getmlst - Download MLST datasets by speciesfrom pubmlst.org.

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

getmlst 0.1.6                                     December 2015                                       GETMLST(1)

       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.

       getmlst --species "Escherichia coli#1"

       getmlst - Download MLST datasets by speciesfrom pubmlst.org.

-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")

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