Bio::ConnectDots::ConnectorSet -- 'connect-the-dots'
use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectorSet; my $db=new Bio::ConnectDots::DB(-database=>'test', -host=>'servername', -user=>'username', -password=>'secret'); my $connectorset=new Bio::ConnectDots::ConnectorSet( -name=>'LocusLink', -module=>'LocusLink', -db=>$db, -file=>'LL_tmpl', -dotsets=>['LocusLink','UniGene','Organism', {'PreferedSymbol'=>'Gene Symbol','Alias Symbol'=>'Gene Symbol','Hugo'=>'Gene Name'}] ); $connectorset->load_file;
This class represents a data source, such as LocusLink, that contain connection information for 'connect-the-dots'.
Email dburdick@systemsbiology.org, natg@shore.net
Copyright (c) 2005 Institute for Systems Biology (ISB). All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
The rest of the documentation describes the methods.
Title : new Usage : $connector_set=new Bio::ConnectDots::ConnectorSet( -name=>'LocusLink', -module=>'LocusLink', -db=>$db, -file=>'LL_tmpl', -dotsets=>['LocusLink','UniGene','Organism', {'PreferedSymbol'=>'Gene Symbol','Alias Symbol'=>'Gene Symbol', 'Hugo'=>'Gene Name'}] ); Function: Create ConnectorSet object, typically for parsing and loading a file into the database Args : -name => name of ConnectorSet -module => subclass module to be loaded. The '.pm' for this module must be in a directory Bio/ConnectDots/ConnectorSet beneath one of your PERL5LIBs -db => Bio::ConnectDots::DB object connected to database -file => name of file to be loaded -dotsets => ARRAY of DotSet names or HASH of label=>name. In the first case, ie, if no label is given, the name is used as the label -load_save => controls whether load files are saved after use. Helpful for debugging default - files not saved 'all' -- files are saved 'last' -- only last file is saved -load_chunksize => number of Dots loaded at a time. Tuning parameter. default 100000 The following arguments are set internally: -db_id => database id for ConnectorSet object -saved_file => name of file loaded when object created Returns : Object whose class is a subclass of Bio::ConnectDots::ConnectorSet determined by -module
Title : load_file Usage : $connectorset->load_file; Function: Parse entries and load into database Returns : Nothing Title : parse_file Usage : $connectorset->parse_file; Function: Parse entries into 'instance' objects and store in object Returns : Nothing Title : put_dot Usage : $connectorset->put_dot('Hugo','CASP7') Function: Add a dot to the 'current' Connector. Used in parse_entry methods Args : label of DotSet Dot value, ie, an actual identifier Returns : ARRAY of values for the label
To install Bio::ConnectDots::DB, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ConnectDots::DB
CPAN shell
perl -MCPAN -e shell install Bio::ConnectDots::DB
For more information on module installation, please visit the detailed CPAN module installation guide.