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arkal / Transgene

This is a repository to host the transgene tool. Transgene takes a snpeffed vcf and a peptide fasta , and returns 3 peptide fastas containing 9-, 10- and 15-mers harboring the called mutations
Apache License 2.0
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Implement support for snpeff 4.0+ and VEP (Resolves #44) #45

Closed arkal closed 6 years ago

arkal commented 6 years ago

Resolves #44 Fixes bugs from #30

  1. Refactor how vcfs are read to allow modular parsing of effect lines from different versions of snpeff and from vep.
  2. Fix bugs in translation of sequences (mostly pertaining to incomplete implementation of translation of genes on the reverse strand)
  3. Add tests for get_exon_start_pos (previously untested), get_codon (implemented in this commit) and doctests for other smaller functions.
  4. Refactor tests to alllow testing of a single tool (or version of snpeff) at a time.