Merge pull request #887 from uclahs-cds/czhu-fix-fuzz

Fix FuzzTest to accommodate the update in callVariant
uclahs-cds · Jan 20, 2025 · 6d8e017 · 6d8e017
2 parents 78b1335 + 8004b9c
commit 6d8e017
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - Fixed `callVariant` that failed on small circRNA with a lot of variants at the step that creates the cleavage graph. #885
 
+- Fixed `fuzzTest`. Parameters missing for `callVariant`.
+
 ### Changed
 
 - Changed variant IDs for circRNAs to use backsplicing site instead of listing all exons/introns. #878

diff --git a/docs/files/fuzz_test_history.tsv b/docs/files/fuzz_test_history.tsv
@@ -29,3 +29,6 @@ v1.2.0	8bb50b1	2023-10-03	comprehensive	562642	0	0	0:00:00.360436	1.536579515902
 v1.2.1	e7a4096	2023-11-28	snv	277035	0	0	0:00:00.138178	0.36248703508333757	0:00:56.331649	118.07408019871977
 v1.2.1	e7a4096	2023-11-28	indel	275106	0	0	0:00:00.196090	0.41617068589153344	0:00:41.637490	99.04928608751558
 v1.2.1	e7a4096	2023-11-28	comprehensive	522929	0	0	0:00:00.378236	15.50100807513127	0:00:41.256473	179.70483365195142
+v1.4.2	c2da21c	2025-01-19	snv	270	0	0	0:00:00.170374	0.37595620821363007	0:00:56.681483	105.92716856631384
+v1.4.2	c2da21c	2025-01-19	indel	275	0	0	0:00:00.170908	0.3764300020522951	0:00:40.836362	93.63957347416282
+v1.4.2	c2da21c	2025-01-19	comprehensive	471	0	0	0:00:00.352437	0.6980351919379612	0:00:38.006367	140.52343056870941
diff --git a/moPepGen/fake.py b/moPepGen/fake.py
@@ -753,7 +753,7 @@ def fake_genomic_annotation(n_genes:int, chrom:str, min_exons:int, max_exons:int
         )
         gene_start = tx_model.transcript.location.start
         gene_end = tx_model.transcript.location.end
-        loc = FeatureLocation(start=gene_start, end=gene_end, seqname=chrom)
+        loc = FeatureLocation(start=gene_start, end=gene_end, seqname=chrom, strand=strand)
         gene_model = GeneAnnotationModel(
             location=loc, chrom=chrom, transcripts=[tx_id], type='gene',
             attributes=copy.deepcopy(tx_model.transcript.attributes)

diff --git a/moPepGen/util/fuzz_test.py b/moPepGen/util/fuzz_test.py
@@ -630,13 +630,15 @@ def call_variants(self):
         args.min_length = 7
         args.max_length = 25
         args.threads = 1
-        args.max_variants_per_node = 9
-        args.additional_variants_per_misc = 2
+        args.max_variants_per_node = (9, )
+        args.additional_variants_per_misc = (2, )
         args.min_nodes_to_collapse = 30
         args.naa_to_collapse = 5
         args.noncanonical_transcripts = False
         args.invalid_protein_as_noncoding = False
         args.debug_level = 1
+        args.timeout_seconds = 300
+        args.coding_novel_orf = False
         call_variant_peptide(args=args)
 
     def brute_force(self):