.. _`bio/mlst`:

MLST
====


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

Scan contig files against traditional PubMLST typing schemes


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule run_mlst:
        input:
            #Input assembly
            assembly="{sample}.fasta",
        output:
            #Tab delimited mlst designation
            mlst="{sample}_mlst.txt",
        params:
        #extra parameters should be space delimited
            # SYNOPSIS
            #   Automatic MLST calling from assembled contigs
            # USAGE
            #   % mlst --list                                            # list known schemes
            #   % mlst [options] <contigs.{fasta,gbk,embl}[.gz]          # auto-detect scheme
            #   % mlst --scheme <scheme> <contigs.{fasta,gbk,embl}[.gz]> # force a scheme
            # GENERAL
            #   --help            This help
            #   --version         Print version and exit(default ON)
            #   --check           Just check dependencies and exit (default OFF)
            #   --quiet           Quiet - no stderr output (default OFF)
            #   --threads [N]     Number of BLAST threads (suggest GNU Parallel instead) (default '1')
            #   --debug           Verbose debug output to stderr (default OFF)
            # SCHEME
            #   --scheme [X]      Don't autodetect, force this scheme on all inputs (default '')
            #   --list            List available MLST scheme names (default OFF)
            #   --longlist        List allelles for all MLST schemes (default OFF)
            #   --exclude [X]     Ignore these schemes (comma sep. list) (default 'ecoli_2,abaumannii')
            # OUTPUT
            #   --csv             Output CSV instead of TSV (default OFF)
            #   --json [X]        Also write results to this file in JSON format (default '')
            #   --label [X]       Replace FILE with this name instead (default '')
            #   --nopath          Strip filename paths from FILE column (default OFF)
            #   --novel [X]       Save novel alleles to this FASTA file (default '')
            #   --legacy          Use old legacy output with allele header row (requires --scheme) (default OFF)
            # SCORING
            #   --minid [n.n]     DNA %identity of full allelle to consider 'similar' [~] (default '95')
            #   --mincov [n.n]    DNA %cov to report partial allele at all [?] (default '10')
            #   --minscore [n.n]  Minumum score out of 100 to match a scheme (when auto --scheme) (default '50')
            # PATHS
            #   --blastdb [X]     BLAST database
            #   --datadir [X]     PubMLST data
            # HOMEPAGE
            #   https://github.com/tseemann/mlst - Torsten Seemann
            extra="--nopath",
        log:
            "logs/{sample}.mlst.log",
        threads: 1
        wrapper:
            "v3.0.1/bio/mlst"

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
-----

* The `extra` param allows for additional program arguments.
* For more inforamtion see https://github.com/tseemann/mlst

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

* ``mlst=2.23.0``

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

* Genomic assembly (fasta format)

**Output:**

* Returns a tab-separated line containing the filename, matching PubMLST scheme name, ST (sequence type) and the allele IDs. Other output formats are also available (eg. CSV, JSON)




Authors
-------

* Torsten Seeman (mlst tool) - https://github.com/tseemann/mlst
* Max Cummins (Snakemake wrapper [unaffiliated with Torsten Seeman])


Code
----

.. code-block:: python

    __author__ = "Max Cummins"
    __copyright__ = "Copyright 2021, Max Cummins"
    __email__ = "max.l.cummins@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

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

    shell(
        "mlst"
        " {snakemake.params.extra}"
        " {snakemake.input.assembly}"
        " > {snakemake.output.mlst}"
        " {log}"
    )


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