.. _`bio/cnvkit/diagram`:

CNVKIT DIAGRAM
==============


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

Draw copy number (either individual bins (.cnn, .cnr) or segments (.cns)) on chromosomes as an ideogram. If both the bin-level log2 ratios and segmentation calls are given, show them side-by-side on each chromosome (segments on the left side, bins on the right side).


**URL**: https://cnvkit.readthedocs.io/en/stable/plots.html?highlight=diagram#diagram

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cnvkit_diagram_cns:
        input:
            "test.cns",
        output:
            "test.cns.pdf",
        log:
            "logs/test.cns.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/diagram"

    rule cnvkit_diagram_cnr:
        input:
            "test.cnr",
        output:
            "test.cnr.pdf",
        log:
            "logs/test.cnr.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/diagram"

    rule cnvkit_diagram_cnn:
        input:
            "test.cnn",
        output:
            "test.cnn.pdf",
        log:
            "logs/test.cnn.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/diagram"

    rule cnvkit_diagram_cnscnr:
        input:
            ["test.cns", "test.cnr"]
        output:
            "test.cnscnr.pdf",
        log:
            "logs/test.cnscnr.log",
        params:
            extra = "" # optional
        wrapper:
            "v3.0.1/bio/cnvkit/diagram"

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

* ``cnvkit=0.9.10``

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

* cns file (optional, if cnr is provided)
* cnr/cnn file (optional, if cns is provided)

**Output:**

* pdf report



Params
------

* ``extra``: additional parameters that will be forwarded to cnvkit diagram




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2023, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    cns_file = [f for f in snakemake.input if f.endswith(".cns")]
    cnr_file = [f for f in snakemake.input if f.endswith(".cnr") or f.endswith(".cnn")]

    if cns_file:
        if len(cns_file) > 1:
            raise Exception(f"Expecting only one input cns file {cns_file}")
        cns_file = f"-s {cns_file[0]}"

    if cnr_file:
        if len(cnr_file) > 1:
            raise Exception(f"Expecting only one input cnr/cnn file {cnr_file}")
        cnr_file = f"{cnr_file[0]}"

    extra = snakemake.params.get("extra", "")

    shell(
        "(cnvkit.py diagram "
        "{cns_file} "
        "{cnr_file} "
        "-o {snakemake.output} "
        "{extra}) "
        "{log}"
    )


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