Usage - $intact_parser->parse ( $intact_files, $map ) Returns - data structure ( hash reference ) Args - 1. [ IntAct data file paths ( fully qualified )] ( array reference ) 2. { UniProtKB accession => UniProtKB id ( strings )} ( hash reference ) 3. { UniProtKB accession => UniProtKB id ( strings )} ( hash reference ), optional Function - parses IntAct data file and optionally filters it by the map
Usage - $intact_parser->work ( $ontology, $data, $parent_protein_name ) Returns - { NCBI ID => { UP AC => OBO::Core::Term object }} ( data structure with all the proteins in the interactions ) Args - 1. OBO::Core::Ontology object, 2. data structure from parse ( ) 3. parent term name for proteins ( string ) # to link new proteins to, e.g. 'cell cycle protein' Function - adds to the input ontology OBO::Core::Term objects along with appropriate relations for interactions and proteins from IntAct data
OBO::Parser::IntActParser - An IntAct to OBO parser/filter.
A parser for IntAct-to-OBO conversion. The conversion is filtered according to the proteins already existing in the input ontology.
Vladimir Mironov <vladimir.n.mironov@gmail.com>
Copyright ( C ) 2006 by Vladimir Mironov
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 OBO::Util::Set, copy and paste the appropriate command in to your terminal.
cpanm
cpanm OBO::Util::Set
CPAN shell
perl -MCPAN -e shell install OBO::Util::Set
For more information on module installation, please visit the detailed CPAN module installation guide.