[Bioperl-l] error reading psi 2.5 file from intact using bioperl-network-1.5.2_100

Brian Osborne bosborne11 at verizon.net
Wed Jan 17 13:14:02 EST 2007


Mikel,

Please send me human_small-01.xml, I'll take a look.

Brian O.


On 1/17/07 11:37 AM, "Mikel Egaña Aranguren"
<mikel.eganaaranguren at cs.man.ac.uk> wrote:

> 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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