.. _`bio/art/profiler_illumina`:

ART_PROFILER_ILLUMINA
=====================


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

Use the art profiler to create a base quality score profile for Illumina read data from a fastq file.

**URL**: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule art_profiler_illumina:
        input:
            "data/{sample}.fq",
        output:
            "profiles/{sample}.txt"
        log:
            "logs/art_profiler_illumina/{sample}.log"
        params: ""
        threads: 2
        wrapper:
            "v3.0.1/bio/art/profiler_illumina"

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
-----

Your input file must have one of the following extensions: fastq, fastq.gz, fq or fq.gz


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

* ``art=2016.06.05``

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

* Path to fastq-formatted input file (first place in the input list of files)

**Output:**

* Path to txt formatted profile (first place in the output list of files)



Params
------

* ``Extra parameters (no keyword mapped parameter)``: 




Authors
-------

* David Laehnemann
* Victoria Sack


Code
----

.. code-block:: python

    __author__ = "David Laehnemann, Victoria Sack"
    __copyright__ = "Copyright 2018, David Laehnemann, Victoria Sack"
    __email__ = "david.laehnemann@hhu.de"
    __license__ = "MIT"


    from snakemake.shell import shell
    import os
    import tempfile
    import re


    # Create temporary directory that will only contain the symbolic link to the
    # input file, in order to sanely work with the art_profiler_illumina cli
    with tempfile.TemporaryDirectory() as temp_input:
        # ensure that .fastq and .fastq.gz input files work, as well
        filename = os.path.basename(snakemake.input[0]).replace(".fastq", ".fq")

        # figure out the exact file extension after the above substitution
        ext = re.search("fq(\.gz)?$", filename)
        if ext:
            fq_extension = ext.group(0)
        else:
            raise IOError(
                "Incompatible extension: This art_profiler_illumina "
                "wrapper requires input files with one of the following "
                "extensions: fastq, fastq.gz, fq or fq.gz. Please adjust "
                "your input and the invocation of the wrapper accordingly."
            )

        os.symlink(
            # snakemake paths are relative, but the symlink needs to be absolute
            os.path.abspath(snakemake.input[0]),
            # the following awkward file name generation has reasons:
            # * the file name needs to be unique to the execution of the
            #   rule, as art will create and mv temporary files with its basename
            #   in the output directory, which causes utter confusion when
            #   executing instances of the rule in parallel
            # * temp file name cannot have any read infixes before the file
            #   extension, because otherwise art does read enumeration magic
            #   that messes up output file naming
            os.path.join(
                temp_input,
                filename.replace(
                    "." + fq_extension, "_preventing_art_magic_spacer." + fq_extension
                ),
            ),
        )

        # include output folder name in the profile_name command line argument and
        # strip off the file extension, as art will add its own ".txt"
        profile_name = os.path.join(
            os.path.dirname(snakemake.output[0]), filename.replace("." + fq_extension, "")
        )

        shell(
            "( art_profiler_illumina {snakemake.params} {profile_name}"
            " {temp_input} {fq_extension} {snakemake.threads} ) 2> {snakemake.log}"
        )


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