refactor!: initial work for cleaning up ExonGenomicCoordsMapper
#252
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…235) * Fix TypeError in `SeqRepoAccess.get_reference_sequence()` when `start` is not provided * Requires both start and end positions to be provided (`get_mane_transcript` and `get_inter_residue_pos`)
* Only call unique function if DataFrame is not empty
* Accidentally used fixture decorator instead of pytest.mark.asyncio * Coroutine was never awaited + did not check expected response
stopping until we find a way to represent output using vrs 2.0-alpha
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* Cleaned up docstrings / comments / typos / naming * Remove unused kwargs in `transcript_to_genomic_coordinates` and `genomic_to_transcript_exon_coordinates` * `transcript` is now required in `transcript_to_genomic_coordinates` * `genomic_to_transcript_exon_coordinates` accepts either `chromosome` or `alt_ac` * Moves methods from `UtaDatabase` that do not query the database to `ExonGenomicCoordsMapper` * `UtaDatabase.chr_to_gene_and_accessions` renamed to `UtaDatabase.get_genes_and_alt_acs` and `chromosome` is now optional
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Initial work for #224
Notes:
transcript_to_genomic_coordinatesandgenomic_to_transcript_exon_coordinatestranscriptis now required intranscript_to_genomic_coordinatesgenomic_to_transcript_exon_coordinatesaccepts eitherchromosomeoralt_acUtaDatabasethat do not query the database toExonGenomicCoordsMapperUtaDatabase.chr_to_gene_and_accessionsrenamed toUtaDatabase.get_genes_and_alt_acsandchromosomeis now optional