.. _`bio/sourmash/compute`:

SOURMASH_COMPUTE
================


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

Build a MinHash signature for a transcriptome, genome, or reads 



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule sourmash_reads:
        input:
            "reads/a.fastq"
        output:
            "reads.sig"
        log:
            "logs/sourmash/sourmash_compute_reads.log"
        threads: 2
        params:
            # optional parameters
            k = "31",
            scaled = "1000",
            extra = ""
        wrapper:
            "v3.0.1/bio/sourmash/compute"


    rule sourmash_transcriptome:
        input:
            "assembly/transcriptome.fasta"
        output:
            "transcriptome.sig"
        log:
            "logs/sourmash/sourmash_compute_transcriptome.log"
        threads: 2
        params:
            # optional parameters
            k = "31",
            scaled = "1000",
            extra = ""
        wrapper:
            "v3.0.1/bio/sourmash/compute"

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

* ``sourmash=4.8.4``

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

* assembly fasta, or reads fastq

**Output:**

* sourmash signature




Authors
-------

* Lisa K. Johnson


Code
----

.. code-block:: python

    """Snakemake wrapper for sourmash compute."""

    __author__ = "Lisa K. Johnson"
    __copyright__ = "Copyright 2018, Lisa K. Johnson"
    __email__ = "ljcohen@ucdavis.edu"
    __license__ = "MIT"

    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    scaled = snakemake.params.get("scaled", "1000")
    k = snakemake.params.get("k", "31")

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

    shell(
        "sourmash compute --scaled {scaled} -k {k} {snakemake.input} -o {snakemake.output}"
        " {extra} {log}"
    )


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