fix: genomic accession mismatch when getting nearest tx junction #356
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* Only focused on `UtaDatabase` for now * `alt_pos_change` was renamed to `pos_change`
Addresses part of #224 * `transcript_to_genomic_coordinates` renamed to `tx_segment_to_genomic` * `genomic_to_transcript_exon_coordinates` renamed to `genomic_to_tx_segment`
Addresses #224 * Move `get_tx_exons_genomic_coords` from `UtaDatabase` to `ExonGenomicCoordsMapper` as a private method (`_get_tx_exons_genomic_coords`)
…x_segment` Addresses #224
Addresses #224 * `genomic_to_tx_segment` will now require inter-residue coordinates to be passed
…exons_genomic_coords
addresses #224 * initial work for cleaning up exon coord data retrieval
…dsMapper`" This reverts commit d4fb059.
addresses #224 * Use `ExonGenomicCoordsMapper._get_all_exon_coords` instead
* include `ord` in `get_alt_ac_start_or_end` response. This represents the exon number (0-based)
* include include `ord` in `UtaDatabase.get_tx_exon_aln_v_data` response. This represents the exon number (0-based)
jarbesfeld
approved these changes
Aug 20, 2024
jsstevenson
requested changes
Aug 20, 2024
Co-authored-by: James Stevenson <james.stevenson@nationwidechildrens.org>
jsstevenson
reviewed
Aug 20, 2024
jsstevenson
reviewed
Aug 20, 2024
|
Made some changes. I reverted back to tuple since it's lightweight. Named tuple / pydantic model seemed a little extra. I can change back if you disagree |
jsstevenson
approved these changes
Aug 21, 2024
korikuzma
added a commit
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Aug 21, 2024
close #329 * When lifting over to GRCh38 assembly, genomic accession and genomic position should be updated accordingly
korikuzma
added a commit
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Aug 21, 2024
close #329 * When lifting over to GRCh38 assembly, genomic accession and genomic position should be updated accordingly
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close #329