Added unit and integration tests

.gitignore

@@ -7,3 +7,4 @@ trace.txt*
 report.html*
 test/output
 conda_env
+__pycache__/

test.yml

@@ -0,0 +1,18 @@
+name: test_env
+channels:
+  - bioconda
+  - conda-forge
+  - anaconda
+dependencies:
+  - python>=3.8
+  - bioconda::gffutils=0.12
+  - bioconda::pysam=0.22.0
+  - conda-forge::pytest=8.0.0
+  - conda-forge::pytest-workflow=2.0.1
+  - conda-forge::logzero=1.7.0
+  - conda-forge::biopython=1.83
+  - conda-forge::python-xxhash=3.4.1
+  - conda-forge::r-base
+  - conda-forge::r-optparse
+  - conda-forge::r-tidyverse
+  - conda-forge::r-randomForest

tests/annotation/test_fusionannotation.py

@@ -0,0 +1,4 @@
+from bin.fusionannotation import FusionAnnotation
+
+def test_breakpoints_to_dict():
+    pass

tests/filtering/test_fusionreadfilter.py

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+from bin.fusionreadfilter import FusionReadFilter
+
+def test_fusionreadfilter():
+    pass

tests/merging/test_merge_data.py

@@ -0,0 +1,4 @@
+#from bin.merge_data import FusionSummary
+
+def test_normalize_counts_cpm():
+    pass

tests/parsing/fusioncatcher_1.txt

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+Very short summary of found candidate somatic fusion genes
+======================================================= ====
+
+Found 8 somatic fusion gene(s), which are as follows:
+  * TMPRSS2--ETV1  (already known fusion)
+  * EWSR1--ATF1  (already known fusion; exon-exon fusion junction)
+  * AKAP9--BRAF  (already known fusion; exon-exon fusion junction)
+  * ETV6--NTRK3  (already known fusion; exon-exon fusion junction)
+  * HOOK3--RET  (already known fusion; exon-exon fusion junction)
+  * EWSR1--FLI1  (already known fusion; exon-exon fusion junction)
+  * BRD4--NUTM1  (already known fusion; exon-exon fusion junction)
+  * CD74--ROS1  (already known fusion; exon-exon fusion junction)
+
+Found 8 somatic fusion transcript(s).
+
+For more detailed information regarding these candidate fusions, see text file 'final-list_candidate-fusion-genes.txt'.

tests/parsing/fusioncatcher_2.tsv

@@ -0,0 +1,9 @@
+Gene_1_symbol(5end_fusion_partner)	Gene_2_symbol(3end_fusion_partner)	Fusion_description	Counts_of_common_mapping_reads	Spanning_pairs	Spanning_unique_reads	Longest_anchor_found	Fusion_finding_method	Fusion_point_for_gene_1(5end_fusion_partner)	Fusion_point_for_gene_2(3end_fusion_partner)	Gene_1_id(5end_fusion_partner)	Gene_2_id(3end_fusion_partner)	Exon_1_id(5end_fusion_partner)	Exon_2_id(3end_fusion_partner)	Fusion_sequence	Predicted_effect
+TMPRSS2	ETV1	known,oncogene,cosmic,chimer2,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,oncokb,mitelman,t43	0	367	16	25	BOWTIE+BLAT	21:41494380:-	7:13935843:-	ENSG00000184012	ENSG00000006468			GGTCCTGACGCAGGCTTCCAACCCCGTCGTCTGCACGCAGCCCAAATCCC*CATCCAGCACGCCAGTGTCCCCACTGCATCATGCATCTCCAAACTCAACT	in-frame
+EWSR1	ATF1	known,oncogene,cosmic,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,m114,oncokb,mitelman,t24,exon-exon	0	363	23	25	BOWTIE	22:29287134:+	12:50814280:+	ENSG00000182944	ENSG00000123268	ENSE00003570564	ENSE00003675908	CAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*CTGCATCAGGAGATATGCAAACATATCAGATCCGAAC	in-frame
+AKAP9	BRAF	known,oncogene,cosmic,chimer2,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,oncokb,mitelman,t34,exon-exon	0	340	21	25	BOWTIE	7:92003235:+	7:140787584:-	ENSG00000127914	ENSG00000157764	ENSE00003484877	ENSE00003680515	ACTTCAGAAAGAACTCAATGTACTTAAATCAGAACAG*GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAG	in-frame
+ETV6	NTRK3	known,oncogene,cosmic,chimer2,cgp,ticdb,tcga,ccle2,18cancers,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,tcga2,oncokb,mitelman,pcawg,tcga3,t32,exon-exon	0	299	23	25	BOWTIE	12:11869969:+	15:87940753:-	ENSG00000139083	ENSG00000140538	ENSE00001788162	ENSE00001134154	CCTGAAGAGCACGCCATGCCCATTGGGAGAATAGCAG*ATGTGCAGCACATTAAGAGGAGAGACATCGTGCTGAA	in-frame
+HOOK3	RET	known,oncogene,cosmic,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,mitelman,t43,exon-exon	0	298	20	25	BOWTIE	8:42968214:+	10:43116584:+	ENSG00000168172	ENSG00000165731	ENSE00003485179	ENSE00001095944	CGCAGCGCGAAGTCAACTTGAAACCTACAAGAGACAG*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTTGG	in-frame
+EWSR1	FLI1	known,oncogene,cosmic,cgp,ticdb,ccle2,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,m85,oncokb,mitelman,ccle,t16,exon-exon	0	282	22	25	BOWTIE	22:29287134:+	11:128807180:+	ENSG00000182944	ENSG00000151702	ENSE00003570564	ENSE00003702967	CAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*GTCCTCCCCTTGGAGGGGCACAAACGATCAGTAAGAA	in-frame
+BRD4	NUTM1	known,oncogene,cosmic,chimer2,cgp,ticdb,ccle2,chimer4kb,chimer4pub,chimer4seq,cancer,oncokb,mitelman,ccle,t32,exon-exon	0	244	20	24	BOWTIE	19:15254152:-	15:34347969:+	ENSG00000141867	ENSG00000184507	ENSE00001187704	ENSE00001367212	GAGTCCAGCTCCTCTGACAGCGAAGACTCCGAAACAG*CATCTGCATTGCCGGGACCGGATATGAGCATGAAACC	in-frame
+CD74	ROS1	known,oncogene,cosmic,chimer2,cgp,ticdb,tcga,ccle2,18cancers,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,tcga2,oncokb,mitelman,pcawg,t29,exon-exon	0	152	22	25	BOWTIE	5:150404680:-	6:117324415:-	ENSG00000019582	ENSG00000047936	ENSE00000841201	ENSE00000762702	TCCTTGGAGCAAAAGCCCACTGACGCTCCACCGAAAG*ATGATTTTTGGATACCAGAAACAAGTTTCATACTTAC	in-frame

tests/parsing/test_fusiontoolparser.py

@@ -0,0 +1,97 @@
+from bin.fusiontoolparser_helper import parse_fusioncatcher_results
+from bin.fusiontoolparser_helper import parse_starfusion_results
+from bin.fusiontoolparser_helper import parse_arriba_results
+
+def test_parse_fusioncatcher_results():
+    infile = "tests/parsing/fusioncatcher_1.txt"
+    infile2 = "tests/parsing/fusioncatcher_2.tsv"
+    assert parse_fusioncatcher_results(infile, infile2) == {
+        '21:41494380:-_7:13935843:-': [
+            'TMPRSS2_ETV1', '21:41494380:-', '7:13935843:-', '16', '367'
+        ], 
+        '22:29287134:+_12:50814280:+': [
+            'EWSR1_ATF1', '22:29287134:+', '12:50814280:+', '23', '363'
+        ], 
+        '7:92003235:+_7:140787584:-': [
+            'AKAP9_BRAF', '7:92003235:+', '7:140787584:-', '21', '340'
+        ], 
+        '12:11869969:+_15:87940753:-': [
+            'ETV6_NTRK3', '12:11869969:+', '15:87940753:-', '23', '299'
+        ], 
+        '8:42968214:+_10:43116584:+': [
+            'HOOK3_RET', '8:42968214:+', '10:43116584:+', '20', '298'
+        ], 
+        '22:29287134:+_11:128807180:+': [
+            'EWSR1_FLI1', '22:29287134:+', '11:128807180:+', '22', '282'
+        ], 
+        '19:15254152:-_15:34347969:+': [
+            'BRD4_NUTM1', '19:15254152:-', '15:34347969:+', '20', '244'
+        ], 
+        '5:150404680:-_6:117324415:-': [
+            'CD74_ROS1', '5:150404680:-', '6:117324415:-', '22', '152'
+        ]
+    }
+
+def test_parse_starfusion_results():
+    infile = "tests/parsing/starfusion.tsv"
+    assert parse_starfusion_results(infile) == {
+        '12:11869969:+_15:87940753:-': [
+            'ETV6_NTRK3', '12:11869969:+', '15:87940753:-', '160', '390'
+        ], 
+        '22:29287134:+_11:128807180:+': [
+            'EWSR1_FLI1', '22:29287134:+', '11:128807180:+', '140', '333'
+        ], 
+        '19:15254152:-_15:34347969:+': [
+            'BRD4_NUTM1', '19:15254152:-', '15:34347969:+', '132', '260'
+        ], 
+        '22:29287134:+_12:50814280:+': [
+            'EWSR1_ATF1', '22:29287134:+', '12:50814280:+', '129', '367'
+        ], 
+        '5:150404680:-_6:117324415:-': [
+            'CD74_ROS1', '5:150404680:-', '6:117324415:-', '125', '140'
+        ], 
+        '7:92003235:+_7:140787584:-': [
+            'AKAP9_BRAF', '7:92003235:+', '7:140787584:-', '120', '348'
+        ], 
+        '8:42968214:+_10:43116584:+': [
+            'HOOK3_RET', '8:42968214:+', '10:43116584:+', '94', '276'
+        ], 
+        '21:41494375:-_7:13935838:-': [
+            'TMPRSS2_ETV1', '21:41494375:-', '7:13935838:-', '76', '321'
+        ], 
+        '2:42301394:+_2:29223584:-': [
+            'EML4_ALK', '2:42301394:+', '2:29223584:-', '61', '256'
+        ]
+    }
+
+def test_parse_arriba_results():
+    infile = "tests/parsing/arriba.tsv"
+    assert parse_arriba_results(infile) == {
+        '12:11869969:+_15:87940753:-': [
+            'ETV6_NTRK3', '12:11869969:+', '15:87940753:-', '130', '300'
+        ], 
+        '7:92003235:+_7:140787584:-': [
+            'AKAP9_BRAF', '7:92003235:+', '7:140787584:-', '113', '299'
+        ], 
+        '22:29287134:+_11:128807180:+': [
+            'EWSR1_FLI1', '22:29287134:+', '11:128807180:+', '70', '299'
+        ], 
+        '8:42968214:+_10:43116584:+': [
+            'HOOK3_RET', '8:42968214:+', '10:43116584:+', '88', '275'
+        ], 
+        '22:29287134:+_12:50814280:+': [
+            'EWSR1_ATF1', '22:29287134:+', '12:50814280:+', '49', '299'
+        ], 
+        '19:15254152:-_15:34347969:+': [
+            'BRD4_NUTM1', '19:15254152:-', '15:34347969:+', '82', '232'
+        ], 
+        '2:42301394:+_2:29223584:-': [
+            'EML4_ALK', '2:42301394:+', '2:29223584:-', '52', '221'
+        ], 
+        '5:150404680:-_6:117324415:-': [
+            'CD74_ROS1', '5:150404680:-', '6:117324415:-', '75', '139'
+        ], 
+        '21:41494375:-_7:13935838:-': [
+            'TMPRSS2_ETV1', '21:41494375:-', '7:13935838:-', '59', '300'
+        ]
+    }

tests/test_fusiontoolparser.yaml

@@ -0,0 +1,11 @@
+- name: Parse results of fusion tools
+  command: >
+    bin/fusiontoolparser.py \
+    --input-fusioncatcher tests/parsing/fusioncatcher_1.txt \
+    --input-fusioncatcher2 tests/parsing/fusioncatcher_2.tsv \
+    --input-starfusion tests/parsing/starfusion.tsv \
+    --input-arriba tests/parsing/arriba.tsv \
+    -o tests/ \
+    -s test
+  files:
+    - path: "tests/Detected_Fusions.csv"