.. _`bio/transdecoder/longorfs`:

TRANSDECODER LONGORFS
=====================


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

TransDecoder.LongOrfs will identify coding regions within transcript sequences (ORFs) that are at least 100 amino acids long. You can lower this via the '-m' parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule transdecoder_longorfs:
        input:
            fasta="test.fa.gz", # required
            gene_trans_map="test.gtm" # optional gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> )
        output:
            "test.fa.transdecoder_dir/longest_orfs.pep"
        log:
            "logs/transdecoder/test-longorfs.log"
        params:
            extra=""
        wrapper:
            "v3.0.1/bio/transdecoder/longorfs"

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.


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

* ``transdecoder=5.7.1``

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

* fasta transcripts

**Output:**

* ORFs peptide file(s)




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for Transdecoder LongOrfs"""

    __author__ = "N. Tessa Pierce"
    __copyright__ = "Copyright 2019, N. Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"

    from os import path
    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    gtm_cmd = ""
    gtm = snakemake.input.get("gene_trans_map", "")
    if gtm:
        gtm_cmd = " --gene_trans_map " + gtm

    output_dir = path.dirname(str(snakemake.output))

    # transdecoder fails if output already exists. No force option available
    shell("rm -rf {output_dir}")

    input_fasta = str(snakemake.input.fasta)
    if input_fasta.endswith("gz"):
        input_fa = input_fasta.rsplit(".gz")[0]
        shell("gunzip -c {input_fasta} > {input_fa}")
    else:
        input_fa = input_fasta

    shell("TransDecoder.LongOrfs -t {input_fa} {gtm_cmd} {log}")


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