Fix ORF prediction crash on soft-masked (lowercase) genome FASTA (2.0.4) - #40
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Genome FASTA files commonly soft-mask repeats with lowercase bases. Gene.get_sequence() doesn't normalize case, so lowercase bases flowed into kozak_score's PWM lookup (indexed only by uppercase ACGTN), crashing with an uncaught KeyError (#26). Also fixes a silent sibling bug: start/stop codon regex matching ("ATG" vs "atg") would silently miss ORFs entirely in soft-masked regions rather than crash. Fixed at the single point tr_seq is obtained in add_orfs(), not in get_sequence() itself, since that's also used by the public write_fasta export where case is meaningful to preserve.
Covers the lowercase-FASTA ORF prediction fix (#26).
Two styles coexist -- self-contained fixtures vs. the pickle-based pipeline chain -- prompted by real debugging time lost to stale cross-run pickle state earlier today.
b06579c's commit message described this fix but only staged the test files -- the source change itself was never committed.
Dependency Review✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.Scanned FilesNone |
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Summary
Closes #26:
add_orf_prediction/Gene.add_orfs()crashed with an uncaughtKeyErrorwhen the genome FASTA has soft-masked (lowercase) sequence.Root cause:
Gene.get_sequence()doesn't normalize case, so lowercase bases flowed intokozak_score()'s PWM lookup, which is indexed only by uppercaseACGTN. Also fixes a silent sibling bug: start/stop codon matching uses a case-sensitive regex against"ATG"/"TAA"/etc., so ORFs entirely within soft-masked regions were previously missed with no warning at all, not just crashed.Fixed at the single point
tr_seqis obtained insideadd_orfs(), not inget_sequence()itself -- that function is also used by the publicwrite_fastaexport, where preserving original case is meaningful to users (e.g. visualizing repeat-masked regions). Checked the other twoget_sequence(protein=True)callers indomains.py; they rely on the same upstreamadd_orfs()fix and don't need separate changes.Also includes a short
tests/README.mddocumenting the two test styles in this repo (self-contained fixtures vs. the pickle-based pipeline chain), prompted by real debugging time lost to stale cross-run pickle state while working on this fix.Bumps version to 2.0.4.
Test plan
pytestsuite passes (15 passed), including the new regression testflake8/blackcleanpython -m build+twine check dist/*pass at 2.0.4