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Andrew Page
Documentation
download_mlst_databases - Downloads all the MLST databases to disk. It requires access to the Internet.
download_mlst_databases - Downloads all the MLST databases to disk. It requires access to the Internet.
get_emm_sequence_type - Given an assembly find the MLST sequence type of the emm gene from the CDC.
get_sequence_type - Given an assembly find the MLST sequence type.
Modules
Bio::MLST::Blast::BlastN - Wrapper around NCBI BlastN
Bio::MLST::Blast::Database - Wrapper around NCBIs makeblastdb command
Bio::MLST::CDC::Convert - Take in a fasta file of emmST sequences and convert it into an MLST format
Bio::MLST::Check - Multilocus sequence type checking using blast
Bio::MLST::CheckMultipleSpecies - High throughput multilocus sequence typing (MLST) checking against several MLST databases.
Bio::MLST::CompareAlleles - Get a list of matching alleles between the sequence and database
Bio::MLST::DatabaseSettings - Read in an XML file of settings and return a hash with the values.
Bio::MLST::Databases - List available MLST databases
Bio::MLST::Download::Database - Represents a single genus-species database on a single species
Bio::MLST::Download::Databases - Represents multiple databases of species
Bio::MLST::Download::Downloadable - Moose Role to download everything data
Bio::MLST::NormaliseFasta - Take in a Fasta file, check for invalid characters and build a corrected file if needed.
Bio::MLST::OutputFasta - Take in two hashes, both containing sequence names and sequences and output fasta files.
Bio::MLST::ProcessFasta - Take in a fasta file, lookup the MLST database and create relevant files.
Bio::MLST::SearchForFiles - Take in a species name and get the allele and profile files.
Bio::MLST::SequenceType - Take in a list of matched alleles and look up the sequence type from the profile.
Bio::MLST::Spreadsheet::File - Create a file representation of the ST results for multiple fasta files.
Bio::MLST::Spreadsheet::Row - Create a row representation of the ST results for a single fasta file.
Bio::MLST::Types - Moose types to use for validation.
Bio::MLST::Validate::Executable - Validates the executable is available in the path before running it.
Bio::MLST::Validate::File - Check to see if a file exists. For validation when classes have input files.
Bio::MLST::Validate::Resource - 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.



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