openvax / gtfparse / 28965619839
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28965619839

Pull #72

github

iskandr 
Add write_gtf: serialize a DataFrame back to GTF (fixes #21)

Adds the inverse of read_gtf. A DataFrame produced by read_gtf -- whether
the attribute column was expanded into per-key columns or left as a raw
'attribute' string -- can be written back out and re-read to recover an
equivalent DataFrame.

This builds on the approach in #46 by Benoitdw, with fixes:

- Python 3.9 compatibility: use typing.Union / typing.Optional instead of
  the `str | Path` union syntax, which requires Python 3.10+ (the project
  targets >=3.9).
- No silent data loss: attribute values are omitted only when None (the
  way read_gtf represents an absent key), not when merely falsy. Values
  like 0 or the empty string are now written and survive a round trip.
- Missing values in the fixed columns are serialized as '.', and null
  scores/frames round-trip correctly.
- The attribute field ends with a trailing ';', matching the canonical
  GTF format emitted by Ensembl/GENCODE and re-parsed by read_gtf.
- A column literally named 'attribute' (unexpanded read) is emitted
  verbatim, so expand_attribute_column=False round-trips too.
- Accepts a pandas DataFrame as well as polars (result_type="pandas").
- Raises ValueError if any required fixed column is missing.

Tests cover round trips for RefSeq and Ensembl fixtures (expanded and
unexpanded), pandas input, header lines, missing-value handling, the
falsy-value regression, and the missing-column error.

Co-authored-by: Benoitdw <bw@oncodna.com>
Claude-Session: https://claude.ai/code/session_014fNxSBm5zvdsDNwN3nhmpS
Pull Request #72: Add write_gtf: serialize a DataFrame back to GTF (fixes #21)

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