TWOBITINFO#
Generate *.chorom.sizes file by *.2bit file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)
Example#
This wrapper can be used in the following way:
rule twoBitInfo:
input:
"{sample}.2bit"
output:
"{sample}.chrom.sizes"
log:
"logs/{sample}.chrom.sizes.log"
params:
"" # optional params string
wrapper:
"v3.0.2-2-g0dea6a1/bio/ucsc/twoBitInfo"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies#
ucsc-twobitinfo=447
Input/Output#
Input:
Path to genome *.2bit file
Output:
Path to output *.chrom.sizes file
Code#
"""Snakemake wrapper for *.2bit to *.fa conversion using UCSC twoBitInfo tool."""
# http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
shell("twoBitInfo {extra} {snakemake.input} {snakemake.output} {log}")