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

[Marc Logghe]

Hi,
What is actually the problem ? Do you have errors ? Is the script not
behaving as you expect ?
You also might attach the input file sample1.txt so that people can try
it.
Regards,
Marc
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> saurabh maheshwari
> Sent: Friday, May 12, 2006 3:56 PM
> To: bioperl-l at bioperl.org; s_maheshwari84
> Subject: [Bioperl-l] problem help me...........please
> 
>   
> 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
>