.. _`bio/samtools/fastq/separate`:

SAMTOOLS FASTQ SEPARATE
=======================


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

Convert a bam file with paired end reads back to unaligned reads in a two separate fastq files with `samtools`. Reads that are not properly paired are discarded (READ_OTHER and singleton reads in `samtools fastq` documentation), as are secondary (0x100) and supplementary reads (0x800).


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_fastq_separate:
        input:
            "mapped/{sample}.bam",
        output:
            "reads/{sample}.1.fq",
            "reads/{sample}.2.fq",
        log:
            "{sample}.separate.log",
        params:
            sort="-m 4G",
            fastq="-n",
        # Remember, this is the number of samtools' additional threads. At least 2 threads have to be requested on cluster sumbission. This value - 2 will be sent to samtools sort -@ argument.
        threads: 3
        wrapper:
            "v3.0.1/bio/samtools/fastq/separate"

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.


Notes
-----

* The `extra` param allows for additional program arguments.
* For more information see, http://www.htslib.org/doc/samtools-fasta.html


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

* ``samtools=1.14``
* ``snakemake-wrapper-utils=0.5.2``




Authors
-------

* David Laehnemann
* Victoria Sack
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "David Laehnemann, Victoria Sack"
    __copyright__ = "Copyright 2018, David Laehnemann, Victoria Sack"
    __email__ = "david.laehnemann@hhu.de"
    __license__ = "MIT"


    import os
    import tempfile
    from pathlib import Path
    from snakemake.shell import shell
    from snakemake_wrapper_utils.snakemake import get_mem

    params_sort = snakemake.params.get("sort", "")
    params_fastq = snakemake.params.get("fastq", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Samtools takes additional threads through its option -@
    # One thread is used bu Samtools sort
    # One thread is used by Samtools fastq
    # So snakemake.threads has to take them into account
    # before allowing additional threads through samtools sort -@
    threads = 0 if snakemake.threads <= 2 else snakemake.threads - 2

    mem = get_mem(snakemake, "MiB")
    mem = "-m {0:.0f}M".format(mem / threads) if mem and threads else ""

    with tempfile.TemporaryDirectory() as tmpdir:
        tmp_prefix = Path(tmpdir) / "samtools_fastq.sort"

        shell(
            "(samtools sort -n"
            " --threads {threads}"
            " {mem}"
            " -T {tmp_prefix}"
            " {params_sort}"
            " {snakemake.input[0]} | "
            "samtools fastq"
            " {params_fastq}"
            " -1 {snakemake.output[0]}"
            " -2 {snakemake.output[1]}"
            " -0 /dev/null"
            " -s /dev/null"
            " -F 0x900"
            " - "
            ") {log}"
        )


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