.. _`bio/ucsc/gtfToGenePred`:

GTFTOGENEPRED
=============


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

Convert a GTF file to genePred format (see https://genome.ucsc.edu/FAQ/FAQformat.html#format9)


**URL**: https://hgdownload.cse.ucsc.edu/admin/exe/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gtfToGenePred:
        input:
            # annotations containing gene, transcript, exon, etc. data in GTF format
            "annotation.gtf",
        output:
            "annotation.genePred",
        log:
            "logs/gtfToGenePred.log",
        params:
            extra="-genePredExt",  # optional parameters to pass to gtfToGenePred
        wrapper:
            "v5.3.0-16-g710597c/bio/ucsc/gtfToGenePred"


    rule gtfToGenePred_CollectRnaSeqMetrics:
        input:
            # annotations containing gene, transcript, exon, etc. data in GTF format
            "annotation.gtf",
        output:
            "annotation.PicardCollectRnaSeqMetrics.genePred",
        log:
            "logs/gtfToGenePred.PicardCollectRnaSeqMetrics.log",
        params:
            convert_out="PicardCollectRnaSeqMetrics",
            extra="-genePredExt -geneNameAsName2",  # optional parameters to pass to gtfToGenePred
        wrapper:
            "v5.3.0-16-g710597c/bio/ucsc/gtfToGenePred"

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 program arguments.
* The `convert_out` param allows to apply some conversions to the `refFlat` output. For example, if set to `PicardCollectRnaSeqMetrics` it makes it compatible with `Picard CollectRnaSeqMetrics` (this one also requires `extra` to be set to `-genePredExt -geneNameAsName2`).


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

* ``ucsc-gtftogenepred=469``
* ``csvkit=2.0.1``

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

* GTF file

**Output:**

* genePred table




Authors
-------

* Brett Copeland
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Brett Copeland"
    __copyright__ = "Copyright 2021, Brett Copeland"
    __email__ = "brcopeland@ucsd.edu"
    __license__ = "MIT"

    import os
    from snakemake.shell import shell


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


    pipes = ""
    if convert_out == "raw":
        pipes = ""
    elif convert_out == "PicardCollectRnaSeqMetrics":
        pipes += " | csvcut -t -c 12,1-10 | csvformat -T"
    else:
        raise ValueError(
            f"Unsupported conversion mode {convert_out}. Please check wrapper documentation."
        )


    shell(
        "(gtfToGenePred {extra} {snakemake.input} /dev/stdout {pipes} > {snakemake.output}) {log}"
    )


.. |nl| raw:: html

   <br>