Skip to content

Commit 4b5ea94

Browse files
committed
fix: handle small transcript populations in random_transcripts_contig
Clamp sample size to available count and skip when no mRNA transcripts exist for a given contig. Fixes CI flake where random.sample() fails on small simulated contigs.
1 parent ff1b9ed commit 4b5ea94

1 file changed

Lines changed: 3 additions & 0 deletions

File tree

tests/anoph/test_dipclust.py

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,9 @@ def random_transcripts_contig(*, api, contig, n):
1111
df_gff = api.genome_features(attributes=["ID", "Parent"])
1212
df_transcripts = df_gff.query(f"type == 'mRNA' and contig == '{contig}'")
1313
transcript_ids = df_transcripts["ID"].dropna().to_list()
14+
n = min(n, len(transcript_ids))
15+
if n == 0:
16+
pytest.skip(f"No mRNA transcripts found for contig '{contig}'")
1417
transcripts = random.sample(transcript_ids, n)
1518
return transcripts
1619

0 commit comments

Comments
 (0)