fixed some tests

fratajcz · Sep 26, 2024 · ddd6640 · ddd6640
1 parent b9de9bf
commit ddd6640
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Showing 3 changed files with 5 additions and 9 deletions.
diff --git 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
diff --git 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
@@ -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):
-Original file line number
+Diff line change
@@ -1,4 +1,3 @@
-    HGNC
     BEND7
     POTEF
     AADAC