Keep all variants, add gene set membership check #168
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…ms around between functions)
…ounts from core logic
… against known gene lists
iskandr
requested changes
Aug 8, 2018
vaxrank/gene_pathway_check.py
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| _DRIVER_VARIANT = 'cancer_driver_variant' | ||
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| class GenePathwayCheck: |
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Something about calling this a "pathway check" seems very odd to me.
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Until we stop supporting Python 2, inherit from object:
vaxrank/gene_pathway_check.py
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| @staticmethod | ||
| def is_present(df, value, column): | ||
| return len(df.loc[df[column] == value]) > 0 |
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What about (df[column] == value).any()?
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Maybe worth noting that this expects the DataFrame to be small
iskandr
reviewed
Aug 8, 2018
test/test_mutant_protein_sequence.py
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| @@ -67,6 +70,8 @@ def test_mutant_amino_acids_in_mm10_chrX_8125624_refC_altA_pS460I(): | |||
| min_alt_rna_reads=1, | |||
| min_variant_sequence_coverage=1, | |||
| variant_sequence_assembly=True) | |||
| core_logic.process_variants() | |||
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Can we make this more "functional" by having process_variants just return its results? Or is there other persistent data that gets used later?
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Idea for a future branch: Make the MHC binding and RNA support columns quantitative instead of binary. |
iskandr
reviewed
Aug 22, 2018
iskandr
approved these changes
Sep 6, 2018
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