NAME

Bio::MLST::CheckMultipleSpecies - High throughput multilocus sequence typing (MLST) checking against several MLST databases.

VERSION

version 2.1.1706216

SYNOPSIS

This is a wrapper for the Bio::MLST::Check module allowing MLST checking against several databases.

The Bio::MLST::Check options to output a concatenated fasta file of allele matches or to output a phylip alignment file are not supported as the loci for sequence typing will vary between species. Including these options will give an error message requesting that the user refine their search.

   use Bio::MLST::CheckMultipleSpecies;
   
   my @fasta_files  = ('isolate_one.fa', 'isolate_two.fa');
   my @species_list = ('Clostridium diff', 'Streptococcus');
   
   my $mlst = Bio::MLST::CheckMultipleSpecies->new( species               => \@species_list,
                                                    raw_input_fasta_files => \@fasta_files,
                                                    spreadsheet_basename  => $spreadsheet_basename,
                                                    output_directory      => $output_directory,
                                                    base_directory        => $base_directory,
                                                    makeblastdb_exec      => $makeblastdb_exec,
                                                    blastn_exec           => $blastn_exec,
                                                    parallel_processes    => $parallel_processes,
                                                    verbose               => 0,);
   $multiple_species->create_result_files;

METHODS

create_result_files

Creates a spreadsheet of results.

SEE ALSO

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