feat!: Add methods for extracting data from fusion callers

src/fusor/translator.py

@@ -493,7 +493,7 @@ async def from_arriba(
                 eventType=EventType("read-through"),
                 eventDescription=arriba.confidence,
             )
-            if "read_through" in arriba.event
+            if "read_through" in arriba.event_type
             else CausativeEvent(
                 eventType=EventType("rearrangement"),
                 eventDescription=arriba.confidence,

tests/conftest.py

@@ -2,13 +2,16 @@
 
 import asyncio
 import logging
+from pathlib import Path
 
 import pytest
 from cool_seq_tool.app import CoolSeqTool
 
 from fusor.fusor import FUSOR
 from fusor.translator import Translator
 
+FIXTURE_DATA_DIR = Path(__file__).parents[0].resolve() / "fixtures"
+
 
 def pytest_addoption(parser):
     """Add custom commands to pytest invocation.
@@ -39,6 +42,12 @@ def event_loop():
     loop.close()
 
 
+@pytest.fixture(scope="session")
+def fixture_data_dir():
+    """Provide test data directory."""
+    return FIXTURE_DATA_DIR
+
+
 @pytest.fixture(scope="session")
 def fusor_instance():
     """Create test fixture for fusor object

tests/fixtures/annotated.fusion.txt

@@ -0,0 +1,2 @@
+sample	geneA	chrA	posA	ortA	featureA	geneB	chrB	posB	ortB	featureB	sv_ort	readsA	readsB	matchA	matchB	repeatA	repeatB	coverageA	coverageB	ratioA	ratioB	qposA	qposB	total_readsA	total_readsB	contig	type
+test	TCF3	chr19	1619111	-	coding	PBX1	chr1	164792493	+	coding	>	62	78	98	93	0.00	0.00	1145	1756	0.38	0.77	98	97	399	227	CCTCGCAGGCAGCACCAGCCTCATGCACAACCACGCGGCCCTCCCCAGCCAGCCAGGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTGTTTTGAGTATCCGAGGAGCCCAGGAGGAGGAACCCACAGACCCCCAGCTGATGCGGCTGGACAACATGCTGTTAGCGGAAGGCGTGGCGGGGG	CTX

tests/fixtures/enfusion_test.csv

@@ -0,0 +1,2 @@
+	Gene1	Gene2	Chr1	Chr2	Break1	Break2	FusionJunctionSequence
+0	TPM3	PDGFRB	1	5	154170465	150126612	ATATATCTAGAG|ATAGACAGATAGAT

tests/fixtures/fusions_arriba_test.tsv

@@ -0,0 +1,2 @@
+#gene1	gene2	strand1(gene/fusion)	strand2(gene/fusion)	breakpoint1	breakpoint2	site1	site2	type	split_reads1	split_reads2	discordant_mates	coverage1	coverage2	confidence	reading_frame	tags	retained_protein_domains	closest_genomic_breakpoint1	closest_genomic_breakpoint2	gene_id1	gene_id2	transcript_id1	transcript_id2	direction1	direction2	filters	fusion_transcript	peptide_sequence	read_identifiers
+BCR	ABL1	+/+	+/+	22:23632600	9:133729451	CDS/splice-site	CDS/splice-site	translocation	4	7	0	4	12	high	in-frame	Mitelman	Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),PH_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%),Variant_SH3_domain(100%)	.	.	ENSG00000186716.15	ENSG00000097007.13	ENST00000305877.8	ENST00000372348.2	downstream	upstream	.	AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG	SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR	BCR-ABL1-10,BCR-ABL1-2,BCR-ABL1-24,BCR-ABL1-28,BCR-ABL1-58,BCR-ABL1-60,BCR-ABL1-76,BCR-ABL1-12,BCR-ABL1-18,BCR-ABL1-4,BCR-ABL1-66

tests/fixtures/genie_test.txt

@@ -0,0 +1,2 @@
+Site1_Hugo_Symbol	Site2_Hugo_Symbol	Site1_Chromosome	Site2_Chromosome	Site1_Position	Site2_Position	Site2_Effect_On_Frame	Annotation
+TPM3	PDGFRB	1	5	154170465	150126612	In_frame	TMP3 (NM_152263.4) - PDGFRB (NM_002609.4) fusion

tests/fixtures/star-fusion.fusion_predictions.abridged.tsv

@@ -0,0 +1,38 @@
+#FusionName	JunctionReadCount	SpanningFragCount	SpliceType	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	LargeAnchorSupport	FFPM	LeftBreakDinuc	LeftBreakEntropy	RightBreakDinuc	RightBreakEntropy	annots
+KIF5B--RET	286	27	ONLY_REF_SPLICE	KIF5B^ENSG00000170759.10	chr10:32017143:-	RET^ENSG00000165731.18	chr10:43114480:+	YES_LDAS	3.2247	GT	1.9656	AG	1.9656	["ChimerKB","ChimerPub","Cosmic","ChimerSeq","INTRACHROMOSOMAL[chr10:11.02Mb]"]
+EML4--ALK	219	39	ONLY_REF_SPLICE	EML4^ENSG00000143924.18	chr2:42295516:+	ALK^ENSG00000171094.17	chr2:29223528:-	YES_LDAS	2.6581	GT	1.6895	AG	1.9086	["Klijn_CellLines","GUO2018CR_TCGA","HaasMedCancer","TCGA_StarF2019","CCLE_StarF2019","chimerdb_pubmed","ChimerSeq","ChimerKB","TumorFusionsNAR2018","Cosmic","YOSHIHARA_TCGA","ChimerPub","INTRACHROMOSOMAL[chr2:12.25Mb]"]
+ETV6--NTRK3	212	26	ONLY_REF_SPLICE	ETV6^ENSG00000139083.10	chr12:11869969:+	NTRK3^ENSG00000140538.16	chr15:87940753:-	YES_LDAS	2.452	GT	1.7819	AG	1.9656	["TCGA_StarF2019","HaasMedCancer","GUO2018CR_TCGA","chimerdb_omim","Cosmic","YOSHIHARA_TCGA","TumorFusionsNAR2018","ChimerPub","Larsson_TCGA","ChimerKB","ChimerSeq","chimerdb_pubmed","INTERCHROMOSOMAL[chr12--chr15]"]
+LMNA--NTRK1	196	34	ONLY_REF_SPLICE	LMNA^ENSG00000160789.19	chr1:156130773:+	NTRK1^ENSG00000198400.11	chr1:156874906:+	YES_LDAS	2.3696	GT	1.7465	AG	1.5058	["ChimerKB","Cosmic","TCGA_StarF2019","ChimerPub","INTRACHROMOSOMAL[chr1:0.68Mb]"]
+FGFR3--TACC3	196	25	ONLY_REF_SPLICE	FGFR3^ENSG00000068078.18	chr4:1806934:+	TACC3^ENSG00000013810.18	chr4:1739702:+	YES_LDAS	2.2769	GT	1.8892	AG	1.7819	["Cosmic","ChimerPub","YOSHIHARA_TCGA","TumorFusionsNAR2018","ChimerKB","ChimerSeq","CCLE_StarF2019","TCGA_StarF2019","GUO2018CR_TCGA","Klijn_CellLines","INTRACHROMOSOMAL[chr4:0.05Mb]","LOCAL_REARRANGEMENT:+:[48117]"]
+NCOA4--RET	183	20	ONLY_REF_SPLICE	NCOA4^ENSG00000266412.5	chr10:46012883:-	RET^ENSG00000165731.18	chr10:43116584:+	YES_LDAS	2.0915	GT	1.9086	AG	1.8323	["GUO2018CR_TCGA","HaasMedCancer","TCGA_StarF2019","ChimerSeq","ChimerKB","YOSHIHARA_TCGA","Cosmic","ChimerPub","TumorFusionsNAR2018","chimerdb_pubmed","INTRACHROMOSOMAL[chr10:2.87Mb]"]
+TPM3--NTRK1	135	16	ONLY_REF_SPLICE	TPM3^ENSG00000143549.19	chr1:154170400:-	NTRK1^ENSG00000198400.11	chr1:156874571:+	YES_LDAS	1.5556	GT	1.9329	AG	1.6895	["ChimerSeq","ChimerPub","Cosmic","TumorFusionsNAR2018","ChimerKB","CCLE_StarF2019","chimerdb_pubmed","Klijn_CellLines","TCGA_StarF2019","HaasMedCancer","INTRACHROMOSOMAL[chr1:2.62Mb]"]
+PAX8--PPARG	116	15	ONLY_REF_SPLICE	PAX8^ENSG00000125618.16	chr2:113235394:-	PPARG^ENSG00000132170.20	chr3:12379704:+	YES_LDAS	1.3496	GT	1.8295	AG	1.9329	["chimerdb_omim","GUO2018CR_TCGA","HaasMedCancer","TCGA_StarF2019","chimerdb_pubmed","ChimerSeq","ChimerKB","Cosmic","Mitelman","YOSHIHARA_TCGA","ChimerPub","TumorFusionsNAR2018","INTERCHROMOSOMAL[chr2--chr3]"]
+SLC45A3--BRAF	119	0	ONLY_REF_SPLICE	SLC45A3^ENSG00000158715.5	chr1:205680394:-	BRAF^ENSG00000157764.13	chr7:140794467:-	YES_LDAS	1.226	GT	1.5628	AG	1.7465	["ChimerSeq","ChimerPub","Cosmic","ChimerKB","INTERCHROMOSOMAL[chr1--chr7]"]
+FGFR3--BAIAP2L1	111	13	ONLY_REF_SPLICE	FGFR3^ENSG00000068078.18	chr4:1806934:+	BAIAP2L1^ENSG00000006453.13	chr7:98362432:-	YES_LDAS	1.2775	GT	1.8892	AG	1.8062	["CCLE_StarF2019","Klijn_CellLines","ChimerPub","Cosmic","ChimerKB","INTERCHROMOSOMAL[chr4--chr7]"]
+SLC34A2--ROS1	77	26	ONLY_REF_SPLICE	SLC34A2^ENSG00000157765.12	chr4:25664330:+	ROS1^ENSG00000047936.10	chr6:117324415:-	YES_LDAS	1.0612	GT	1.8892	AG	1.7465	["Cosmic","ChimerPub","ChimerKB","ChimerSeq","chimerdb_pubmed","CCLE_StarF2019","TCGA_StarF2019","GUO2018CR_TCGA","Klijn_CellLines","INTERCHROMOSOMAL[chr4--chr6]"]
+CD74--ROS1	58	6	ONLY_REF_SPLICE	CD74^ENSG00000019582.14	chr5:150404680:-	ROS1^ENSG00000047936.10	chr6:117324415:-	YES_LDAS	0.6593	GT	1.7819	AG	1.7465	["ChimerPub","Cosmic","TumorFusionsNAR2018","ChimerKB","ChimerSeq","chimerdb_pubmed","TCGA_StarF2019","GUO2018CR_TCGA","Klijn_CellLines","INTERCHROMOSOMAL[chr5--chr6]"]
+RN7SKP80--RN7SKP118	33	0	INCL_NON_REF_SPLICE	RN7SKP80^ENSG00000202058.1	chr22:42565086:-	RN7SKP118^ENSG00000201201.1	chr16:67321742:-	YES_LDAS	0.34	TT	1.9656	CG	1.8256	["TCGA_StarF2019","CCLE_StarF2019","INTERCHROMOSOMAL[chr22--chr16]"]
+EGFR--SEPT14	9	13	ONLY_REF_SPLICE	EGFR^ENSG00000146648.17	chr7:55200413:+	SEPT14^ENSG00000154997.8	chr7:55796092:-	YES_LDAS	0.2266	GT	1.8892	AG	1.9899	["GUO2018CR_TCGA","TCGA_StarF2019","YOSHIHARA_TCGA","INTRACHROMOSOMAL[chr7:0.58Mb]"]
+AC021660.2--GPR15	8	0	INCL_NON_REF_SPLICE	AC021660.2^ENSG00000248839.1	chr3:98525247:+	GPR15^ENSG00000154165.4	chr3:98532009:+	YES_LDAS	0.0824	CT	1.8892	AC	1.9656	["INTRACHROMOSOMAL[chr3:0.01Mb]","NEIGHBORS[6565]"]
+EEF1A1P13--EFHC1	6	0	INCL_NON_REF_SPLICE	EEF1A1P13^ENSG00000250182.3	chr5:14651703:-	EFHC1^ENSG00000096093.15	chr6:52482342:+	YES_LDAS	0.0618	CA	1.7056	CT	0.3534	["INTERCHROMOSOMAL[chr5--chr6]"]
+AC098590.1--AC099789.1	5	0	INCL_NON_REF_SPLICE	AC098590.1^ENSG00000213851.3	chr4:43410174:-	AC099789.1^ENSG00000225475.1	chr1:56619540:-	YES_LDAS	0.0515	CT	1.8323	AC	1.6049	["CCLE_StarF2019","INTERCHROMOSOMAL[chr4--chr1]"]
+RPL14--USP27X-AS1	5	0	INCL_NON_REF_SPLICE	RPL14^ENSG00000188846.13	chr3:40462056:+	USP27X-AS1^ENSG00000234390.4	chrX:49877691:-	YES_LDAS	0.0515	CT	1.5850	TC	1.5850	["INTERCHROMOSOMAL[chr3--chrX]"]
+TMPRSS2--ERG	5	0	ONLY_REF_SPLICE	TMPRSS2^ENSG00000184012.11	chr21:41508081:-	ERG^ENSG00000157554.18	chr21:38584945:-	YES_LDAS	0.0515	GT	1.6895	AG	1.9219	["ChimerSeq","Cosmic","ChimerPub","YOSHIHARA_TCGA","TumorFusionsNAR2018","Larsson_TCGA","ChimerKB","CCLE_StarF2019","chimerdb_pubmed","GUO2018CR_TCGA","TCGA_StarF2019","INTRACHROMOSOMAL[chr21:2.80Mb]"]
+LINC00158--AP001341.1	3	1	ONLY_REF_SPLICE	LINC00158^ENSG00000185433.8	chr21:25420708:-	AP001341.1^ENSG00000222042.1	chr21:25175445:-	YES_LDAS	0.0412	GT	1.9086	AG	1.4295	["TCGA_StarF2019","INTRACHROMOSOMAL[chr21:0.05Mb]","NEIGHBORS[51995]"]
+AC021660.2--GPR15	3	0	INCL_NON_REF_SPLICE	AC021660.2^ENSG00000248839.1	chr3:98525260:+	GPR15^ENSG00000154165.4	chr3:98532011:+	YES_LDAS	0.0309	AT	1.6895	CA	1.8892	["INTRACHROMOSOMAL[chr3:0.01Mb]","NEIGHBORS[6565]"]
+AC021660.2--GPR15	3	0	INCL_NON_REF_SPLICE	AC021660.2^ENSG00000248839.1	chr3:98525337:+	GPR15^ENSG00000154165.4	chr3:98532012:+	YES_LDAS	0.0309	GA	1.5058	AG	1.8892	["INTRACHROMOSOMAL[chr3:0.01Mb]","NEIGHBORS[6565]"]
+CLSPN--C1orf216	3	0	INCL_NON_REF_SPLICE	CLSPN^ENSG00000092853.13	chr1:35720748:-	C1orf216^ENSG00000142686.7	chr1:35719497:-	YES_LDAS	0.0309	TG	1.5656	CG	1.6729	["INTRACHROMOSOMAL[chr1:0.00Mb]","NEIGHBORS[746]"]
+ENO1--PDE6A	3	0	INCL_NON_REF_SPLICE	ENO1^ENSG00000074800.15	chr1:8867988:-	PDE6A^ENSG00000132915.10	chr5:149867239:-	YES_LDAS	0.0309	GT	1.4256	TG	1.8295	["INTERCHROMOSOMAL[chr1--chr5]"]
+RF00100--RN7SKP76	3	0	INCL_NON_REF_SPLICE	RF00100^ENSG00000202198.1	chr6:52995864:+	RN7SKP76^ENSG00000201289.1	chr16:61743234:-	YES_LDAS	0.0309	TT	1.9656	AT	1.8256	["INTERCHROMOSOMAL[chr6--chr16]"]
+RN7SK--RN7SKP76	3	0	INCL_NON_REF_SPLICE	RN7SK^ENSG00000283293.1	chr6:52995864:+	RN7SKP76^ENSG00000201289.1	chr16:61743234:-	YES_LDAS	0.0309	TT	1.9656	AT	1.8256	["INTERCHROMOSOMAL[chr6--chr16]"]
+EPSTI1--TGS1	2	0	ONLY_REF_SPLICE	EPSTI1^ENSG00000133106.14	chr13:42991978:-	TGS1^ENSG00000137574.10	chr8:55790182:+	YES_LDAS	0.0206	GT	1.3996	AG	1.9086	["INTERCHROMOSOMAL[chr13--chr8]"]
+KLHL18--ELP6	2	0	ONLY_REF_SPLICE	KLHL18^ENSG00000114648.11	chr3:47322708:+	ELP6^ENSG00000163832.15	chr3:47511226:-	YES_LDAS	0.0206	GT	1.9899	AG	1.9656	["INTRACHROMOSOMAL[chr3:0.15Mb]"]
+MCOLN2--NEK7	2	0	ONLY_REF_SPLICE	MCOLN2^ENSG00000153898.12	chr1:84997008:-	NEK7^ENSG00000151414.14	chr1:198232553:+	YES_LDAS	0.0206	GT	1.5301	AG	1.8892	["INTRACHROMOSOMAL[chr1:113.16Mb]"]
+PLEC--TSPAN4	2	0	ONLY_REF_SPLICE	PLEC^ENSG00000178209.15	chr8:143950184:-	TSPAN4^ENSG00000214063.10	chr11:850288:+	YES_LDAS	0.0206	GT	1.6729	AG	1.9329	["INTERCHROMOSOMAL[chr8--chr11]"]
+SEPT2--SFI1	2	0	ONLY_REF_SPLICE	SEPT2^ENSG00000168385.17	chr2:241315982:+	SFI1^ENSG00000198089.15	chr22:31607937:+	YES_LDAS	0.0206	GT	1.4566	AG	1.8062	["INTERCHROMOSOMAL[chr2--chr22]"]
+SNX25--NEK1	2	0	ONLY_REF_SPLICE	SNX25^ENSG00000109762.15	chr4:185320864:+	NEK1^ENSG00000137601.16	chr4:169590809:-	YES_LDAS	0.0206	GT	1.7232	AG	1.6402	["INTRACHROMOSOMAL[chr4:15.59Mb]"]
+UBE2K--FAM208A	2	0	ONLY_REF_SPLICE	UBE2K^ENSG00000078140.13	chr4:39755739:+	FAM208A^ENSG00000163946.13	chr3:56628614:-	YES_LDAS	0.0206	GT	1.9219	AG	1.6895	["INTERCHROMOSOMAL[chr4--chr3]"]
+XXYLT1-AS2--RNF145	2	0	ONLY_REF_SPLICE	XXYLT1-AS2^ENSG00000230266.1	chr3:195148105:+	RNF145^ENSG00000145860.11	chr5:159174158:-	YES_LDAS	0.0206	GT	1.8256	AG	1.5656	["INTERCHROMOSOMAL[chr3--chr5]"]
+NSF--AC091132.5	1	1	ONLY_REF_SPLICE	NSF^ENSG00000073969.18	chr17:46704854:+	AC091132.5^ENSG00000267246.1	chr17:45551537:-	YES_LDAS	0.0206	GT	1.6729	AG	1.9329	["INTRACHROMOSOMAL[chr17:1.03Mb]"]
+TXNDC11--SNX29	1	1	ONLY_REF_SPLICE	TXNDC11^ENSG00000153066.12	chr16:11730645:-	SNX29^ENSG00000048471.13	chr16:12524702:+	YES_LDAS	0.0206	GT	1.9086	AG	1.9086	["INTRACHROMOSOMAL[chr16:0.23Mb]"]
+UBE2R2--WNK1	1	1	ONLY_REF_SPLICE	UBE2R2^ENSG00000107341.4	chr9:33817934:+	WNK1^ENSG00000060237.16	chr12:813642:+	YES_LDAS	0.0206	GT	1.9656	AG	1.7232	["INTERCHROMOSOMAL[chr9--chr12]"]

tests/test_fusion_caller_models.py

@@ -0,0 +1,99 @@
+"""Module for testing fusion caller classes"""
+
+from pathlib import Path
+
+import pytest
+
+from fusor.fusion_caller_models import (
+    JAFFA,
+    Arriba,
+    Cicero,
+    EnFusion,
+    FusionCatcher,
+    Genie,
+    STARFusion,
+)
+
+
+def test_get_jaffa_records(fixture_data_dir):
+    """Test that get_jaffa_records works correctly"""
+    path = Path(fixture_data_dir / "jaffa_results.csv")
+    jaffa_instance = JAFFA()
+    records = jaffa_instance.load_records(path)
+    assert len(records) == 491
+
+    path = Path(fixture_data_dir / "jaffa_resultss.csv")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert jaffa_instance.load_records(path)
+
+
+def test_get_star_fusion_records(fixture_data_dir):
+    """Test that get_star_fusion_records works correctly"""
+    path = Path(fixture_data_dir / "star-fusion.fusion_predictions.abridged.tsv")
+    sf_instance = STARFusion()
+    records = sf_instance.load_records(path)
+    assert len(records) == 37
+
+    path = Path(fixture_data_dir / "star-fusion.fusion_predictions.abridged.tsvs")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert sf_instance.load_records(path)
+
+
+def test_get_fusion_catcher_records(fixture_data_dir):
+    """Test that get_fusion_catcher_records works correctly"""
+    path = Path(fixture_data_dir / "final-list_candidate-fusion-genes.txt")
+    fc_instance = FusionCatcher()
+    fusions_list = fc_instance.load_records(path)
+    assert len(fusions_list) == 355
+
+    path = Path(fixture_data_dir / "final-list_candidate-fusion-genes.txts")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert fc_instance.load_records(path)
+
+
+def test_get_arriba_records(fixture_data_dir):
+    """Test that get_arriba_records works correctly"""
+    path = Path(fixture_data_dir / "fusions_arriba_test.tsv")
+    arriba = Arriba()
+    fusions_list = arriba.load_records(path)
+    assert len(fusions_list) == 1
+
+    path = Path(fixture_data_dir / "fusionsd_arriba_test.tsv")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert arriba.load_records(path)
+
+
+def test_get_cicero_records(fixture_data_dir):
+    """Test that get_cicero_records works correctly"""
+    path = Path(fixture_data_dir / "annotated.fusion.txt")
+    cicero = Cicero()
+    fusions_list = cicero.load_records(path)
+    assert len(fusions_list) == 1
+
+    path = Path(fixture_data_dir / "annnotated.fusion.txt")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert cicero.load_records(path)
+
+
+def test_get_enfusion_records(fixture_data_dir):
+    """Test that get_enfusion_records works correctly"""
+    path = Path(fixture_data_dir / "enfusion_test.csv")
+    enfusion = EnFusion()
+    fusions_list = enfusion.load_records(path)
+    assert len(fusions_list) == 1
+
+    path = Path(fixture_data_dir / "enfusions_test.csv")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert enfusion.load_records(path)
+
+
+def test_get_genie_records(fixture_data_dir):
+    """Test that get_genie_records works correctly"""
+    path = Path(fixture_data_dir / "genie_test.txt")
+    genie = Genie()
+    fusions_list = genie.load_records(path)
+    assert len(fusions_list) == 1
+
+    path = Path(fixture_data_dir / "genie_tests.txt")
+    with pytest.raises(ValueError, match=f"{path} does not exist"):
+        assert genie.load_records(path)

tests/test_translators.py

@@ -369,7 +369,7 @@ async def test_arriba(
         strand2="-/-",
         breakpoint1="1:154170465",
         breakpoint2="5:150126612",
-        event="translocation",
+        event_type="translocation",
         confidence="high",
         direction1="upstream",
         direction2="downstream",