MICROPHASER BUILD_REFERENCE

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/microphaser/build_reference?label=version%20update%20pull%20requests

Create a reference of all normal peptides in a sample

Example

This wrapper can be used in the following way:

rule microphaser_build:
    input:
        # all normal peptides from the complete proteome as nucleotide sequences
        ref_peptides="germline/peptides.fasta",
    output:
        # a binary of the normal peptides amino acid sequences
        bin="out/peptides.bin",
        # the amino acid sequences in FASTA format
        peptides="out/peptides.fasta",
    log:
        "logs/microphaser/build_reference.log"
    params:
        extra="--peptide-length 9",  # optional, desired peptide length in amino acids.
    wrapper:
        "v3.8.0-1-g149ef14/bio/microphaser/build_reference"

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.

Notes

Software dependencies

  • microphaser=0.8.0

Input/Output

Input:

  • peptide reference (nucleotide sequences from microphaser germline)

Output:

  • peptide reference in amino acid FASTA format

  • binary peptide reference for filtering

Authors

  • Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "microphaser build_reference "
    "{extra} "
    "--reference {snakemake.input.ref_peptides} "
    "--output {snakemake.output.bin} "
    "> {snakemake.output.peptides} "
    "{log}"
)