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.