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feat!: create method for GRCh38 to MANE protein representation #211

Merged
merged 34 commits into from
Oct 20, 2023
Merged

feat!: create method for GRCh38 to MANE protein representation #211

merged 34 commits into from
Oct 20, 2023

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korikuzma
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@korikuzma korikuzma commented Oct 16, 2023 •
edited

Addresses #151 for GRCh38 (will do liftover/check at a later time). This is needed for VarCat

Notes:

  • MANETranscript updates:
    • Add method grch38_to_mane_p
      • Given GRCh38 representation, will return MANE protein representation. Also allows for longest compatible remaining representation to be returned if no compatible MANE representation found.
    • Updates get_longest_compatible_transcript
      • gene is now optional
      • Adds end_annotation_layer as a parameter. This will allow you to either return protein or cdna representation when set.
  • MANETranscriptMappings updates:
    • get_gene_mane_data always returns list. If no MANE data found, will return empty list (previously returned None)
  • UTADatabase updates:
    • get_transcripts_from_gene renamed to get_transcripts
      • gene is now an optional parameter

@korikuzma
wip: update schema example + rm GeneNormalizer + comment out chr code
5a1a21d
@korikuzma
wip: update tmp versions
34a6422
@korikuzma
wip: initial work for reorganizing modules
ad8febf
@korikuzma
update deps
1894458
@korikuzma
rm gene-normalizer dep + get_mapped_mane_data
036fdc1
@korikuzma
bump version
8d88e14
@korikuzma
fix version
2266295
@korikuzma
refactor: use ResidueMode for residue_mode type
0bbc511 
- Inconsistent with using ResidueMode vs str
@korikuzma
fix routers
d2a8d50
@korikuzma
Merge branch 'issue-192' into issue-185
892a881
@korikuzma
style: use ruff + black
d5d40cf
@korikuzma
bump pre-commit versions
ae54496
@korikuzma
refactor: use AnnotationLayer enum
1734779 
- Some places we were not using it when we should have been
@korikuzma
rm unnecessary lower
8170d0b
@korikuzma
Merge branch 'issue-185' into issue-193
183e871
@korikuzma
Merge branch 'issue-193' into issue-202
cbd712f
@korikuzma
build: replace pandas with polars (#178)
b616b92
@korikuzma
rm other flake8 references
bf46216
@korikuzma
Merge branch 'issue-193' into issue-202
3cc1747
@korikuzma
Merge branch 'issue-202' into issue-178
924b425
@korikuzma
wip
e581d6d
@korikuzma
feat: create method for GRCh38 to MANE protein representation
78c4fbb
@korikuzma
Merge branch 'main' into issue-151
c3c430d
@korikuzma
cleanup
a1496c0
@korikuzma
use enum
3d4c54e
@korikuzma
more cleanup
7fb17cf
@korikuzma
rename get_transcripts_from_gene to get_transcripts
e0223ff
@korikuzma korikuzma added enhancement New feature or request priority:high High priority labels Oct 16, 2023
@korikuzma korikuzma self-assigned this Oct 16, 2023
@korikuzma korikuzma removed the request for review from jsstevenson October 16, 2023 22:22
@korikuzma korikuzma marked this pull request as draft October 16, 2023 22:22
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Added test for #212 which pointed out a bug for braf v600e

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This refactor work has made me think about #63, specifically this comment

@korikuzma korikuzma marked this pull request as ready for review October 16, 2023 22:49
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Done making changes. Ready for review!

jsstevenson
jsstevenson previously approved these changes Oct 19, 2023
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lgtm, two small things

  1. I think changing arguments for public methods probably entails an API break (i.e. a "!")
  2. made a note about including an extra linebreak in docstrings for public methods/any methods that could conceivably have API pages generated for them

cool_seq_tool/mappers/mane_transcript.py Show resolved Hide resolved
@korikuzma korikuzma changed the title feat: create method for GRCh38 to MANE protein representation feat!: create method for GRCh38 to MANE protein representation Oct 19, 2023
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Need to actually return both cdna and protein representation

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Actually, I'm going to hold off on this

@korikuzma korikuzma merged commit af67d8e into main Oct 20, 2023
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@korikuzma korikuzma deleted the issue-151 branch October 20, 2023 14:13
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