[Bioperl-l] bioperl-network warnings when loading the DIP dataset

Brian Osborne osborne1 at optonline.net
Sun Oct 1 17:49:47 EDT 2006


Florin,

This is fixed in CVS now. What had happened is that the DIP file had some
minimal protein (node) entries where the only id available was DIP's
internal identifier. Not ideal to have to use these as accessions but
there's no other choice.

Thank you for the note, and in the future write to bioperl-l since there may
be others who are interested in hearing about what you've encountered.

Brian O.


On 10/1/06 2:32 PM, "Florin Iucha" <florin at iucha.net> wrote:

> Hello,
> 
> I have downloaded a CVS snapshot [1] of your module, bioperl-network, and
> I am using it to read the 20060402 edition release of the DIP [2] dataset.
> 
> Starting with the simple program you show in the man page:
> 
>    my $io = Bio::Network::IO->new(-format => 'psi',
>                                   -file   => $ARGV[0]);
> 
>    my $network = $io->next_network;
> 
> I get 772 instances of:
> 
>    Use of uninitialized value in string eq at
>    /usr/local/share/perl/5.8.8/Bio/Network/IO/psi.pm line 326.
> 
> I don't know if it is just an annoyance or something bad, so you might
> want to take a look at it.
> 
> Thank you for your work,
> florin
> 
> [1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-network/
> [2] http://dip.doe-mbi.ucla.edu/




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