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.