.. _`bio/cooltools/eigs_trans`:

COOLTOOLS EIGS_TRANS
====================


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

Calculate trans eigenvectors 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_eigs_trans:
        input:
            cooler="CN.mm9.1000kb.mcool",  ## Multiresolution cooler file
            track="mm9_1000000_gc.bed",
        output:
            vecs="CN_{resolution,[0-9]+}.trans.vecs.tsv",
            lam="CN_{resolution,[0-9]+}.trans.lam.tsv",
            bigwig="CN_{resolution,[0-9]+}.trans.bw",
        params:
            ## Add optional parameters
            track_col_name="GC",
            extra="",
        log:
            "logs/CN_{resolution}_trans_eigs.log",
        wrapper:
            "v3.0.1/bio/cooltools/eigs_trans"

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
-----

["Output files can have a {resolution} wildcard that specifies the resolution for the analysis, then it doesn't need to be specified as a parameter."]

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

* ``ucsc-bedgraphtobigwig``
* ``cooltools=0.6.1``

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

* a multiresolution cooler file (.mcool)
* (optional) phasing track file

**Output:**

* vecs
* lams
* bigwig



Params
------

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


* ``track_col_name``: Name of the column in the track file to use


* ``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
    import tempfile

    ## Extract arguments
    # view = snakemake.input.get("view", "") # Not yet implemented
    # if view:
    #     view = f"--view {view}"
    view = ""

    track = snakemake.input.get("track", "")
    track_col_name = snakemake.params.get("track_col_name", "")
    if track and track_col_name:
        track = f"--phasing-track {track}::{track_col_name}"
    elif track:
        track = f"--phasing-track {track}"

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

    bigwig = snakemake.output.get("bigwig", "")
    if bigwig:
        bigwig = "--bigwig"

    resolution = snakemake.params.get("resolution", snakemake.wildcards.get("resolution"))
    assert (
        resolution
    ), "Please specify resolution either as a `wildcard` or as a `parameter`"

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "cooltools eigs-trans"
            " {snakemake.input.cooler}::resolutions/{resolution} "
            " {track}"
            " {view} "  # Not yet implemented, hardcoded to ""
            " {bigwig}"
            " {extra} "
            " -o {tmpdir}/out"
            " {log}"
        )

        shell("mv {tmpdir}/out.trans.vecs.tsv {snakemake.output.vecs}")
        shell("mv {tmpdir}/out.trans.lam.txt {snakemake.output.lam}")
        if bigwig:
            shell("mv {tmpdir}/out.trans.bw {snakemake.output.bigwig}")


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