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Published 20 hours ago • verified publisher icon kundajelab

Migrate from pysam to pyfaidx

Open Avsecz opened this issue 5 years ago • 2 comments

since the pysam dependency cause trouble (when the conda channels as misconfigured) and since chromosome name parsing is very fragile in pysam (https://github.com/kipoi/kipoi/issues/330#issuecomment-420054392), I propose to migrate from pysam.FastaFile to pyfaidx.Fasta.

Avsecz avatar Oct 01 '18 22:10 Avsecz