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Bio_MLST_check-1.122350-TRIAL
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Documentation

download_mlst_databases
get_sequence_type

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::Check
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::Download::Downloadable
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

Other files