Add write gtf feature - Issue #21 - #46
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Benoitdw wants to merge 2 commits into
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gamazeps
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Apr 11, 2024
| def test_write_gtf(tmp_path): | ||
| gtf_dict = read_gtf(REFSEQ_GTF_PATH) | ||
| write_gtf(gtf_dict, tmp_path/"dummy_gtf.gtf") | ||
| assert isinstance(read_gtf(str(tmp_path/"dummy_gtf.gtf")), DataFrame) |
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Check for equality of this gtf and the original one too ?
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Looks good to me at least :) @iskandr all good with you too ? |
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Thanks @Benoitdw — sorry this sat so long! I've adopted your I made a few fixes on top of your version so it could land:
Closing this in favor of #72 — really appreciate the original contribution, which is what got the feature moving. 🙏 |
iskandr
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Jul 8, 2026
…tions Addresses the review findings on the first draft: - Faithful missing-value handling. read_gtf represents an absent attribute as null (numeric *_version columns) or the empty string (string columns) and cannot tell absent from present-but-empty. The writer now omits both null and "" so that read -> write -> read reproduces the parsed frame exactly, including column order, on multi-feature GTFs (GENCODE). A non-empty falsy value such as "0" is still written (the original #46 bug). - Vectorized. The attribute field and full line are built with polars expressions (concat_str/format) instead of per-row Python; ~200k rows x 6 attributes now writes in ~0.1s. - gzip output. A path ending in .gz is gzip-compressed, mirroring read_gtf which transparently reads gzipped GTFs. - Dropped the redundant fixed-column filter; fixed columns are always written in canonical order (the missing-column guard runs first). - Documented that "\"" and ";" in attribute values cannot round-trip (a limitation shared with read_gtf, which strips quotes and splits on ";"). Tests now cover both directions across RefSeq/Ensembl/GENCODE/StringTie fixtures: write(read(...)) recovers the parsed frame and is byte-idempotent (a fixed point); read(write(...)) recovers a DataFrame's values. Plus gzip, pandas input, the "0"-vs-empty-vs-null semantics, "." for missing fixed values, header lines, the structural-character limitation, and the missing-column error. Co-authored-by: Benoitdw <[email protected]> Claude-Session: https://claude.ai/code/session_014fNxSBm5zvdsDNwN3nhmpS
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Fixe #21