.. _`bio/rsem/generate-data-matrix`:

RSEM GENERATE DATA MATRIX
=========================


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

Run rsem-generate-data-matrix to combine a set of single-sample rsem results into a single matrix.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule rsem_generate_data_matrix:
        input:
            # one or more expression files created by rsem-calculate-expression
            ["a.genes.results", "b.genes.results"],
        output:
            # a tsv containing each sample in the input as a column
            "genes.results",
        params:
            # optional additional parameters
            extra="",
        log:
            "logs/rsem/generate_data_matrix.log",
        wrapper:
            "v3.0.1/bio/rsem/generate-data-matrix"

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
-----

* For more information, see https://github.com/deweylab/RSEM.


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

* ``rsem=1.3.3``

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

* a list of rsem results files

**Output:**

* Quantification results summarized by allele/gene/isoform per sample




Authors
-------

* Brett Copeland


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", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    shell(
        "rsem-generate-data-matrix {extra} "
        "{snakemake.input} > {snakemake.output} "
        "{log}"
    )


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