CCO::Parser::NCBIParser - A NCBI taxonomy to OBO translator.
This parser converts chosen parts of the NCBI taxonomy-tree into an OBO file. Some taxa are given to the parser and the whole tree till the root is reconstructed in a given OBO ontology, using scientific names.
The dump files (nodes.dmp and names.dmp) should be obtained from:
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
TODO: include ranks and disjoints only in correlating ranks.
Mikel Egana Aranguren
http://www.mikeleganaranguren.com
eganaarm@cs.man.ac.uk
Copyright (C) 2006 by Mikel Egana Aranguren
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.
Usage - $NCBIParser->work() Returns - the parsed OBO ontology Args - old OBO file, new OBO file, cco ids file, nodes dump file, names dump file, taxon 1, taxon 2, ... Function - converts NCBI taxonomy into an OBO file
To install CCO::Util::Set, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CCO::Util::Set
CPAN shell
perl -MCPAN -e shell install CCO::Util::Set
For more information on module installation, please visit the detailed CPAN module installation guide.