.. _`bio/pretext/graph`:

PRETEXT MAP
===========


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

Embeds bedgraph data into Pretext contact maps.

**URL**: https://github.com/wtsi-hpag/PretextGraph

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pretext_graph:
        input:
            bedgraph="{a}.bedgraph",
            map="map.pretext",
        output:
            "{a}.pretext",
        log:
            "logs/{a}.pretext_graph.log",
        params:
            graph_name="graph_name",
            extra="",
        wrapper:
            "v3.0.4/bio/pretext/graph"

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
-----

* The `extra` param allows for additional arguments.


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

* ``pretextgraph=0.0.6``

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

* BEDgraph file

**Output:**

* pretext contact map




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell


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


    if snakemake.input[0].endswith(".gz"):
        pipe = "gunzip -c"
    elif snakemake.input[0].endswith(".bz2"):
        pipe = "bunzip2 -c"
    else:
        pipe = "cat"


    shell(
        "({pipe}"
        " {snakemake.input.bedgraph} | "
        "PretextGraph"
        " -i {snakemake.input.map}"
        " -n {snakemake.params.graph_name}"
        " {extra}"
        " -o {snakemake.output}"
        ") {log}"
    )


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