NAME

Bio::MLST::SequenceType - Take in a list of matched alleles and look up the sequence type from the profile.

VERSION

version 2.1.1706216

SYNOPSIS

Take in a list of matched alleles and look up the sequence type from the profile.

  use Bio::MLST::SequenceType;
  my $st = Bio::MLST::SequenceType->new(
    profiles_filename  => 't/data/Escherichia_coli_1/profiles/escherichia_coli.txt',
    matching_names     => ['adk-2','purA-3','recA-1'],
    non_matching_names => []
  );
  $st->sequence_type();

METHODS

allele_to_number

Maps the allele name to the corresponding locus sequence number.

sequence_type

Returns the sequence type (an integer).

nearest_sequence_type

Returns the nearest matching sequence type if there is no exact match, randomly chosen if there is more than 1 with equal identity.

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007