getmlst - Download MLST datasets by speciesfrom pubmlst.org.
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
- -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.
- Flage to force downloading of specific scheme name (e.g.
getmlst --species "Escherichia coli#1"
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.