GenomicMedLab cool-seq-tool issues

GenomicMedLab / cool-seq-tool

https://coolseqtool.readthedocs.io

MIT License

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docs: use correct app name + update transcript selection algorithm

#379 korikuzma closed 2 days ago
0
fix: Check if MANE transcript exists in UTA, if not select longest compatible

#378 jarbesfeld opened 2 weeks ago
3
genomic_to_tx_segment should check if a MANE Select transcript is in UTA

#377 jarbesfeld opened 2 weeks ago
0
chore: remove unused action

#376 jsstevenson closed 4 weeks ago
0
fix!: Expect user to supply valid, case-sensitive HGNC symbol

#375 jarbesfeld closed 1 month ago
2
Expect gene symbol to be formatted correctly

#374 jarbesfeld closed 1 month ago
3
Ensure proper gene symbol comparison

#373 jarbesfeld closed 1 month ago
0
Add warning for when a coordinate occurs outside of 100 base pairs of the start/end of a transcript

#372 katiestahl opened 2 months ago
0
Add parameter for using GRCh37 sequences

#371 jarbesfeld opened 2 months ago
1
fix: make gene optional param for converting genomic coords as long a…

#370 katiestahl closed 2 months ago
0
Do not require gene when genomic accession and transcript are provided to genomic_to_tx_segment

#369 jarbesfeld closed 2 months ago
0
Gene should be an optional parameter for genomic_to_tx_segment when transcript and genomic accession are provided

#368 jarbesfeld closed 2 months ago
0
MANE transcript data was not found for the gene C1orf159

#367 jarbesfeld closed 1 month ago
17
Ensure that start position does not exceed end position for a transcript segment

#366 jarbesfeld opened 2 months ago
0
refactor: remove duplicate `genomic_ac` check

#365 korikuzma closed 3 months ago
0
test: update tests for `ExonGenomicCoordsMapper`

#364 korikuzma closed 2 months ago
6
Migrate staging changes to main branch

#363 korikuzma closed 3 months ago
0
Break up `_genomic_to_tx_segment` into smaller methods

#362 korikuzma opened 3 months ago
0
Choosing the Correct Adjacent Exon along Exon Boundaries

#361 jarbesfeld opened 3 months ago
3
refactor: rename `_get_alt_ac_start_and_end` + flatten output

#360 korikuzma closed 3 months ago
0
refactor: rename `is_start` kwarg in private methods to `is_seg_start`

#359 korikuzma closed 3 months ago
1
refactor: reorder classes and methods in `exon_genomic_coords` module

#358 korikuzma closed 3 months ago
0
refactor!: rename `ExonCoord` to `_ExonCoord` to indicate internal use

#357 korikuzma closed 3 months ago
2
fix: genomic accession mismatch when getting nearest tx junction

#356 korikuzma closed 3 months ago
1
docs: link to stable, not latest

#355 jsstevenson closed 3 months ago
0
Update fixtures and offsets for test_exon_genomic_coords

#354 jarbesfeld closed 3 months ago
0
feat: enable direct import of CST from package root

#353 jsstevenson closed 3 months ago
0
feat!: update `ExonGenomicCoordsMapper` + `UtaDatabase`

#352 korikuzma closed 3 months ago
2
feat!: return Pydantic model in `UtaDatabase.get_tx_exon_aln_v_data`

#351 korikuzma closed 3 months ago
0
feat!: return Pydantic model in `get_alt_ac_start_or_end`

#350 korikuzma closed 3 months ago
1
refactor: remove unnecessary literal from `AnnotationLayer` enum

#349 korikuzma closed 3 months ago
0
feat!: remove `UtaDatabase.get_tx_exons_genomic_coords`

#348 korikuzma closed 3 months ago
0
feat!: remove `UtaDatabase.get_tx_exons` + cleanup exon work

#347 korikuzma closed 3 months ago
0
[OLD] feat!: update `ExonGenomicCoordsMapper`

#346 korikuzma closed 3 months ago
3
Wrong location in `ExonGenomicCoordsMapper.transcript_to_genomic_coordinates`

#345 jsstevenson closed 3 months ago
3
feat!: remove optional `coordinate_type` from `genomic_to_tx_segment`

#344 korikuzma closed 3 months ago
2
feat!: rename `start`/`end` to `genomic_start`/`genomic_end` in `genomic_to_tx_segment`

#343 korikuzma closed 3 months ago
1
Add information about Ensembl transcripts to docs

#342 korikuzma opened 4 months ago
0
Add coordinate type to usage docs

#341 korikuzma opened 4 months ago
0
refactor: remove optional `strand` field from `genomic_to_tx_segment`

#340 korikuzma closed 3 months ago
1
feat!: move `get_tx_exons_genomic_coords` to `ExonGenomicCoordsMapper`

#339 korikuzma closed 3 months ago
2
feat!: rename ExonGenomicCoordsMapper methods

#338 korikuzma closed 3 months ago
0
feat!: rename residue mode to coordinate type

#337 korikuzma closed 3 months ago
0
Move pydantic models to their respective module

#336 korikuzma opened 4 months ago
0
Rename residue mode to coordinate type

#335 korikuzma closed 3 months ago
3
feat!: Return Pydantic models instead of dicts in UtaDatabase

#334 korikuzma closed 3 months ago
0
docs: remove VRS schema support section

#333 korikuzma closed 4 months ago
0
Counterintuitive/wrong? offset from genomic to transcript mapping

#332 jsstevenson closed 3 months ago
3
docs: fix source link

#331 jsstevenson closed 4 months ago
0
Add start/end residue mode parameter

#330 korikuzma closed 4 months ago
2