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feat!: add starting_assembly as argument when using genomic_to_tx_segment #391

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merged 21 commits into from
Jan 8, 2025
Merged

feat!: add starting_assembly as argument when using genomic_to_tx_segment #391

merged 21 commits into from
Jan 8, 2025

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jarbesfeld
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closes #390

@jarbesfeld jarbesfeld added enhancement New feature or request priority:high High priority stale-exempt labels Jan 3, 2025
@jarbesfeld jarbesfeld requested a review from korikuzma January 3, 2025 18:00
@jarbesfeld jarbesfeld self-assigned this Jan 3, 2025
korikuzma
korikuzma requested changes Jan 6, 2025
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I think you also need to pull in changes from main in both of your PRs

src/cool_seq_tool/mappers/exon_genomic_coords.py Outdated Show resolved Hide resolved
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@jarbesfeld jarbesfeld requested a review from korikuzma January 6, 2025 20:05
@jarbesfeld jarbesfeld changed the base branch from issue-383 to main January 7, 2025 13:59
@jarbesfeld jarbesfeld mentioned this pull request Jan 7, 2025
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korikuzma
korikuzma reviewed Jan 7, 2025
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Holding off my review until #384 gets merged

@korikuzma korikuzma changed the base branch from main to issue-383 January 7, 2025 17:04
Base automatically changed from issue-383 to main January 7, 2025 17:53
@jarbesfeld jarbesfeld requested a review from korikuzma January 7, 2025 18:26
korikuzma
korikuzma requested changes Jan 7, 2025
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@jarbesfeld jarbesfeld changed the title feat!: Specify assembly when using genomic_to_tx_segment feat!: add starting_assembly as argument when using genomic_to_tx_segment Jan 7, 2025
@jarbesfeld jarbesfeld requested a review from korikuzma January 7, 2025 22:08
korikuzma
korikuzma reviewed Jan 8, 2025
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src/cool_seq_tool/mappers/exon_genomic_coords.py
if not genomic_ac_validation:
grch38_ac = await self.uta_db.get_newest_assembly_ac(genomic_ac)
if grch38_ac:
genomic_ac = grch38_ac[0]
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Is it worth adding something in the docstrings (for both private + public method) about version will be ignored for GRCh37?

@jarbesfeld jarbesfeld requested a review from korikuzma January 8, 2025 16:59
@jarbesfeld jarbesfeld requested a review from korikuzma January 8, 2025 17:02
@jarbesfeld jarbesfeld merged commit a43932f into main Jan 8, 2025
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@jarbesfeld jarbesfeld deleted the issue-390 branch January 8, 2025 17:46
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Require assembly parameter for genomic_to_tx_segment
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