feat!: update ExonGenomicCoordsMapper + UtaDatabase
#352
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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)
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ExonGenomicCoordsMapperExonGenomicCoordsMapper + UtaDatabase
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Co-authored-by: James Stevenson <james.stevenson@nationwidechildrens.org>
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@jsstevenson I moved + modified a UtaDatabase method in 615d747 so will re-request your review |
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Close #345 and #332 * Update and fix bugs in`ExonGenomicCoordsMapper` * Change output for public methods in `ExonGenomicCoordsMapper` (leverage VRS Sequence Location and improve structure for transcript segment data). Renamed `warnings` to `errors`. * Resolve offset / genomic location bugs (#345 and #332) * Remove `mane_transcript` instance variable and use `mane_transcript_mappings` instead. * Refactor code that was unnecessary or extra. * Rename arguments in `genomic_to_tx_segment`: `alt_ac` -> `genomic_ac`, `genomic_start` -> ` seg_start_genomic`, `genomic_end` -> `seg_end_genomic` * pin `ga4gh.vrs` to `2.0.0a10` * Remove `get_genes_and_alt_acs` from `UtaDatabase`. Moved this to `ExonGenomicCoordsMapper` and renamed to `_get_genomic_ac_gene`. Will return single gene since genomic accessions are not needed anymore. --------- Co-authored-by: Jeremy Arbesfeld <jarbesfeld@gmail.com>
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Close #345 and #332 * Update and fix bugs in`ExonGenomicCoordsMapper` * Change output for public methods in `ExonGenomicCoordsMapper` (leverage VRS Sequence Location and improve structure for transcript segment data). Renamed `warnings` to `errors`. * Resolve offset / genomic location bugs (#345 and #332) * Remove `mane_transcript` instance variable and use `mane_transcript_mappings` instead. * Refactor code that was unnecessary or extra. * Rename arguments in `genomic_to_tx_segment`: `alt_ac` -> `genomic_ac`, `genomic_start` -> ` seg_start_genomic`, `genomic_end` -> `seg_end_genomic` * pin `ga4gh.vrs` to `2.0.0a10` * Remove `get_genes_and_alt_acs` from `UtaDatabase`. Moved this to `ExonGenomicCoordsMapper` and renamed to `_get_genomic_ac_gene`. Will return single gene since genomic accessions are not needed anymore. --------- Co-authored-by: Jeremy Arbesfeld <jarbesfeld@gmail.com>
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So sorry for this large PR. 😓
Close #345 and #332
ExonGenomicCoordsMapperExonGenomicCoordsMapper(leverage VRS Sequence Location and improve structure for transcript segment data). Renamedwarningstoerrors.ExonGenomicCoordsMapper.transcript_to_genomic_coordinates#345 and Counterintuitive/wrong? offset from genomic to transcript mapping #332)mane_transcriptinstance variable and usemane_transcript_mappingsinstead.genomic_to_tx_segment:alt_ac->genomic_ac,genomic_start->seg_start_genomic,genomic_end->seg_end_genomicga4gh.vrsto2.0.0a10get_genes_and_alt_acsfromUtaDatabase. Moved this toExonGenomicCoordsMapperand renamed to_get_genomic_ac_gene. Will return single gene since genomic accessions are not needed anymore.Addresses #224 . I still want to re-order private methods and see if there are any places we can clean up. Since we need to get a release out ASAP suggested changes for refactoring will be done in a separate PR.