work

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

NAME

CCO::Parser::NCBIParser - A NCBI taxonomy to OBO translator.

DESCRIPTION

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.

AUTHOR

Mikel Egana Aranguren

http://www.mikeleganaranguren.com

eganaarm@cs.man.ac.uk

COPYRIGHT AND LICENSE

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.

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.

	Global
`s`	Focus search bar
`?`	Bring up this help dialog

	GitHub
`g` `p`	Go to pull requests
`g` `i`	go to github issues (only if github is preferred repository)

	POD
`g` `a`	Go to author
`g` `c`	Go to changes
`g` `i`	Go to issues
`g` `d`	Go to dist
`g` `r`	Go to repository/SCM
`g` `s`	Go to source
`g` `b`	Go to file browse

	Search terms
module: (e.g. module:Plugin)
distribution: (e.g. distribution:Dancer auth)
author: (e.g. author:SONGMU Redis)
version: (e.g. version:1.00)

work

NAME

DESCRIPTION

AUTHOR

COPYRIGHT AND LICENSE

Module Install Instructions