.. _`bio/pyroe/idtoname`:

PYROE ID-TO-NAME
================


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

Create a 2-column tab-separated file mapping IDs to names


**URL**: https://pyroe.readthedocs.io/en/latest/geneid_to_name.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_pyroe_idtoname:
        input:
            "annotation.{format}",
        output:
            "id2name.{format}.tsv",
        threads: 1
        log:
            "logs/{format}.log",
        params:
            extra="",
        wrapper:
            "v3.0.1/bio/pyroe/idtoname"

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
-----

Format is automatically inferred from input files.

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

* ``pyroe=0.9.3``

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

* Path to genome annotation (GTF or GFF3)

**Output:**

* Path to gene id <-> gene names mapping



Params
------

* ``extra``: Optional parameters to be passed to pyroe




Authors
-------



Code
----

.. code-block:: python

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2023, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"


    from snakemake.shell import shell


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

    if str(snakemake.input).endswith(("gtf", "gtf.gz")):
        extra += " --format GTF "
    elif str(snakemake.input).endswith(("gff", "gff.gz", "gff3", "gff3.gz")):
        extra += " --format GFF3 "

    shell("pyroe id-to-name {extra} {snakemake.input} {snakemake.output} {log}")


.. |nl| raw:: html

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