updatemlst.pl

Written by Keith Jolley
Copyright (c) 2003, University of Oxford

General

This Perl script will set up local Linux PostgreSQL profile databases for publicly available MLST schemes by downloading configurations, allele sequences and allelic profiles from pubmlst.org. Once set up, it contains options to keep the databases up-to-date. You can link the resulting profiles databases to your own isolate database systems. The user running the script must have sufficient permissions to create new databases.

Options

updatemlst.pl has a number of command line options which can be combined:

• s - setup. Run with this option to initially set up the databases. When this option is selected, all other options are ignored. The script will connect to pubmlst.org and download a configuration file describing all the databases available. You will be presented with a menu to choose which database to set up.
• u <dbase code> - update. Run with this option to update a local database that has already been set up.
• q - quiet. Only error messages are displayed. This is useful when running the updates from a cron job.
• f - force. Overwrites the local database without prompting, even when there are discrepancies between the downloaded version and values stored locally. You may want to run with this option if there have been large-scale changes to the primary profiles database or a new clonal complex has been introduced.

Databases currently available

Local databases can be set up automatically by updatemlst.pl for the following schemes (the name of the local database created is in parentheses - this is the database code needed to run with the update option):

• Acinetobacter baumannii (abaumannii_profiles)
• Bacillus cereus (bcereus_profiles)
• Bordetella spp. (bordetella_profiles)
• Burkholderia cepacia complex (bcc_profiles)
• Campylobacter fetus (cfetus_profiles)
• Campylobacter helveticus (chelveticus_profiles)
• Campylobacter jejuni and C. coli (campylobacter_profiles)
• Campylobacter lari (clari_profiles)
• Campylobacter upsaliensis (cupsaliensis_profiles)
• Candida tropicalis (ctropicalis_profiles)
• Helicobacter pylori (helicobacter_profiles)
• Klebsiella pneumoniae (kpneumoniae_profiles)
• Neisseria spp. (neisseria_profiles)
• Porphyromonas gingivalis (pgingivalis_profiles)
• Pseudomonas aeruginosa (paeruginosa_profiles)
• Staphylococcus aureus (saureus_profiles)
• Streptococcus agalactiae (sgalactiae_profiles)
• Streptococcus uberis (suberis_profiles)
• Vibrio vulnificus (vvulnificus_profiles)