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getmlst - Download MLST datasets by speciesfrom

GETMLST(1) User Commands GETMLST(1)


getmlst - Download MLST datasets by speciesfrom


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


Download MLST datasets from this site: by parsing an xml file (
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.


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


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.
December 2015 getmlst 0.1.6