NAME

Bio::MLST::CompareAlleles - Get a list of matching alleles between the sequence and database

VERSION

version 2.0.1510612

SYNOPSIS

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.

use Bio::MLST::CompareAlleles;

my $compare_alleles = Bio::MLST::CompareAlleles->new(

  sequence_filename => 'contigs.fa',
  allele_filenames => ['abc.tfa','efg.tfa']
);
$compare_alleles->found_sequence_names;
$compare_alleles->found_non_matching_sequence_names
$compare_alleles->matching_sequences;
$compare_alleles->non_matching_sequences

METHODS

found_sequence_names

Return a list of the sequence names which match.

found_non_matching_sequence_names

Return a list of the sequence names which dont match.

matching_sequences

Return a Hash containing the sequnces that match.

non_matching_sequences

Return a Hash containing the sequnces that dont match.

contamination

Flag which is set if more than one 100% match is found for a single locus.

new_st

Flag which is set if the results contain a novel combination of sequences or a new sequence.

SEE ALSO

• Bio::MLST::Check

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