.. _`bio/pear`:

PEAR
====


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

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pear_merge:
        input:
            read1="reads/reads.left.fq.gz",
            read2="reads/reads.right.fq.gz"
        output:
            assembled="pear/reads_pear_assembled.fq.gz",
            discarded="pear/reads_pear_discarded.fq.gz",
            unassembled_read1="pear/reads_pear_unassembled_r1.fq.gz",
            unassembled_read2="pear/reads_pear_unassembled_r2.fq.gz",
        log:
            'logs/pear.log'
        params:
            pval=".01",
            extra=""
        threads: 4
        resources:
            mem_mb=4000 # define amount of memory to be used by pear
        wrapper:
            "v5.3.0-16-g710597c/bio/pear"

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
---------------------

* ``pear=0.9.6``

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

* paired fastq files

**Output:**

* merged fastq




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    __author__ = "N. Tessa Pierce"
    __copyright__ = "Copyright 2019, N. Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"

    from os import path
    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    r1 = snakemake.input.get("read1")
    r2 = snakemake.input.get("read2")
    assert r1 is not None and r2 is not None, "r1 and r2 files are required as input"

    assembled = snakemake.output.get("assembled")
    assert assembled is not None, "require 'assembled' outfile"
    gzip = True if assembled.endswith(".gz") else False

    out_base, out_end = assembled.rsplit(".f")
    out_end = ".f" + out_end

    df_assembled = out_base + ".assembled.fastq"
    df_discarded = out_base + ".discarded.fastq"
    df_unassembled_r1 = out_base + ".unassembled.forward.fastq"
    df_unassembled_r2 = out_base + ".unassembled.reverse.fastq"

    df_outputs = [df_assembled, df_discarded, df_unassembled_r1, df_unassembled_r2]

    discarded = snakemake.output.get("discarded", out_base + ".discarded" + out_end)
    unassembled_r1 = snakemake.output.get(
        "unassembled_read1", out_base + ".unassembled_r1" + out_end
    )
    unassembled_r2 = snakemake.output.get(
        "unassembled_read2", out_base + ".unassembled_r2" + out_end
    )

    final_outputs = [assembled, discarded, unassembled_r1, unassembled_r2]


    def move_files(in_list, out_list, gzip):
        for f, o in zip(in_list, out_list):
            if f != o:
                if gzip:
                    shell("gzip -9 -c {f} > {o}")
                    shell("rm -f {f}")
                else:
                    shell("cp {f} {o}")
                    shell("rm -f {f}")
            elif gzip:
                shell("gzip -9 {f}")


    pval = float(snakemake.params.get("pval", ".01"))
    max_mem = snakemake.resources.get("mem_mb", "4000")
    extra = snakemake.params.get("extra", "")

    shell(
        "pear -f {r1} -r {r2} -p {pval} -j {snakemake.threads} -y {max_mem} {extra} -o {out_base} {log}"
    )

    move_files(df_outputs, final_outputs, gzip)


.. |nl| raw:: html

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