.. _`bio/pyroe/makesplicedintronic`:

PYROE MAKE-SPLICED+INTRONIC
===========================


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

Build splici reference files for Alevin-fry. The splici index reference of a given species consists of the transcriptome of the species, i.e., the spliced transcripts and the intronic sequences of the species.


**URL**: https://pyroe.readthedocs.io/en/latest/building_splici_index.html#preparing-a-spliced-intronic-transcriptome-reference

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_pyroe_makesplicedintronic:
        input:
            fasta="genome.fasta",
            gtf="annotation.gtf",
            spliced="extra_spliced.fasta",  # Optional path to additional spliced sequences (FASTA)
            unspliced="extra_unspliced.fasta",  # Optional path to additional unspliced sequences (FASTA)
        output:
            fasta="splici_full/spliced_intronic_sequences.fasta",
            gene_id_to_name="splici_full/gene_id_to_name.tsv",
            t2g="splici_full/t2g.tsv",
        threads: 1
        log:
            "logs/pyroe.log",
        params:
            read_length=91,  # Required
            flank_trim_length=5,  # Optional l
            extra="",  # Optional parameters
        wrapper:
            "v3.0.1/bio/pyroe/makesplicedintronic"

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
---------------------

* ``pyroe=0.9.3``
* ``bedtools=2.31.1``

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

* ``gtf``: Path to the genome annotation (GTF formatted)
* ``fasta``: Path to the genome sequence (Fasta formatted)
* ``spliced``: Optional path to additional spliced sequences (Fasta formatted)
* ``unspliced``: Optional path to unspliced sequences (Fasta formatted)

**Output:**

* ``fasta``: Path to spliced+intronic sequences (Fasta formatted)
* ``gene_id_to_name``: Path to a TSV formatted text file containing gene_id <-> gene_name correspondence
* ``t2g``: Path to a TSV formatted text file containing the transcript_id <-> gene_name <-> splicing status correspondence



Params
------

* ``read_length``: The read length of the single-cell experiment being processed (determines flank size). Default is 100.

* ``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 tempfile import TemporaryDirectory
    from snakemake.shell import shell


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

    # pyroe uses the flank-length value to name its output files
    # in the result directory. We need this value to acquired output
    # files and let snakemake-wrapper choose its output file names.
    read_length = snakemake.params.get("read_length", 101)
    flank_trim_length = snakemake.params.get("flank_trim_length", 5)
    flank_length = read_length - flank_trim_length

    spliced = snakemake.input.get("spliced", "")
    if spliced:
        spliced = "--extra-spliced " + spliced


    unspliced = snakemake.input.get("unspliced", "")
    if unspliced:
        unspliced = "--extra-unspliced " + unspliced


    with TemporaryDirectory() as tempdir:
        shell(
            "pyroe make-spliced+intronic "
            "{extra} {spliced} "
            "{unspliced} "
            "{snakemake.input.fasta} "
            "{snakemake.input.gtf} "
            "{read_length} "
            "{tempdir} "
            "{log}"
        )

        if snakemake.output.get("fasta", False):
            shell(
                "mv --verbose "
                "{tempdir}/splici_fl{flank_length}.fa "
                "{snakemake.output.fasta} {log}"
            )

        if snakemake.output.get("gene_id_to_name", False):
            shell(
                "mv --verbose "
                "{tempdir}/gene_id_to_name.tsv "
                "{snakemake.output.gene_id_to_name} {log}"
            )

        if snakemake.output.get("t2g", False):
            shell(
                "mv --verbose "
                "{tempdir}/splici_fl{flank_length}_t2g_3col.tsv "
                "{snakemake.output.t2g} {log} "
            )


.. |nl| raw:: html

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