NAME

Bio::MLST::ProcessFasta - Take in a fasta file, lookup the MLST database and create relevant files.

VERSION

version 2.1.1630910

SYNOPSIS

Take in a fasta file, lookup the MLST database and create relevant files.

use Bio::MLST::ProcessFasta;
Bio::MLST::ProcessFasta->new(
  'species'           => 'E.coli',
  'base_directory'    => '/path/to/dir',
  'fasta_file'        => 'myfasta.fa',
  'makeblastdb_exec'  => 'makeblastdb',
  'blastn_exec'       => 'blastn',
  'output_directory'  => '/path/to/output',
  'output_fasta_files'=> 1,
);

METHODS

concat_name

Output the name of the concatinated multifasta file

concat_sequence

Output the sequences of the concatinated multifasta file

_spreadsheet_row_obj

A row in the output spreadsheet

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