openvax / pyensembl
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LAST BUILD ON BRANCH v2.10.0
branch: v2.10.0
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coverage: 85.426% (+0.5%) from 84.971%
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Preserve FASTA-header versions in SequenceData (closes #351) (#355)

* Preserve FASTA-header versions in SequenceData (#351)

`_parse_header_id` no longer strips ENS .N version suffixes — the
versioned form is preserved as the canonical FASTA identifier, with
the version treated as authoritative source-of-truth for the
sequence's identity. Also added pipe-delimited (GENCODE) header
handling: the leading field before `|` is now the identifier rather
than the whole pipe-packed blob with everything-after-the-first-dot
silently dropped.

`SequenceData` now maintains:
  - `_fasta_dictionary` keyed on whichever form the header carried
    (versioned when available, bare otherwise)
  - `_stripped_index: bare_ens_id -> versioned_id`, so bare-ID
    lookups still resolve against a versioned FASTA (GENCODE case)
  - `_versions: id -> int`, exposed via the new `fasta_version(id)`
    accessor for downstream sanity-checking of FASTA / GTF alignment

`lookup_sequence_with_version_fallback` resolves both directions —
versioned caller against bare FASTA (existing Ensembl path) and
bare caller against versioned FASTA (new GENCODE path) — without
the runtime `.rsplit` on every miss the old helper did. Defensive
fallback for callers that hold a `SequenceData` without the new
attributes (e.g. unpickled old object).

Bumped the on-disk pickle filename to `<fasta>.v2.pickle` so stale
caches from the previous bare-key layout get ignored instead of
loaded.

Closes #351. Companion to gtfparse#67 (attribute_aliases +
cast_version_columns), which together close out the GENCODE
compatibility regression originally reported in #335.

* Address PR #355 review: drop pickle schema bump, surface fasta_version

* Reverted FASTA_PICKLE_SCHEMA_VERSION + the .v2.pickle filename suffix.
  v1 (bare-keyed) pickles load cleanly under the new code path - the
  rebuilt _stripped_index stays empty, but lookups still resolve via
  the version-stripped retry path so Ensembl-style callers see no
 ... (continued)

60 of 61 new or added lines in 5 files covered. (98.36%)

1653 of 1935 relevant lines covered (85.43%)

3.42 hits per line

Relevant lines Covered
1935 RELEVANT LINES 1653 COVERED LINES
3.42 HITS PER LINE
Source Files on v2.10.0

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25816710251 v2.10.0 Preserve FASTA-header versions in SequenceData (closes #351) (#355) * Preserve FASTA-header versions in SequenceData (#351) `_parse_header_id` no longer strips ENS .N version suffixes — the versioned form is preserved as the canonical FASTA iden... push web-flow github
85.43
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