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j-andrews7 / VAMPIRE

Variant and Epigenetic anNotation for Underlying Significance and Regulation
MIT License
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variant code duplication #37

Open Crumbs350 opened 7 years ago

Crumbs350 commented 7 years ago

gene_expression and activity both use the same or similar Variant class. Also sequence.py has similar logic which is used by motifs.py and others. Need to merge these for combined vcf read utility. See vcf.py for start.

Crumbs350 commented 7 years ago

Note: vcf combined class being created with the intent of doing analytics on the final results files more easily.

j-andrews7 commented 7 years ago

I may convert much of this code to instead use pysam, which should drastically simplify this and make reading/writing the VCF files much easier. I'm sure the file reading will work, but I want to test it and see how it handles adding INFO fields before implementing anything.