package

biopipen.utils

Utilities for indexing reference files

Functions
  • bam_index(bam, bamdir, tool, samtools, sambamba, ncores, ext, force) Index a bam file</>
  • tabix_index(infile, preset, tmpdir, tabix) (str | os.pathlike) Index input file using tabix</>

Common docstrings for biopipen procs.

Functions

Do gene name conversion

Classes
Functions
  • gene_name_conversion(genes, infmt, outfmt, dup, species, notfound, suppress_messages) Convert gene names using MyGeneInfo</>