MICROPHASER BUILD_REFERENCE¶
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:
"v1.19.1/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¶
- For more information see, https://github.com/koesterlab/microphaser.
Software dependencies¶
microphaser=0.7.0
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}"
)