From c2da21cffbfb7e8f34b382f9a4b0d6bb2f9f8427 Mon Sep 17 00:00:00 2001 From: zhuchcn Date: Sun, 19 Jan 2025 13:51:50 -0800 Subject: [PATCH 1/2] fix (fuzzTest): parameters missing for callVariant --- CHANGELOG.md | 2 ++ moPepGen/fake.py | 2 +- moPepGen/util/fuzz_test.py | 6 ++++-- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f2e759ef..ad1b325d 100644 --- 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/moPepGen/fake.py b/moPepGen/fake.py index e64c630b..5eb1f76b 100644 --- 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 index ab40233f..7941d7cb 100644 --- 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): From 8004b9cb76c9ea674f7e7268e4295d447e360369 Mon Sep 17 00:00:00 2001 From: zhuchcn Date: Sun, 19 Jan 2025 15:58:42 -0800 Subject: [PATCH 2/2] doc (fuzzTest): fuz test log added --- docs/files/fuzz_test_history.tsv | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/files/fuzz_test_history.tsv b/docs/files/fuzz_test_history.tsv index 59bbb306..ec702a11 100644 --- 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