[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 13:12:41 EST 2007


Ramona,

The current tests read bovin_small_intact.xml and sv40_small.xml
successfully, both IntAct PSI files, but I don't recall ever testing
human_small-07.xml. Can you send me this file? Don't send it to bioperl-l
though.

Brian O.


On 1/17/07 9:33 AM, "magnusgeist" <ramona.schmid at freenet.de> wrote:

> 
> 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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