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feat!: update ExonGenomicCoordsMapper + UtaDatabase #352

Merged
merged 45 commits into from
Aug 21, 2024
Merged

feat!: update ExonGenomicCoordsMapper + UtaDatabase #352

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6559e14
feat!: Return Pydantic models instead of dicts in UtaDatabase
korikuzma Jul 31, 2024
e494b4f
feat!: rename residue mode to coordinate type
korikuzma Jul 31, 2024
f9561be
feat!: rename ExonGenomicCoordsMapper methods
korikuzma Jul 31, 2024
c944cb1
wip
korikuzma Jul 31, 2024
d4fb059
feat!: move `get_tx_exons_genomic_coords` to `ExonGenomicCoordsMapper`
korikuzma Jul 31, 2024
2303bc5
move test fixture
korikuzma Jul 31, 2024
43ec73f
Merge branch 'issue-224-get_tx_exons_genomic_coords' into issue-224-r…
korikuzma Jul 31, 2024
8b4ec13
feat!: rename `start`/`end` to `seg_start`/`seg_end` in `genomic_to_t…
korikuzma Aug 1, 2024
a707a2e
refactor: remove optional `coordinate_type` from `genomic_to_tx_segment`
korikuzma Aug 1, 2024
f099596
Merge branch 'staging' into issue-224-rename-mapper-methods
korikuzma Aug 1, 2024
f891033
Merge branch 'issue-224-rename-mapper-methods' into issue-224-get_tx_…
korikuzma Aug 1, 2024
de06317
Merge branch 'issue-224-get_tx_exons_genomic_coords' into issue-224-r…
korikuzma Aug 1, 2024
1f43803
Merge branch 'issue-224-rm-strand' into issue-224-rename-start-end
korikuzma Aug 1, 2024
74f0ab1
Merge branch 'issue-224-rename-start-end' into issue-224-assume-inter…
korikuzma Aug 1, 2024
97002e5
feat!: remove `UtaDatabase.get_tx_exons` + cleanup exon work
korikuzma Aug 6, 2024
ae318b4
Revert "feat!: move `get_tx_exons_genomic_coords` to `ExonGenomicCoor…
korikuzma Aug 6, 2024
2c38fa5
Merge branch 'clean-up-exon' into issue-224-rm-strand
korikuzma Aug 6, 2024
ec346ec
cleanup
korikuzma Aug 6, 2024
c6d63ec
feat!: remove `UtaDatabase.get_tx_exons_genomic_coords`
korikuzma Aug 6, 2024
7347436
Merge branch 'remove-get_tx_exons_genomic_coords' into issue-224-rm-s…
korikuzma Aug 6, 2024
758fe65
docstrings
korikuzma Aug 6, 2024
05064b5
Merge branch 'remove-get_tx_exons_genomic_coords' into issue-224-rm-s…
korikuzma Aug 6, 2024
fa87175
Merge branch 'issue-224-rm-strand' into issue-224-rename-start-end
korikuzma Aug 6, 2024
750e2b3
Merge branch 'issue-224-rename-start-end' into issue-224-assume-inter…
korikuzma Aug 6, 2024
1d030d3
seg_ -> genomic_
korikuzma Aug 6, 2024
55c9296
Merge branch 'issue-224-rename-start-end' into issue-224-assume-inter…
korikuzma Aug 6, 2024
8162f64
feat!: return Pydantic model in `get_alt_ac_start_or_end`
korikuzma Aug 6, 2024
6209114
feat!: return Pydantic model in `UtaDatabase.get_tx_exon_aln_v_data`
korikuzma Aug 6, 2024
f088820
wip
korikuzma Aug 8, 2024
18a4b82
docstrings
korikuzma Aug 8, 2024
1afa541
wip: rm mane transcript
korikuzma Aug 8, 2024
1f798ae
dry
korikuzma Aug 9, 2024
b166d31
clean up getting gene/alt ac
korikuzma Aug 9, 2024
c8f3947
Merge branch 'staging' into issue-224-new-structure
korikuzma Aug 12, 2024
493bb8a
Update test fixture values and offsets for negative strand transcript…
jarbesfeld Aug 13, 2024
805788e
ruff format fix
jarbesfeld Aug 19, 2024
f853d9d
fix offsets
korikuzma Aug 19, 2024
8d24226
add seg_ prefix to genomic_start and genomic_end
korikuzma Aug 19, 2024
e944f1f
clean up tx_segment_to_genomic
korikuzma Aug 19, 2024
0953785
cleanup
korikuzma Aug 19, 2024
2707df6
rm _get_exon_number (not used)
korikuzma Aug 20, 2024
370f9f2
TxSegment -> _TxSegment
korikuzma Aug 20, 2024
0534304
update json_schema_extra examples
korikuzma Aug 20, 2024
0b9c10e
Update src/cool_seq_tool/sources/uta_database.py
korikuzma Aug 20, 2024
615d747
pr suggestions
korikuzma Aug 20, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ dependencies = [
"hgvs",
"biocommons.seqrepo",
"pydantic == 2.*",
"ga4gh.vrs",
"ga4gh.vrs ~= 2.0.0a10",
"wags-tails ~= 0.1.3",
"bioutils",
]
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1 change: 0 additions & 1 deletion src/cool_seq_tool/app.py
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Expand Up @@ -107,7 +107,6 @@ def __init__(
self.ex_g_coords_mapper = ExonGenomicCoordsMapper(
self.seqrepo_access,
self.uta_db,
self.mane_transcript,
self.mane_transcript_mappings,
self.liftover,
)
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