.. _`bio/subread/featurecounts`:

SUBREAD FEATURECOUNTS
=====================


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

FeatureCounts assign mapped reads or fragments (paired-end data) to genomic features such as genes, exons and promoters.


**URL**: http://subread.sourceforge.net/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule feature_counts:
        input:
            # list of sam or bam files
            samples="{sample}.bam",
            annotation="annotation.gtf",
            # optional input
            #chr_names="",           # implicitly sets the -A flag
            #fasta="genome.fasta"    # implicitly sets the -G flag
        output:
            multiext(
                "results/{sample}",
                ".featureCounts",
                ".featureCounts.summary",
                ".featureCounts.jcounts",
            ),
        threads: 2
        params:
            strand=0,  # optional; strandness of the library (0: unstranded [default], 1: stranded, and 2: reversely stranded)
            r_path="",  # implicitly sets the --Rpath flag
            extra="-O --fracOverlap 0.2 -J -p",
        log:
            "logs/{sample}.log",
        wrapper:
            "v3.0.2/bio/subread/featurecounts"

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 `strand` param allows to specify the strandness of the library (0: unstranded, 1: stranded, and 2: reversely stranded)
* The `extra` param allows for additional program arguments.


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

* ``subread=2.0.6``

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

* a list of .sam or .bam files
* GTF, GFF or SAF annotation file
* optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
* optional a fasta index file

**Output:**

* Feature counts file including read counts (tab separated)
* Summary file including summary statistics (tab separated)
* Junction counts file including count number of reads supporting each exon-exon junction (tab separated)




Authors
-------



Code
----

.. code-block:: python

    __author__ = "Antonie Vietor"
    __copyright__ = "Copyright 2020, Antonie Vietor"
    __email__ = "antonie.v@gmx.de"
    __license__ = "MIT"

    import tempfile
    from snakemake.shell import shell

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

    # optional input files and directories
    strand = snakemake.params.get("strand", 0)

    fasta = snakemake.input.get("fasta", "")
    if fasta:
        fasta = f"-G {fasta}"

    chr_names = snakemake.input.get("chr_names", "")
    if chr_names:
        chr_names = f"-A {chr_names}"

    r_path = snakemake.params.get("r_path", "")
    if r_path:
        r_path = f"--Rpath {r_path}"


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "featureCounts"
            " -T {snakemake.threads}"
            " -s {strand}"
            " -a {snakemake.input.annotation}"
            " {fasta}"
            " {chr_names}"
            " {r_path}"
            " {extra}"
            " --tmpDir {tmpdir}"
            " -o {snakemake.output[0]}"
            " {snakemake.input.samples}"
            " {log}"
        )


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