.. _`bio/bedtools/split`:

BEDTOOLS SPLIT
==============


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

Splits a BED file balancing the number of subfiles not just by number of lines, but also by total number of base pairs in each sub file.


**URL**: https://bedtools.readthedocs.io/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    scattergather:
        n_bed=2,


    rule bedtools_split:
        input:
            bed="a.bed",
        output:
            scatter.n_bed("results/a.{scatteritem}.bed"),
        log:
            "logs/a.split.log",
        params:
            ## Add optional parameters for spliting order
            extra="--algorithm size",
        wrapper:
            "v3.0.1/bio/bedtools/split"

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
-----

* This program/wrapper does not handle multi-threading.
* 'bedtools split' is currently undocumented, even though it was added to 'bedtools' on version `2.23.0` (https://bedtools.readthedocs.io/en/latest/content/history.html#version-2-23-0-22-feb-2015).


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

* ``bedtools=2.31.1``

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

* ``bed``: Path to BED file

**Output:**

* Several BED files



Params
------

* ``extra``: additional program arguments (except for `-i`, `-n`, or `-p`)




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2023, Filipe G. Vieira"
    __license__ = "MIT"

    import tempfile
    from snakemake.shell import shell

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

    n_subfiles = len(snakemake.output)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "bedtools split"
            " --input {snakemake.input.bed}"
            " --number {n_subfiles}"
            " {extra}"
            " --prefix {tmpdir}/out"
            " {log}"
        )

        for i in range(n_subfiles):
            out_tmp = f"{tmpdir}/out.{i+1:05d}.bed"
            out = snakemake.output[i]
            shell("cat {out_tmp} > {out}")


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