Andrew Page > Bio-MLST-Check

Bio-MLST-Check

This Release Bio-MLST-Check-1.133090  [Download] [Browse 05 Nov 2013
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Repository https://github.com/sanger-pathogens/mlst_check.git
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License The GNU General Public License, Version not specified
Special Files
INSTALL
LICENSE
Makefile.PL
MANIFEST
META.yml
README

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.      

Documentation

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.  

Other Files

README.md