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Bio-MLST-Check-2.1.1706216
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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::FilterAlleles
Filter Alleles
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.

Examples

Other files