1 03q25.1 "DAC|CES5A1" arylacetamide deacetylase (esterase) "Lipases|Arylacetamide deacetylase family" "464|465" 1996-12-27 2012-07-13 2021-11-05 13 ENSG00000114771 OTTHUMG00000159876 uc003eze.4 L32179 NM_001086 CCDS33877 P22760 "8063807|9299245" MGI:1915008 RGD:631440 600338 S09.991 3.1.1.3 HGNC:17 "ENST00000232892.12|NM_001086.3" HGNC:17 -HGNC:24427 AADACL2 arylacetamide deacetylase like 2 protein-coding gene gene with protein product Approved 3q25.1 03q25.1 MGC72001 Arylacetamide deacetylase family 465 2005-03-18 2016-05-26 2018-05-03 344752 ENSG00000197953 OTTHUMG00000155914 uc003ezc.4 BC065724 NM_207365 CCDS3161 Q6P093 25715734 MGI:3646333 RGD:1563197 HGNC:24427 "ENST00000356517.4|NM_207365.4" -HGNC:32037 AADACL3 arylacetamide deacetylase like 3 protein-coding gene gene with protein product Approved 1p36.21 01p36.21 OTTHUMG00000001887 Arylacetamide deacetylase family 465 2006-06-30 2016-05-26 2018-05-03 126767 ENSG00000188984 OTTHUMG00000001887 uc057ckc.1 NM_001103170 CCDS41253 Q5VUY0 MGI:2685281 RGD:1563257 HGNC:32037 "ENST00000359318.8|NM_001103170.3" -HGNC:32038 AADACL4 arylacetamide deacetylase like 4 protein-coding gene gene with protein product Approved 1p36.21 01p36.21 OTTHUMG00000001889 Arylacetamide deacetylase family 465 2006-06-30 2016-05-26 2018-04-17 343066 ENSG00000204518 OTTHUMG00000001889 uc001auf.3 NM_001013630 CCDS30590 Q5VUY2 "MGI:2685282|MGI:2685284|MGI:2685880|MGI:3650257|MGI:3650721|MGI:3652194" RGD:1565761 HGNC:32038 "ENST00000376221.2|NM_001013630.2" HGNC:29260 NCEH1 neutral cholesterol ester hydrolase 1 protein-coding gene gene with protein product Approved 3q26.31 03q26.31 "KIAA1363|NCEH" "alkylacetylglycerol acetylhydrolase|acetylalkylglycerol acetylhydrolase" AADACL1 arylacetamide deacetylase-like 1 Arylacetamide deacetylase family 465 2005-02-25 2009-07-23 2009-07-23 2019-11-20 57552 ENSG00000144959 OTTHUMG00000156872 uc003fig.4 AB037784 NM_020792 CCDS54681 Q6PIU2 "10718198|17052608|22771767" MGI:2443191 RGD:1311104 613234 S09.992 3.1.1.71 HGNC:29260 "ENST00000475381.7|NM_020792.6" HGNC:33905 POTEF POTE ankyrin domain family member F protein-coding gene gene with protein product Approved 2q21.1 02q21.1 "POTEACTIN|POTE2alpha" A26C1B "ANKRD26-like family C, member 1B|POTE ankyrin domain family, member F" POTE ankyrin domain containing 685 2007-11-27 2008-11-26 2015-11-18 2015-11-18 728378 ENSG00000196604 OTTHUMG00000153628 uc010fmh.3 EF523384 NM_001099771 CCDS46409 A5A3E0 17101985 MGI:1914825 RGD:1584390 HGNC:33905 "ENST00000409914.7|NM_001099771.2" HGNC:23514 BEND7 BEN domain containing 7 protein-coding gene gene with protein product Approved 10p13 10p13 FLJ40283 C10orf30 chromosome 10 open reading frame 30 BEN domain containing 422 2003-11-21 2008-10-03 2008-10-03 2016-10-05 222389 ENSG00000165626 OTTHUMG00000017699 uc001imm.3 BC031618 NM_152751 "CCDS41490|CCDS7099" Q8N7W2 MGI:2443100 RGD:1305898 HGNC:23514 "ENST00000466271.3|NM_001369863.1" diff --git a/speos/tests/test_preprocessor.py b/speos/tests/test_preprocessor.py index f3a8dd0..dc5df90 100644 --- a/speos/tests/test_preprocessor.py +++ b/speos/tests/test_preprocessor.py @@ -9,7 +9,7 @@ import logging -logging.disable() +#logging.disable() class GWASMapperTest(unittest.TestCase): @@ -657,8 +657,8 @@ def test_label_extension(self): def test_label_extension_other_symbol(self): config = Config() - mapping = [{"name": "UNK-immune_dysregulation", - "ground_truth": "Immune_Dysregulation_genes.bed", + mapping = [{"name": "UNK-dummy", + "ground_truth": "dummy_mendelian.bed", "features_file": "", "match_type": "perfect", "significant": "True", @@ -671,12 +671,13 @@ def test_label_extension_other_symbol(self): with open(mapping_file_path, "w") as file: json.dump(mapping, file) gwasmapper = GWASMapper(mapping_file=mapping_file_path) - mappings = gwasmapper.get_mappings(tags="immune_dysregulation", fields="name") + mappings = gwasmapper.get_mappings(tags="dummy", fields="name") adjacencies = self.adjacencymapper.get_mappings(tags="DummyUndirectedGraph", fields="name") prepro = PreProcessor(config, mappings, adjacencies, **self.prepro_kwargs) prepro.build_graph(features=False) pos, neg = prepro.find_pos_and_neg_idx() + self.assertEqual(len(pos), 3) def test_directed_graph(self):