PRIMERCLIP

Primer trimming on sam file, https://github.com/swiftbiosciences/primerclip

Example

This wrapper can be used in the following way:

rule primerclip:
    input:
        v2.6.0-35-g755343f_file="v2.6.0-35-g755343f_file",
        alignment_file="mapped/{sample}.bam"
    output:
        alignment_file="mapped/{sample}.trimmed.bam"
    log:
        "logs/primerclip/{sample}.log"
    params:
        extra=""
    wrapper:
        "v2.6.0-35-g755343f/bio/primerclip"

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

• samtools==1.9
• primerclip==0.3.8

Input/Output

Input:

• sam file
• master primer file

Output:

• sam file

Authors

• Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


from os import path

from snakemake.shell import shell

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

master_file = snakemake.input.master_file
in_alignment_file = snakemake.input.alignment_file
out_alignment_file = snakemake.output.alignment_file

# Check inputs/arguments.
if not isinstance(master_file, str):
    raise ValueError("master_file, path to the master file")

if not isinstance(in_alignment_file, str):
    raise ValueError("in_alignment_file, path to the input alignment file")

if not isinstance(out_alignment_file, str):
    raise ValueError("out_alignment_file, path to the output file")

samtools_input_command = "samtools view -h " + in_alignment_file

samtools_output_command = " | head -n -3 | samtools view -Sh"

if out_alignment_file.endswith(".cram"):
    samtools_output_command += "C -o " + out_alignment_file
elif out_alignment_file.endswith(".sam"):
    samtools_output_command += " -o " + out_alignment_file
else:
    samtools_output_command += "b -o " + out_alignment_file

shell(
    "{samtools_input_command} |"
    " primerclip"
    " {master_file}"
    " /dev/stdin"
    " /dev/stdout"
    " {samtools_output_command}"
    " {log}"
)