NAME

       getmlst - Download MLST datasets by speciesfrom pubmlst.org.

SYNOPSIS

       getmlst [-h] [--repository_url URL] --species NAME [--force_scheme_name]

DESCRIPTION

       Download   MLST   datasets   from   this   site:   http://pubmlst.org/data/   by   parsing  an  xml  file
       (http://pubmlst.org/data/dbases.xml).

       Data is downloaded for a species determined by the user:

              - profiles (maps STs to allele numbers)

              - numbered sequences for each locus in the scheme

       In addition, the alleles are concatenated together for use with SRST2.

       A log file is also generated in the working directory, detailing the time, date and location of all files
       downloaded, as well as the <retrieved> tag which tells us when the XML entry was last updated.

       If  the  species  name  input  by  the user matches multiple <species> in the xml file, the script simply
       reports the possible matches so the user can try again.

OPTIONS

       -h, --help
              show this help message and exit

       --repository_url URL
              URL for MLST repository XML index

       --species NAME
              The name of the species that you want to download (e.g. "Escherichia coli")

       --force_scheme_name
              Flage to force downloading of specific scheme name (e.g. "Clostridium difficile")

EXAMPLE

       getmlst --species "Escherichia coli#1"

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.