.. _`bio/preseq/lc_extrap`:

PRESEQ LC_EXTRAP
================


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

``preseq`` estimates the library complexity of existing sequencing data to then estimate the yield of future experiments based on their design.


**URL**: https://github.com/smithlabcode/preseq

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule preseq_lc_extrap_bam:
        input:
            "samples/{sample}.sorted.bam"
        output:
            "test_bam/{sample}.lc_extrap"
        params:
            "-v"   #optional parameters
        log:
            "logs/test_bam/{sample}.log"
        wrapper:
            "v3.0.1/bio/preseq/lc_extrap"

    rule preseq_lc_extrap_bed:
        input:
            "samples/{sample}.sorted.bed"
        output:
            "test_bed/{sample}.lc_extrap"
        params:
            "-v"   #optional parameters
        log:
            "logs/test_bed/{sample}.log"
        wrapper:
            "v3.0.1/bio/preseq/lc_extrap"

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

* ``preseq=3.2.0``

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

* bed files containing duplicates and sorted by chromosome, start position, strand position and finally strand OR
* bam files containing duplicates and sorted by using bamtools or samtools sort.

**Output:**

* lc_extrap (.lc_extrap)




Authors
-------

* Antonie Vietor


Code
----

.. code-block:: python

    __author__ = "Antonie Vietor"
    __copyright__ = "Copyright 2020, Antonie Vietor"
    __email__ = "antonie.v@gmx.de"
    __license__ = "MIT"

    import os
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    params = ""
    if (os.path.splitext(snakemake.input[0])[-1]) == ".bam":
        if "-bam" not in (snakemake.input[0]):
            params = "-bam "

    shell(
        "(preseq lc_extrap {params} {snakemake.params} {snakemake.input[0]} -output {snakemake.output[0]}) {log}"
    )


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