[Bioperl-l] Another error reading psi 1 file from intact using bioperl-network-1.5.2_100

Mikel Egaña Aranguren mikel.eganaaranguren at cs.man.ac.uk
Sun Jan 21 10:26:43 EST 2007


Hello;

I'm trying to get some annotations from the interactions of an intact 
file (in psi 1, otherwise won't parse as it has already been commented 
in this list).

The file I'm using is:
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi1/species/schpo_small.xml

I'm interested in the name of each interaction (e.g. 
<shortLabel>spc7_mal2_1</shortLabel>), and I try to get it doing the 
following:

    for my $interaction ($network->interactions){
        my $ac = $interaction->annotation;
        print "--- ANNOTATIONS\n";
        print $ac->get_num_of_annotations(),"\n";
        foreach my $key ( $ac->get_all_annotation_keys() ) {
                my @values = $ac->get_Annotations($key);
                foreach my $value ( @values ) {
                        print "Annotation ",$key," stringified value 
",$value->as_text,"\n";
            }
    }

And the number of annotations is 0, even though I'm sure it works as I 
can access the nodes (the proteins). Is this a bug or am I doing 
something wrong?

thanks a lot

regards


Mikel Egaña Aranguren(e)k dio:
> Hello everyone;
>
> I get exactly the same error when parsing the intact file from
> ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/species/human_small-01.xml
>
> and I was about to send an email; help would be much appreciated.
>
> thanks a lot
>
> Mikel
>
>
> magnusgeist(e)k dio:
>   
>> dear all,
>>
>> trying to read files in psi 2.5 format from intact like this:
>>
>> my $io = Bio::Network::IO->new(-format => 'psi',
>>                                                     -source => 'intact',
>>                                                     -file   =>
>> 'human_small-07.xml');
>>
>> 		my $graph = $io->next_network;
>>
>> returns the following error: Can't call method "att" on an undefined value
>> at /vol/pi/lib/perl-5.8.0/Bio/Network/IO/psi.pm line 396.
>>
>> doing the same with files from dip:
>>
>> my $io = Bio::Network::IO->new(	-format => 'psi',
>>                              	-file   => 'Hsapi20070107.mif');
>> 				
>> my $graph = $io->next_network;	
>>
>> does not result in any problems.
>>
>> would be great if one of you could help!
>> thank you very much in advance.
>> magnusgeist
>>   
>>     
>
>
>   


-- 

Mikel Egaña Aranguren - http://www.mikeleganaaranguren.com

PhD student - Manchester University Computer Science

Cell Cycle Ontology
	http://www.cellcycleontology.org

Gene Ontology Next Generation 
	http://www.gong.manchester.ac.uk

Metabolik BioHacklab
	http://www.sindominio.net/metabolik/weblog

X-Evian
	http://x-evian.org/


	



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