Bio::MLST::ProcessFasta - Take in a fasta file, lookup the MLST database and create relevant files.
version 2.1.1706216
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, );
Output the name of the concatinated multifasta file
Output the sequences of the concatinated multifasta file
A row in the output spreadsheet
Bio::MLST::Check
Andrew J. Page <ap13@sanger.ac.uk>
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
To install Bio::MLST::Check, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MLST::Check
CPAN shell
perl -MCPAN -e shell install Bio::MLST::Check
For more information on module installation, please visit the detailed CPAN module installation guide.