.. _`bio/pretext/map`:

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


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

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pretext_map:
        input:
            "a.bam",
        output:
            "map.pretext",
        log:
            "logs/pretext_map.log",
        params:
            extra="--sortby length --sortorder descend --mapq 10",
        wrapper:
            "v3.0.4/bio/pretext/map"

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

* ``pretextmap=0.1.9``
* ``samtools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* SAM/BAM/CRAM 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
    from snakemake_wrapper_utils.samtools import infer_out_format


    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"
    elif infer_out_format(snakemake.input[0]) in ["SAM", "BAM", "CRAM"]:
        pipe = "samtools view -h"
    else:
        pipe = "cat"


    shell(
        "({pipe}"
        " {snakemake.input} | "
        "PretextMap"
        " {extra}"
        " -o {snakemake.output}"
        ") {log}"
    )


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