getmlst1
Download mlst datasets by speciesfrom pubmlst.org.
Usage
getmlst [-h]
[--repository_url
URL]
--species
NAME
[--force_scheme_name]
Overview
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")
Examples
getmlst --species "Escherichia coli#1"
Releases
Unchanged in 5 releases since Debian 9 (Stretch).