.. _`bio/tabix/query`:

TABIX QUERY
===========


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

Query given file with tabix.

**URL**: https://www.htslib.org/doc/tabix.html#QUERYING_AND_OTHER_OPTIONS

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule tabix:
        input:
            ## list the VCF/BCF as the first input
            ## and the index as the second input
            "{prefix}.bed.gz",
            "{prefix}.bed.gz.tbi",
        output:
            "{prefix}.output.bed",
        log:
            "logs/tabix/query/{prefix}.log",
        params:
            region="1",
            extra="",
        wrapper:
            "v3.0.1/bio/tabix/query"

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 `region` param (required) allows to specify region of interest to retrieve.
* The `extra` param allows for additional program arguments.


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

* ``htslib=1.18``

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

* Bgzip compressed file (e.g. BED.gz, GFF.gz, or VCF.gz)
* Tabix index file

**Output:**

* Uncompressed subset of the input file from the given region




Authors
-------

* William Rowell


Code
----

.. code-block:: python

    __author__ = "William Rowell"
    __copyright__ = "Copyright 2020, William Rowell"
    __email__ = "wrowell@pacb.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    shell(
        "tabix {extra} {snakemake.input[0]} {snakemake.params.region} > {snakemake.output} {log}"
    )


.. |nl| raw:: html

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