Modules
Run blast and find the top hit
Take in a fasta file and create a tempory blast database
Take in an assembly file in Fasta format, and a list of allele files (in multifasta format) and return a list of the alleles and IDs.
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
Take in a Fasta file, check for invalid characters and build a corrected file if needed. This is needed for NCBI makeblastdb which doesnt like the pipe character in the sequence name
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 row representation of the ST results for a single fasta file.
Create a row representation of the ST results for a single fasta file.
Validates the executable is available in the path before running it
Does a file exist?
Provides
in lib/Bio/MLST/Exceptions.pm
in lib/Bio/MLST/Types.pm