.. _`bio/transdecoder/predict`:

TRANSDECODER PREDICT
====================


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

Predict the likely coding regions from the ORFs identified by Transdecoder.LongOrfs. Optionally include results from homology searches (blast/hmmer results) as ORF retention criteria.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule transdecoder_predict:
        input:
            fasta="test.fa.gz", # required input; optionally gzipped
            pfam_hits="pfam_hits.txt", # optionally retain ORFs with hits by inputting pfam results here (run separately)
            blastp_hits="blastp_hits.txt", # optionally retain ORFs with hits by inputting blastp results here (run separately)
            # you may also want to add your transdecoder longorfs result here - predict will fail if you haven't first run longorfs
            #longorfs="test.fa.transdecoder_dir/longest_orfs.pep"
        output:
            "test.fa.transdecoder.bed",
            "test.fa.transdecoder.cds",
            "test.fa.transdecoder.pep",
            "test.fa.transdecoder.gff3"
        log:
            "logs/transdecoder/test-predict.log"
        params:
            extra=""
        wrapper:
            "v3.0.1/bio/transdecoder/predict"

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 assembly

**Output:**

* candidate coding regions (pep, cds, gff3, bed output formats)




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for Transdecoder Predict"""

    __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)

    addl_outputs = ""
    pfam = snakemake.input.get("pfam_hits", "")
    if pfam:
        addl_outputs += " --retain_pfam_hits " + pfam

    blast = snakemake.input.get("blastp_hits", "")
    if blast:
        addl_outputs += " --retain_blastp_hits " + blast

    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.Predict -t {input_fa} {addl_outputs} {extra} {log}")


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