.. _`bio/bustools/count`:

BUSTOOLS COUNT
==============


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

BUS files can be converted into a barcode-feature matrix

**URL**: https://github.com/BUStools/bustools#count

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_bustools_count:
        input:
            bus="file.bus",
            ecmap="matrix.ec",
            txnames="transcripts.txt",
            genemap="t2g.txt",
        output:
            multiext(
                "buscount",
                ".barcodes.txt",
                ".CUPerCell.txt",
                ".cu.txt",
                ".genes.txt",
                ".hist.txt",
                ".mtx",
            ),
        threads: 1
        params:
            extra="",
        log:
            "bustools.log",
        wrapper:
            "v3.0.1/bio/bustools/count"

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
-----

When multiple bus files are provided, only one count matrix is returned.

When an output endswith: ".hist.txt", then `--hist` parameter is automatically used.

When an output endswith: ".genes.txt", then `--genemap` parameter is automatically used.

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

* ``bustools=0.43.1``

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

* ``bus``: Single bus-file, or List of bus-files
* ``genemap``: Transcript to gene mapping
* ``txnames``: List of transcripts
* ``ecmap``: Equivalence classes for transcripts

**Output:**

* barcodes, equivalence classes, and count matrix



Params
------

* ``extra``: Optional parameters, besides `--output`, `--ecmap`, and `--genemap`




Authors
-------



Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # coding: utf-8

    """Snakemake wrapper for bustools count"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os.path import commonprefix

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Get IO files and prefixes
    bus_files = snakemake.input["bus"]
    if isinstance(bus_files, list):
        bus_files = " ".join(bus_files)

    out_prefix = commonprefix(snakemake.output)[:-1]

    # Fill extra parameters if needed
    extra = snakemake.params.get("extra", "")
    if any(outfile.endswith(".hist.txt") for outfile in snakemake.output):
        if "--hist" not in extra:
            extra += " --hist"

    if any(outfile.endswith(".genes.txt") for outfile in snakemake.output):
        if "--genecounts" not in extra:
            extra += " --genecounts"

    shell(
        "bustools count {extra} "
        "--output {out_prefix} "
        "--genemap {snakemake.input.genemap} "
        "--ecmap {snakemake.input.ecmap} "
        "--txnames {snakemake.input.txnames} "
        "{bus_files} "
        "{log}"
    )


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