PYFASTAQ REPLACE_BASES

Replaces all occurrences of one letter with another.

Example

This wrapper can be used in the following way:

rule replace_bases:
    input:
        "{sample}.rna.fa"
    output:
        "{sample}.dna.fa",
    params:
        old_base = "U",
        new_base = "T",
    log:
        "logs/fastaq/replace_bases/test/{sample}.log"
    wrapper:
        "0.72.0/bio/pyfastaq/replace_bases"

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

  • pyfastaq==3.17.0

Authors

  • Michael Hall

Code

__author__ = "Michael Hall"
__copyright__ = "Copyright 2019, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"


from snakemake.shell import shell


log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "fastaq replace_bases"
    " {snakemake.input[0]}"
    " {snakemake.output[0]}"
    " {snakemake.params.old_base}"
    " {snakemake.params.new_base}"
    " {log}"
)