Speed up unit tests

.github/workflows/tests.yml

@@ -34,6 +34,8 @@ jobs:
           pip install pypandoc==1.7.2
           pip install coverage
           pip install coveralls
+          pip install pytest
+          pip install pytest-cov
       - name: Install Python dependencies
         run: |
           pip install polars==0.16.18
@@ -48,7 +50,7 @@ jobs:
       - name: Run tests
         env:
           TEST_FLAG: 1
-        run: coverage run --source=pvactools.lib,pvactools.tools -m unittest discover -v -s tests
+        run: pytest --cov pvactools.lib --cov pvactools.tools --cov-report term-missing --durations=0 tests/test*.py
       - name: Coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

tests/test_data/pvacsplice/results/Test.filtered.gtf.tsv

@@ -0,0 +1,130 @@
+feature	cds_chrom	cds_start	cds_stop	transcript_id	transcript_biotype	tag	transcript_version	transcript_support_level	exon_number	gene_name	gene_id
+transcript	chr1	93179919	93278477	ENST00000343253	protein_coding	CCDS,basic	11	5	NA	CCDC18	ENSG00000122483
+transcript	chr1	93180363	93278607	ENST00000401026	protein_coding	CCDS,basic	7	1	NA	CCDC18	ENSG00000122483
+transcript	chr1	93180724	93278730	ENST00000370276	protein_coding	CCDS,basic	6	5	NA	CCDC18	ENSG00000122483
+transcript	chr1	93180724	93278730	ENST00000690025	protein_coding	basic	1	NA	NA	CCDC18	ENSG00000122483
+CDS	chr1	93183362	93183495	ENST00000343253	protein_coding	CCDS,basic	11	5	2	CCDC18	ENSG00000122483
+CDS	chr1	93183362	93183495	ENST00000401026	protein_coding	CCDS,basic	7	1	2	CCDC18	ENSG00000122483
+CDS	chr1	93183362	93183495	ENST00000370276	protein_coding	CCDS,basic	6	5	2	CCDC18	ENSG00000122483
+CDS	chr1	93183362	93183495	ENST00000690025	protein_coding	basic	1	NA	2	CCDC18	ENSG00000122483
+CDS	chr1	93183978	93184146	ENST00000343253	protein_coding	CCDS,basic	11	5	3	CCDC18	ENSG00000122483
+CDS	chr1	93183978	93184146	ENST00000401026	protein_coding	CCDS,basic	7	1	3	CCDC18	ENSG00000122483
+CDS	chr1	93183978	93184146	ENST00000370276	protein_coding	CCDS,basic	6	5	3	CCDC18	ENSG00000122483
+CDS	chr1	93183978	93184146	ENST00000690025	protein_coding	basic	1	NA	3	CCDC18	ENSG00000122483
+CDS	chr1	93186345	93186503	ENST00000343253	protein_coding	CCDS,basic	11	5	4	CCDC18	ENSG00000122483
+CDS	chr1	93186345	93186503	ENST00000401026	protein_coding	CCDS,basic	7	1	4	CCDC18	ENSG00000122483
+CDS	chr1	93186345	93186503	ENST00000370276	protein_coding	CCDS,basic	6	5	4	CCDC18	ENSG00000122483
+CDS	chr1	93186345	93186503	ENST00000690025	protein_coding	basic	1	NA	4	CCDC18	ENSG00000122483
+CDS	chr1	93192000	93192106	ENST00000343253	protein_coding	CCDS,basic	11	5	5	CCDC18	ENSG00000122483
+CDS	chr1	93192000	93192106	ENST00000401026	protein_coding	CCDS,basic	7	1	5	CCDC18	ENSG00000122483
+CDS	chr1	93192000	93192106	ENST00000370276	protein_coding	CCDS,basic	6	5	5	CCDC18	ENSG00000122483
+CDS	chr1	93192000	93192106	ENST00000690025	protein_coding	basic	1	NA	5	CCDC18	ENSG00000122483
+CDS	chr1	93193616	93193744	ENST00000343253	protein_coding	CCDS,basic	11	5	6	CCDC18	ENSG00000122483
+CDS	chr1	93193616	93193744	ENST00000401026	protein_coding	CCDS,basic	7	1	6	CCDC18	ENSG00000122483
+CDS	chr1	93193616	93193744	ENST00000370276	protein_coding	CCDS,basic	6	5	6	CCDC18	ENSG00000122483
+CDS	chr1	93193616	93193744	ENST00000690025	protein_coding	basic	1	NA	6	CCDC18	ENSG00000122483
+CDS	chr1	93201892	93201988	ENST00000343253	protein_coding	CCDS,basic	11	5	7	CCDC18	ENSG00000122483
+CDS	chr1	93201892	93201988	ENST00000401026	protein_coding	CCDS,basic	7	1	7	CCDC18	ENSG00000122483
+CDS	chr1	93201892	93201988	ENST00000370276	protein_coding	CCDS,basic	6	5	7	CCDC18	ENSG00000122483
+CDS	chr1	93201892	93201988	ENST00000690025	protein_coding	basic	1	NA	7	CCDC18	ENSG00000122483
+CDS	chr1	93205510	93205631	ENST00000343253	protein_coding	CCDS,basic	11	5	8	CCDC18	ENSG00000122483
+CDS	chr1	93205510	93205631	ENST00000401026	protein_coding	CCDS,basic	7	1	8	CCDC18	ENSG00000122483
+CDS	chr1	93205510	93205631	ENST00000370276	protein_coding	CCDS,basic	6	5	8	CCDC18	ENSG00000122483
+CDS	chr1	93205510	93205631	ENST00000690025	protein_coding	basic	1	NA	8	CCDC18	ENSG00000122483
+CDS	chr1	93207107	93207398	ENST00000343253	protein_coding	CCDS,basic	11	5	9	CCDC18	ENSG00000122483
+CDS	chr1	93207107	93207398	ENST00000401026	protein_coding	CCDS,basic	7	1	9	CCDC18	ENSG00000122483
+CDS	chr1	93207107	93207398	ENST00000370276	protein_coding	CCDS,basic	6	5	9	CCDC18	ENSG00000122483
+CDS	chr1	93207107	93207398	ENST00000690025	protein_coding	basic	1	NA	9	CCDC18	ENSG00000122483
+CDS	chr1	93210802	93210926	ENST00000343253	protein_coding	CCDS,basic	11	5	10	CCDC18	ENSG00000122483
+CDS	chr1	93210802	93210926	ENST00000401026	protein_coding	CCDS,basic	7	1	10	CCDC18	ENSG00000122483
+CDS	chr1	93210802	93210926	ENST00000370276	protein_coding	CCDS,basic	6	5	10	CCDC18	ENSG00000122483
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+CDS	chr1	93212101	93212261	ENST00000343253	protein_coding	CCDS,basic	11	5	11	CCDC18	ENSG00000122483
+CDS	chr1	93212101	93212261	ENST00000401026	protein_coding	CCDS,basic	7	1	11	CCDC18	ENSG00000122483
+CDS	chr1	93212101	93212261	ENST00000370276	protein_coding	CCDS,basic	6	5	11	CCDC18	ENSG00000122483
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+CDS	chr1	93214746	93214966	ENST00000343253	protein_coding	CCDS,basic	11	5	12	CCDC18	ENSG00000122483
+CDS	chr1	93214746	93214966	ENST00000370276	protein_coding	CCDS,basic	6	5	12	CCDC18	ENSG00000122483
+CDS	chr1	93216636	93216746	ENST00000343253	protein_coding	CCDS,basic	11	5	13	CCDC18	ENSG00000122483
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+CDS	chr1	93216636	93216746	ENST00000370276	protein_coding	CCDS,basic	6	5	13	CCDC18	ENSG00000122483
+CDS	chr1	93216636	93216746	ENST00000690025	protein_coding	basic	1	NA	13	CCDC18	ENSG00000122483
+CDS	chr1	93217738	93217869	ENST00000343253	protein_coding	CCDS,basic	11	5	14	CCDC18	ENSG00000122483
+CDS	chr1	93217738	93217869	ENST00000401026	protein_coding	CCDS,basic	7	1	14	CCDC18	ENSG00000122483
+CDS	chr1	93217738	93217869	ENST00000370276	protein_coding	CCDS,basic	6	5	14	CCDC18	ENSG00000122483
+CDS	chr1	93217738	93217869	ENST00000690025	protein_coding	basic	1	NA	14	CCDC18	ENSG00000122483
+CDS	chr1	93221609	93221743	ENST00000343253	protein_coding	CCDS,basic	11	5	15	CCDC18	ENSG00000122483
+CDS	chr1	93221609	93221743	ENST00000401026	protein_coding	CCDS,basic	7	1	15	CCDC18	ENSG00000122483
+CDS	chr1	93221609	93221743	ENST00000370276	protein_coding	CCDS,basic	6	5	15	CCDC18	ENSG00000122483
+CDS	chr1	93221609	93221743	ENST00000690025	protein_coding	basic	1	NA	15	CCDC18	ENSG00000122483
+CDS	chr1	93221859	93221936	ENST00000343253	protein_coding	CCDS,basic	11	5	16	CCDC18	ENSG00000122483
+CDS	chr1	93221859	93221936	ENST00000401026	protein_coding	CCDS,basic	7	1	16	CCDC18	ENSG00000122483
+CDS	chr1	93221859	93221936	ENST00000370276	protein_coding	CCDS,basic	6	5	16	CCDC18	ENSG00000122483
+CDS	chr1	93221859	93221936	ENST00000690025	protein_coding	basic	1	NA	16	CCDC18	ENSG00000122483
+CDS	chr1	93226333	93226449	ENST00000343253	protein_coding	CCDS,basic	11	5	17	CCDC18	ENSG00000122483
+CDS	chr1	93226333	93226449	ENST00000401026	protein_coding	CCDS,basic	7	1	17	CCDC18	ENSG00000122483
+CDS	chr1	93226333	93226449	ENST00000370276	protein_coding	CCDS,basic	6	5	17	CCDC18	ENSG00000122483
+CDS	chr1	93226333	93226449	ENST00000690025	protein_coding	basic	1	NA	17	CCDC18	ENSG00000122483
+CDS	chr1	93232426	93232593	ENST00000343253	protein_coding	CCDS,basic	11	5	18	CCDC18	ENSG00000122483
+CDS	chr1	93232426	93232593	ENST00000401026	protein_coding	CCDS,basic	7	1	18	CCDC18	ENSG00000122483
+CDS	chr1	93232426	93232593	ENST00000370276	protein_coding	CCDS,basic	6	5	18	CCDC18	ENSG00000122483
+CDS	chr1	93232426	93232593	ENST00000690025	protein_coding	basic	1	NA	18	CCDC18	ENSG00000122483
+CDS	chr1	93236248	93236390	ENST00000343253	protein_coding	CCDS,basic	11	5	19	CCDC18	ENSG00000122483
+CDS	chr1	93236248	93236390	ENST00000401026	protein_coding	CCDS,basic	7	1	19	CCDC18	ENSG00000122483
+CDS	chr1	93236248	93236390	ENST00000370276	protein_coding	CCDS,basic	6	5	19	CCDC18	ENSG00000122483
+CDS	chr1	93236248	93236390	ENST00000690025	protein_coding	basic	1	NA	19	CCDC18	ENSG00000122483
+CDS	chr1	93239310	93239473	ENST00000343253	protein_coding	CCDS,basic	11	5	20	CCDC18	ENSG00000122483
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+CDS	chr1	93239683	93239896	ENST00000343253	protein_coding	CCDS,basic	11	5	21	CCDC18	ENSG00000122483
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+CDS	chr1	93239683	93239896	ENST00000690025	protein_coding	basic	1	NA	21	CCDC18	ENSG00000122483
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+CDS	chr1	93246105	93246204	ENST00000401026	protein_coding	CCDS,basic	7	1	22	CCDC18	ENSG00000122483
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+CDS	chr1	93246838	93246954	ENST00000343253	protein_coding	CCDS,basic	11	5	23	CCDC18	ENSG00000122483
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+CDS	chr1	93254471	93254614	ENST00000343253	protein_coding	CCDS,basic	11	5	24	CCDC18	ENSG00000122483
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+CDS	chr1	93256335	93256538	ENST00000343253	protein_coding	CCDS,basic	11	5	25	CCDC18	ENSG00000122483
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+CDS	chr1	93264701	93264901	ENST00000370276	protein_coding	CCDS,basic	6	5	27	CCDC18	ENSG00000122483
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