[Bioperl-l] problems with Bio::Graph::ProteinGraph

Maria Persico maria at cbm.bio.uniroma2.it
Fri Oct 22 03:01:29 EDT 2004

Hi All,

I am experiencing some problems with Bio::Graph::ProteinGraph: this may be
a stupid problem but... sorry, ....I am a beginner:
I did a copy-paste of the synopsis in the
http://doc.bioperl.org/bioperl-live/Bio/Graph/ProteinGraph.html web page

I want to read a dip file that I downloaded from DIP database website.

my script was:

#!/usr/bin/perl -w
use strict;

use Bio::Graph::SimpleGraph;
use Bio::Graph::IO;
use XML::Twig;
my $n1;
my $n2;
my $graphio;
my $graph;
my $gr;
my @seqs;
my $g1;
my $g2;
my $io;
my $out;
### read in from file
    my $graphio = Bio::Graph::IO::dip2->new(-file=>'yeast-dip',
#my $graph   = $graphio->next_network();
    while (my $graph   = $graphio->next_network()){
print $out->write_network($graph);

The message that I receive is:

Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.0/Bio/Graph/IO/dip2.pm line 72, <GEN1> line
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.0/Bio/Graph/IO/dip2.pm line 72, <GEN1> line
Use of uninitialized value in exists at
/usr/lib/perl5/site_perl/5.8.0/Bio/Graph/IO/dip2.pm line 73, <GEN1> line

I copied the module dip.pm in dip2.pm and I put some print for some
of the variables I am interested....the
variables are print out , the error message is the same for each line
of the file that is read and the script ends
Can't call method "write_network" on an undefined value at ./graph.pl line
21, <GEN1> line 15161.

what's the problem???



Maria Persico
MINT database, Cesareni Group
Universita' di Tor Vergata, via della Ricerca Scientifica
00133 Roma, Italy
Tel: +39 0672594315
FAX: +39 0672594766
e-mail: maria at cbm.bio.uniroma2.it

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