.. _`bio/pretext/snapshot`:

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


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

Commandline image generator for Pretext contact maps.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pretext_snapshot_png:
        input:
            "map.pretext",
        output:
            all=directory("all_maps/"),
            full="full_map.png",
        log:
            "logs/pretext_snapshot_png.log",
        params:
            extra="--resolution 1080",
        wrapper:
            "v3.0.1/bio/pretext/snapshot"


    rule pretext_snapshot_jpg:
        input:
            "map.pretext",
        output:
            all=directory("all_maps/"),
            full="full_map.jpg",
        log:
            "logs/pretext_snapshot_jpg.log",
        params:
            extra="--resolution 1080",
        wrapper:
            "v3.0.1/bio/pretext/snapshot"

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
-----

* Outputs must all have the same format (PNG/BMP/JPG).
* The `extra` param allows for additional arguments.


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

* ``pretextsnapshot=0.0.4``

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

* pretext contact map

**Output:**

* full image (mandatory)
* all images (optional)
* specific sequences (optional)




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

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


    import tempfile
    from pathlib import Path
    from snakemake.shell import shell


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


    out_maps = snakemake.output.keys()
    sequences = "=" + ", =".join(snakemake.output.keys())


    format = Path(snakemake.output.full).suffix.removeprefix(".")
    if format == "jpg":
        format = "jpeg"


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "PretextSnapshot"
            " --map {snakemake.input[0]}"
            " {extra}"
            " --sequences {sequences:q}"
            " --format {format}"
            " --folder {tmpdir}"
            " --prefix out_"
            " {log}"
        )

        if snakemake.output.get("full"):
            shell("mv {tmpdir}/out_FullMap.{format} {snakemake.output.full}")
        if snakemake.output.get("all"):
            Path(snakemake.output.all).mkdir(parents=True, exist_ok=True)
            shell("mv {tmpdir}/out_*.{format} {snakemake.output.all}/.")


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