.. _`bio/pindel/pindel2vcf`:

PINDEL2VCF
==========


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/pindel/pindel2vcf?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/pindel/pindel2vcf

Convert pindel output to vcf.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pindel2vcf:
        input:
            ref="genome.fasta",
            pindel="pindel/all_{type}"
        output:
            "pindel/all_{type}.vcf"
        params:
            refname="hg38",  # mandatory, see pindel manual
            refdate="20170110",  # mandatory, see pindel manual
            extra=""  # extra params (except -r, -p, -R, -d, -v)
        log:
            "logs/pindel/pindel2vcf.{type}.log"
        wrapper:
            "v3.0.1/bio/pindel/pindel2vcf"

    rule pindel2vcf_multi_input:
        input:
            ref="genome.fasta",
            pindel=["pindel/all_D", "pindel/all_INV"]
        output:
            "pindel/all.vcf"
        params:
            refname="hg38",  # mandatory, see pindel manual
            refdate="20170110",  # mandatory, see pindel manual
            extra=""  # extra params (except -r, -p, -R, -d, -v)
        log:
            "logs/pindel/pindel2vcf.log"
        wrapper:
            "v3.0.1/bio/pindel/pindel2vcf"

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

* ``pindel=0.2.5b9``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster, Patrik Smeds"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell

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

    expected_endings = [
        "INT",
        "D",
        "SI",
        "INV",
        "INV_final",
        "TD",
        "LI",
        "BP",
        "CloseEndMapped",
        "RP",
    ]


    def split_file_name(file_parts, file_ending_index):
        return (
            "_".join(file_parts[:file_ending_index]),
            "_".join(file_parts[file_ending_index:]),
        )


    def process_input_path(input_file):
        """
        :params input_file: Input file from rule, ex /path/to/file/all_D or /path/to/file/all_INV_final
        :return: ""/path/to/file", "all"

        """
        file_path, file_name = os.path.split(input_file)
        file_parts = file_name.split("_")
        # seperate ending and name, to name: all ending: D or name: all ending: INV_final
        file_name, file_ending = split_file_name(
            file_parts, -2 if file_name.endswith("_final") else -1
        )
        if not file_ending in expected_endings:
            raise Exception("Unexpected variant type: " + file_ending)
        return file_path, file_name


    with tempfile.TemporaryDirectory() as tmpdirname:
        input_flag = "-p"
        input_file = snakemake.input.get("pindel")
        if isinstance(input_file, list) and len(input_file) > 1:
            input_flag = "-P"
            input_path, input_name = process_input_path(input_file[0])
            input_file = os.path.join(input_path, input_name)
            for variant_input in snakemake.input.pindel:
                if not variant_input.startswith(input_file):
                    raise Exception(
                        "Unable to extract common path from multi file input, expect path is: "
                        + input_file
                    )
                if not os.path.isfile(variant_input):
                    raise Exception('Input "' + input_file + '" is not a file!')
                os.symlink(
                    os.path.abspath(variant_input),
                    os.path.join(tmpdirname, os.path.basename(variant_input)),
                )
            input_file = os.path.join(tmpdirname, input_name)
        shell(
            "pindel2vcf {snakemake.params.extra} {input_flag} {input_file} -r {snakemake.input.ref} -R {snakemake.params.refname} -d {snakemake.params.refdate} -v {snakemake.output[0]} {log}"
        )


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