NAME
Bio::MLST::ProcessFasta - Take in a fasta file, lookup the MLST database and create relevant files.
VERSION
version 2.1.1706216
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
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