NGS-DISAMBIGUATE

Disambiguation algorithm for reads aligned to two species (e.g. human and mouse genomes) from Tophat, Hisat2, STAR or BWA mem.

Software dependencies

• ngs-disambiguate ==2016.11.10
• bamtools ==2.4.0

Example

This wrapper can be used in the following way:

rule disambiguate:
    input:
        a="mapped/{sample}.a.bam",
        b="mapped/{sample}.b.bam"
    output:
        a_ambiguous='disambiguate/{sample}.graft.ambiguous.bam',
        b_ambiguous='disambiguate/{sample}.host.ambiguous.bam',
        a_disambiguated='disambiguate/{sample}.graft.bam',
        b_disambiguated='disambiguate/{sample}.host.bam',
        summary='qc/disambiguate/{sample}.txt'
    params:
        algorithm="bwa",
        # optional: Prefix to use for output. If omitted, a
        # suitable value is guessed from the output paths. Prefix
        # is used for the intermediate output paths, as well as
        # sample name in summary file.
        prefix="{sample}",
        extra=""
    wrapper:
        "0.32.0/bio/ngs-disambiguate"

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.

Authors

• Julian de Ruiter

Code

"""Snakemake wrapper for ngs-disambiguate (from Astrazeneca)."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


from os import path

from snakemake.shell import shell


# Extract arguments.
prefix = snakemake.params.get("prefix", None)
extra = snakemake.params.get("extra", "")

output_dir = path.dirname(snakemake.output.a_ambiguous)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# If prefix is not given, we use the summary path to derive the most
# probable sample name (as the summary path is least likely to contain)
# additional suffixes. This is better than using a random id as prefix,
# the prefix is also used as the sample name in the summary file.
if prefix is None:
    prefix = path.splitext(path.basename(snakemake.output.summary))[0]

# Run command.
shell(
    "ngs_disambiguate"
    " {extra}"
    " -o {output_dir}"
    " -s {prefix}"
    " -a {snakemake.params.algorithm}"
    " {snakemake.input.a}"
    " {snakemake.input.b}")

# Move outputs into expected positions.
output_base = path.join(output_dir, prefix)

output_map = {
    output_base + ".ambiguousSpeciesA.bam":
        snakemake.output.a_ambiguous,
    output_base + ".ambiguousSpeciesB.bam":
        snakemake.output.b_ambiguous,
    output_base + ".disambiguatedSpeciesA.bam":
        snakemake.output.a_disambiguated,
    output_base + ".disambiguatedSpeciesB.bam":
        snakemake.output.b_disambiguated,
    output_base + "_summary.txt":
        snakemake.output.summary
}

for src, dest in output_map.items():
    if src != dest:
        shell('mv {src} {dest}')