.. _`bio/ptrimmer`:

PTRIMMER
========


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

Tool to trim off the primer sequence from mutiplex amplicon sequencing


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule ptrimmer_pe:
        input:
            r1="resources/a.lane1_R1.fastq.gz",
            r2="resources/a.lane1_R2.fastq.gz",
            primers="resources/primers.txt"
        output:
            r1="results/a.lane1_R1.fq.gz",
            r2="results/a.lane1_R2.fq.gz"
        log:
            "logs/ptrimmer/a.lane.log"
        wrapper:
            "v3.0.1/bio/ptrimmer"

    rule ptrimmer_se:
        input:
            r1="resources/a.lane1_R1.fastq.gz",
            primers="resources/primers.txt"
        output:
            r1="results/a.lane1_R1.fq",
        log:
            "logs/ptrimmer/a.lane1.log"
        wrapper:
            "v3.0.1/bio/ptrimmer"

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

* ``ptrimmer=1.3.3``




Authors
-------

* Felix Mölder


Code
----

.. code-block:: python

    __author__ = "Felix Mölder"
    __copyright__ = "Copyright 2020, Felix Mölder"
    __email__ = "felix.moelder@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from pathlib import Path
    import ntpath

    input_reads = "-f {r1}".format(r1=snakemake.input.r1)

    out_r1 = ntpath.basename(snakemake.output.r1)
    output_reads = "-d {o1}".format(o1=out_r1)

    if snakemake.input.get("r2", ""):
        seqmode = "pair"
        input_reads = "{reads} -r {r2}".format(reads=input_reads, r2=snakemake.input.r2)
        out_r2 = ntpath.basename(snakemake.output.r2)
        output_reads = "{reads} -e {o2}".format(reads=output_reads, o2=out_r2)
    else:
        seqmode = "single"

    primers = snakemake.input.primers

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

    ptrimmer_params = "-t {mode} {in_reads} -a {primers} {out_reads}".format(
        mode=seqmode, in_reads=input_reads, primers=primers, out_reads=output_reads
    )

    process_r1 = "mv {out_read} {final_output_path}".format(
        out_read=out_r1, final_output_path=snakemake.output.r1
    )

    process_r2 = ""
    if snakemake.input.get("r2", ""):
        process_r2 = "&& mv {out_read} {final_output_path}".format(
            out_read=out_r2, final_output_path=snakemake.output.r2
        )

    shell("(ptrimmer {ptrimmer_params} && {process_r1} {process_r2}) {log}")


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