[Bioperl-l] problem help me...........please

[saurabh maheshwari]

hello
I am a studnt at Center for DNA Finger Printing and Diagnostics(CDFD).
I am working on protein protein interaction but I am unable to use the protein interaction module i.e. ProteinGraph.pm..
Actially I am facing lots of problem in the programme I have written Please help me since last four months I am not able to solve the same problem..
I am pasting my programe here also I am attaching it also. ......

#!usr/bin/perl
use lib "/usr/local/bioxapps/bioperl/library/";
use strict;
use Bio::Graph::SimpleGraph;
use Bio::Graph::IO;
our @ISA=qw( Bio::SeqI);
use Bio::Graph::Edge;
use Bio::Graph::IO::dip;
use Bio::Graph::IO::psi_xml;
use Clone qw(clone);
use vars  qw(@ISA);
use Bio::AnnotatableI;
use Bio::IdentifiableI;
our @ISA = qw(Bio::Graph::SimpleGraph);
@ISA = qw(Bio::Graph::IO);
our @ISA=qw(Expoerter);
use Bio::Graph::ProteinGraph;
use Class::AutoClass;
use Bio::Graph::SimpleGraph::Traversal;

my $graphio = Bio::Graph::IO->new(-file   => '/users/saurabh/perl_program/sample1.txt',-format => 'dip');
print "$graphio";
my $graph   = $graphio->next_network();
print "$graph->nodes\t";
$graph->remove_dup_edges();
my @un=$graph->unconnected_nodes();
print "\nthe unconnected nodes are =@un";
my @n=$graph->subgraph();
print "\subgraph=@n\n";
#print "Please the protein-id whose clusering coefficient is to be detemined\n";
#my $v=<STDIN>;
my $density = $graph->density();
print "\ngraph density=$density\n";
my @graphs = $graph->components();
print "\nno of Connected components=$#graphs\n";
print "\nplease enter the protein-id whom you want to remove from the network\n";
my $no=<STDIN>;
$graph->remove_nodes($graph->nodes_by_id($no));
my $count = $graph->edge_count();
print "\nno of edges=$count\n ";
my $ncount = $graph->node_count();
print "\nno of nodes=$ncount\n ";

print"\nenter the protein  whose interactions is to be find "; 
my $x=<STDIN>;
my $node = $graph->nodes_by_id($x);
#print " this is $node\n";
my @neighbors = $graph->neighbors($node); 
print "to check";
print join",",map{$_->object_id()} @neighbors;
my @nodes = $graph->nodes();
print "\nno of nodes = @nodes\t\n";
my @hubs;
foreach my $nodi (@nodes) 
 {
  if ($graph->neighbor_count($node) > 10) 
      {
       push @hubs, $nodi;
      }
  }
  
foreach my $r(@hubs)
  {
     my @y=@$r;
      print "the following proteins have > 10 interactors=@y\n";
  }
  #siblingual protein

 my @edgeref = $graph->articulation_points();
 print "no of articulation points=$#edgeref\n";
 print "please enter the protein whom you want to check for articulation point \n ";
 my $nod=<STDIN>;
  # make pathgen graph
  my $grap = Bio::Graph::IO->new(-file   => 'org.txt',-format => 'dip');
  my $gra   = $grap->next_network();
  $graph->remove_dup_edges();
  $graph->union($gra);
  my @duplicates = $graph->dup_edges();
  print "these interactions exist in cere and c.elegan\n=@duplicates";
  print "please enter the first protein for identifiaction of shortest path\n";
  my $p1=<STDIN>;
  print "please enter the second  protein for identifiaction of shortest path\n";
  my $p2=<STDIN>;
  
    my @a=$graph->shortest_paths();
 print "shortest path=@a\t\n";
    
  

with Regards
SAURABH MAHESHWARI
M.Sc. (BIOINFORMATICS)
JAMIA MILLIA ISLAMIA
NEW DELHI
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