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

Mikel Egaña Aranguren mikel.eganaaranguren at cs.man.ac.uk
Wed Jan 17 11:37:35 EST 2007


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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