.. _`bio/blast/makeblastdb`:

BLAST MAKEBLASTDB FOR FASTA FILES
=================================


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

Makeblastdb produces local `BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_ databases from nucleotide or protein FASTA files. For more information please see `BLAST documentation <https://www.ncbi.nlm.nih.gov/books/NBK279690/>`_.


**URL**: https://blast.ncbi.nlm.nih.gov/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule blast_makedatabase_nucleotide:
        input:
            fasta="genome/{genome}.fasta"
        output:
            multiext("results/{genome}.fasta",
                ".ndb",
                ".nhr",
                ".nin",
                ".not",
                ".nsq",
                ".ntf",
                ".nto"
            )
        log:
            "logs/{genome}.log"
        params:
            "-input_type fasta -blastdb_version 5 -parse_seqids"
        wrapper:
            "v3.0.1/bio/blast/makeblastdb"

    rule blast_makedatabase_protein:
        input:
            fasta="protein/{protein}.fasta"
        output:
            multiext("results/{protein}.fasta",
                ".pdb",
                ".phr",
                ".pin",
                ".pot",
                ".psq",
                ".ptf",
                ".pto"
            )
        log:
            "logs/{protein}.log"
        params:
            "-input_type fasta -blastdb_version 5"
        wrapper:
            "v3.0.1/bio/blast/makeblastdb"

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

* ``blast=2.15.0``

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

* ``fasta``: Path to FASTA file

**Output:**

* Path to database multiple files with different extensions (e.g. .nin, .nsq, .nhr for nucleotides or .pin, .psq, .phr for proteins)



Params
------

* ``Optional parameters basides `-in`, `-dtype`, and `-out```: 




Authors
-------



Code
----

.. code-block:: python

    __author__ = "Antonie Vietor"
    __copyright__ = "Copyright 2021, Antonie Vietor"
    __email__ = "antonie.v@gmx.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

    log = snakemake.log
    out = snakemake.output[0]

    db_type = ""
    (out_name, ext) = path.splitext(out)

    if ext.startswith(".n"):
        db_type = "nucl"
    elif ext.startswith(".p"):
        db_type = "prot"

    shell(
        "makeblastdb"
        " -in {snakemake.input.fasta}"
        " -dbtype {db_type}"
        " {snakemake.params}"
        " -logfile {log}"
        " -out {out_name}"
    )


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