Bio::Network::Node - describe a Node, either a protein or protein complex
use Bio::Network::Node; my $node = Bio::Network::Node->new(-protein => [($seq1,$seq2)]); # or get nodes from a network: my @nodes = $graph->nodes; for my $node (@nodes) { my @proteins = $node->proteins for my $protein (@proteins) { print "Sequence is ", $protein->seq; } }
This class describes nodes in a network of interactions. A node is either a protein, a Sequence object, or a protein complex, which is a collection of Sequence objects.
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Brian Osborne bosborne at alum.mit.edu
Maintained by Brian Osborne
Name : new Purpose : Constructor for an Node object Usage : my $node = Bio::Network::Node->new(-protein => $seqobj) or my $node = Bio::Network::Node->new(-protein => [($seqobj1,$seqobj2)]) or my $node = Bio::Network::Node->new(-protein => [ [(2, $seqobj1)], [(1, $seqobj2)], [(3, $seqobj3)] ]; Returns : A new Bio::Network::Node object Arguments : -protein => 1 Sequence object or -protein => Reference to an array containing 1 or more Sequence objects or -protein => Reference to an array of arrays where the elements are arrays containing a number denoting the number of subunits of a protein in the protein complex and a Sequence object Notes :
Name : proteins Purpose : Get the proteins in a Node or get a count of proteins in the Node Usage : my $count = $node->proteins or my @proteins = $node->proteins Returns : Gets an array of Sequence objects or a count of the number of Sequence objects Arguments : None
Name : Purpose : Usage : Returns : Arguments :
Name : is_complex Purpose : Get or set whether a node is a protein or a protein complex Usage : if ($node->is_complex){ ... } or $node->is_complex(1) Returns : 1 if the Node has more than 1 proteins, 0 if not Arguments : None
Name : subunit_number Purpose : Get or set the number of a given protein in a protein complex. Usage : $num = $node->subunit_number($protein) or $node->subunit_number($protein,$number) Returns : A number, whether get or set Arguments : None or a Sequence object in a given Node
To install Bio::Network::IO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Network::IO
CPAN shell
perl -MCPAN -e shell install Bio::Network::IO
For more information on module installation, please visit the detailed CPAN module installation guide.