Documentation
Downloads all the MLST databases to disk. It requires access to the Internet.
Downloads all the MLST databases to disk. It requires access to the Internet.
Given an assembly find the MLST sequence type of the emm gene from the CDC.
Given an assembly find the MLST sequence type.
Modules
Wrapper around NCBI BlastN
Wrapper around NCBIs makeblastdb command
Take in a fasta file of emmST sequences and convert it into an MLST format
Multilocus sequence type checking using blast
High throughput multilocus sequence typing (MLST) checking against several MLST databases.
Get a list of matching alleles between the sequence and database
Read in an XML file of settings and return a hash with the values.
List available MLST databases
Represents a single genus-species database on a single species
Represents multiple databases of species
Moose Role to download everything data
Take in a Fasta file, check for invalid characters and build a corrected file if needed.
Take in two hashes, both containing sequence names and sequences and output fasta files.
Take in a fasta file, lookup the MLST database and create relevant files.
Take in a species name and get the allele and profile files.
Take in a list of matched alleles and look up the sequence type from the profile.
Create a file representation of the ST results for multiple fasta files.
Create a row representation of the ST results for a single fasta file.
Moose types to use for validation.
Validates the executable is available in the path before running it.
Check to see if a file exists. For validation when classes have input files.
Check to see if a file exists or if a uri is valid. For validation when classes have input files which may be local or on the web.