22 results (0.104 seconds)
Andrew Page
Modules
Bio::MLST::Blast::BlastN - Run blast and find the top hit
Bio::MLST::Blast::Database - Take in a fasta file and create a tempory blast database
Bio::MLST::CompareAlleles - 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.
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::NormaliseFasta - 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
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 row representation of the ST results for a single fasta file.
Bio::MLST::Spreadsheet::Row - Create a row representation of the ST results for a single fasta file.
Bio::MLST::Validate::Executable - Validates the executable is available in the path before running it
Bio::MLST::Validate::File - Does a file exist?
Provides
Bio::MLST::Exceptions in lib/Bio/MLST/Exceptions.pm
Bio::MLST::Types in lib/Bio/MLST/Types.pm



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