.. _`bio/ngs-disambiguate`:

NGS-DISAMBIGUATE
================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/ngs-disambiguate?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/ngs-disambiguate

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



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    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:
            "v3.0.4/bio/ngs-disambiguate"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``ngs-disambiguate=2018.05.03``
* ``bamtools=2.5.1``

Input/Output
------------
**Input:**

* species a bam file (name sorted)
* species b bam file (name sorted)

**Output:**

* bam file with ambiguous alignments for species a
* bam file with ambiguous alignments for species b
* bam file with unambiguous alignments for species a
* bam file with unambiguous alignments for species b




Authors
-------

* Julian de Ruiter


Code
----

.. code-block:: python

    """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}")


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