package
biopipen.utils
module
biopipen.utils.reference
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</>
module
biopipen.utils.common_docstrs
Common docstrings for biopipen procs.
Functions
format_placeholder
(
**kwargs
)
(Callable) — A decorator to format a docstring placeholder.</>indent_docstr
(
docstr
,indent
)
(str) — Indent the docstring.</>
module
biopipen.utils.gene
Do gene name conversion
Classes
QueryGenesNotFound
— When genes cannot be found</>
Functions
gene_name_conversion
(
genes
,infmt
,outfmt
,dup
,species
,notfound
,suppress_messages
)
— Convert gene names using MyGeneInfo</>