.. _`bio/last/lastdb`:

LASTDB
======


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

LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule lastdb_transcript:
        input:
            "test-transcript.fa"
        output:
            "test-transcript.fa.prj",
        params:
            protein_input=False,
            extra=""
        log:
            "logs/lastdb/test-transcript.log"
        wrapper:
            "v3.0.1/bio/last/lastdb"

    rule lastdb_protein:
        input:
            "test-protein.fa"
        output:
            "test-protein.fa.prj",
        params:
            protein_input=True,
            extra=""
        log:
            "logs/lastdb/test-protein.log"
        wrapper:
            "v3.0.1/bio/last/lastdb"

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

* ``last=1513``




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    __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=False, stderr=True)

    protein_cmd = ""
    protein = snakemake.params.get("protein_input", False)

    if protein:
        protein_cmd = " -p "

    shell("lastdb {extra} {protein_cmd} -P {snakemake.threads} {snakemake.input} {log}")


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