---
name: "getmlst"
section: "1"
platform: "linux"
package: "srst2"
version: "0.2.0-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getmlst"
---

# getmlst(1)

Download MLST datasets by speciesfrom pubmlst.org.

## 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.