Kevin’s Snakemake Helpers¶
To use these, pip install
this package in the same python environment as
snakemake, then use from kdmsnakemake import *
in the top of your Snakefile.
Helper functions¶
-
kdmsnakemake.
make_regions
(rdict, window=1000000.0)[source]¶ Splits a reference into window sized windows.
- Makes a list of regions for each reference in a dict of {refname:
- refpath: entries.
Parameters: - rdict – dict of {refname: refpath, …}
- window – Size of windows
Returns: dict of {refname: {region: coordinates, …}, …}
-
kdmsnakemake.
make_chromosomes
(rdict, chrom_regex='^chr')[source]¶ Splits a reference into chromosome chunks
Makes a list of regions for each reference in a dict of {refname: refpath} entries. Sequences matching chrom_regex appear as their own entires, all other sequences appear under a “scaffols” pseudo-chromosome.
Parameters: - rdict – dict of {refname: refpath, …}
- chrom_regex – Regular expression that (case-insensitively) matches proper chromosomes.
Returns: dict of {refname: {chromosome_set: [refseq_name, …]}, …}