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

Brian Osborne bosborne11 at verizon.net
Sun Jan 21 17:52:18 EST 2007


Mikel,

Currently only nodes have annotations, the interactions do not have
annotations. See the latest psi.pm, it explains what the nodes and
interactions contain.

Brian O.


On 1/21/07 10:26 AM, "Mikel Egaña Aranguren"
<mikel.eganaaranguren at cs.man.ac.uk> wrote:

> 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
>>>   
>>>     
>> 
>> 
>>   
> 





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