.. _`bio/nanosim-h`:

NANOSIM-H
=========


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

NanoSim-H is a simulator of Oxford Nanopore reads that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of Nanopore sequencing technology.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule nanosimh:
        input:
            "{sample}.fa"
        output:
            reads = "{sample}.simulated.fa",
            log = "{sample}.simulated.log",
            errors = "{sample}.simulated.errors.txt"
        params:
            extra = "",
            num_reads = 10,
            perfect_reads = True,
            min_read_len = 10,
        log:
            "logs/nanosim-h/test/{sample}.log"
        wrapper:
            "v3.0.1/bio/nanosim-h"

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

* ``nanosim-h=1.1.0.4``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    """Snakemake wrapper for NanoSim-H."""

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2019, Michael Hall"
    __email__ = "mbhall88@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell


    def is_header(query):
        return query.startswith(">")


    def get_length_of_longest_sequence(fh):
        current_length = 0
        all_lengths = []
        for line in fh:
            if not is_header(line):
                current_length += len(line.rstrip())
            else:
                all_lengths.append(current_length)
                current_length = 0
        all_lengths.append(current_length)

        return max(all_lengths)


    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    prefix = snakemake.params.get("prefix", snakemake.output.reads.rpartition(".")[0])
    num_reads = snakemake.params.get("num_reads", 10000)
    profile = snakemake.params.get("profile", "ecoli_R9_2D")
    perfect_reads = snakemake.params.get("perfect_reads", False)
    min_read_len = snakemake.params.get("min_read_len", 50)
    max_read_len = snakemake.params.get("max_read_len", 0)

    # need to do this as the default read length of infinity can cause nanosim-h to
    # hang if the reference is short
    if max_read_len == 0:
        with open(snakemake.input[0]) as fh:
            max_read_len = get_length_of_longest_sequence(fh)

    perfect_reads_flag = "--perfect " if perfect_reads else ""
    # Formats the log redrection string
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Executed shell command
    shell(
        "nanosim-h {extra} "
        "{perfect_reads_flag} "
        "--max-len {max_read_len} "
        "--min-len {min_read_len} "
        "--profile {profile} "
        "--number {num_reads} "
        "--out-pref {prefix} "
        "{snakemake.input} {log}"
    )


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