.. _`bio/cooltools/pileup`:

COOLTOOLS PILEUP
================


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

Pileup features for a resolution in an .mcool file

**URL**: https://github.com/open2c/cooltools

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cooltools_pileup:
        input:
            cooler="CN.mm9.1000kb.mcool",  ## Multiresolution cooler file
            features="CN.mm9.toy_features.bed",  ## Feature file
            expected="CN.mm9.toy_expected.tsv",  ## Expected file
            view="CN.mm9.toy_regions.bed",  ## File with the region names and coordinates
        output:
            "CN_{resolution,[0-9]+}.pileup.npz",
        params:
            ## Add optional parameters
            features_format="bed",  ## Format of the features file
            extra="--aggregate mean",  ## Add extra parameters
        threads: 4
        log:
            "logs/CN_{resolution}_pileup.log",
        wrapper:
            "v3.0.1/bio/cooltools/pileup"

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

* ``cooltools=0.6.1``

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

* a multiresolution cooler file (.mcool)
* a file with features to pileup
* (optional) file with expected
* (optional) view, a bed-style file with region coordinates and names to use for analysis

**Output:**

* A file (.npz or .h5) with piled up snippets. Can have a {resolution} wildcard that specifies the resolution for the analysis, then it doesn't need to be specified as a parameter.




Params
------

* ``resolution``: Optional, can be instead specified as a wildcard in the output


* ``extra``: Any additional arguments to pass




Authors
-------

* Ilya Flyamer


Code
----

.. code-block:: python

    __author__ = "Ilya Flyamer"
    __copyright__ = "Copyright 2022, Ilya Flyamer"
    __email__ = "flyamer@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

    ## Extract arguments
    view = snakemake.input.get("view", "")
    if view:
        view = f"--view {view}"
    expected = snakemake.input.get("expected", "")
    if expected:
        expected = f"--expected {expected}"

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

    resolution = snakemake.params.get(
        "resolution", snakemake.wildcards.get("resolution", 0)
    )
    if not resolution:
        raise ValueError("Please specify resolution either as a wildcard or as a parameter")

    shell(
        "(cooltools pileup"
        " {snakemake.input.cooler}::resolutions/{resolution}"
        " {snakemake.input.features}"
        " {expected}"
        " --features-format {snakemake.params.features_format}"
        " {view}"
        " -p {snakemake.threads}"
        " {extra}"
        " -o {snakemake.output}) {log}"
    )


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