.. _`bio/purge_dups/get_seqs`:

PURGE_DUPS GET_SEQS
===================


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

Purge haplotigs and overlaps in an assembly based on read depth

**URL**: https://github.com/dfguan/purge_dups

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule purge_dups_get_seqs:
        input:
            fas="genome.fasta",
            bed="purge_dups.bed",
        output:
            hap="out/get_seqs.hap.fasta",
            purged="out/get_seqs.purged.fasta",
        log:
            "logs/get_seqs.log",
        params:
            extra="",
        threads: 1
        wrapper:
            "v3.0.1/bio/purge_dups/get_seqs"

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.


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

* ``purge_dups=1.2.6``

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

* BED file
* FASTA file

**Output:**

* purged FASTA file




Authors
-------

* Filipe Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    import tempfile
    from pathlib import Path
    from snakemake.shell import shell


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


    if Path(snakemake.input.bed).stat().st_size:
        with tempfile.TemporaryDirectory() as tmpdir:
            shell(
                "get_seqs {extra} -p {tmpdir}/out {snakemake.input.bed} {snakemake.input.fas} {log}"
            )

            if snakemake.output.get("hap"):
                shell("cat {tmpdir}/out.hap.fa > {snakemake.output.hap}")
            if snakemake.output.get("purged"):
                shell("cat {tmpdir}/out.purged.fa > {snakemake.output.purged}")
    else:
        # If BED file empty, copy input to output since `get_seqs` will segfault
        log = Path(snakemake.log[0])
        log.write_text(
            "WARN: Input BED file is empty. Input FASTA file will be copied to output."
        )
        shell("cp {snakemake.input.fas} {snakemake.output.hap}")
        Path(snakemake.output.purged).touch()


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