FATOTWOBIT

Convert *.fa file to *.2bit file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)

URL:

Example

This wrapper can be used in the following way:

# Example: from *.fa file
rule faToTwoBit_fa:
    input:
        "{sample}.fa"
    output:
        "{sample}.2bit"
    log:
        "logs/{sample}.fa_to_2bit.log"
    params:
        "" # optional params string
    wrapper:
        "0.77.0-2-gf3a6529/bio/ucsc/faToTwoBit"

# Example: from *.fa.gz file
rule faToTwoBit_fa_gz:
    input:
        "{sample}.fa.gz"
    output:
        "{sample}.2bit"
    log:
        "logs/{sample}.fa-gz_to_2bit.log"
    params:
        "" # optional params string
    wrapper:
        "0.77.0-2-gf3a6529/bio/ucsc/faToTwoBit"

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-fatotwobit==377

Input/Output

Input:

  • Path(s) to genome *.fa or *.fa.gz files

Output:

  • Path to output ‘*.2bit’ file

Authors

  • Roman Cherniatchik

Code

"""Snakemake wrapper for *.2bit to *.fa conversion using UCSC faToTwoBit 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("faToTwoBit {extra} {snakemake.input} {snakemake.output} {log}")