[Bioperl-l] human_small-01.xml file

Brian Osborne bosborne11 at verizon.net
Sat Jan 20 21:46:42 EST 2007


Mikel and Ramona,

I took at look at the human-small-01.xml file that Mikel sent me, from
Intact. The problem is that the PSI MI parser expects to find a field called
proteinInteractorRef for every protein in every file it sees. The file you
sent me has no such field, it looks like they use the field interactorRef
instead. 

Other files from IntAct, like a slightly older 2.5 file bovine_small.xml
that's used in the test suite, do have the proteinInteractorRef field. I'll
need to take a closer look.

Brian O.


On 1/18/07 5:17 AM, "Mikel Egaña Aranguren"
<mikel.eganaaranguren at cs.man.ac.uk> wrote:

> Hi,
> 
> gzipped and attached the xml file
> 
> thanks
> 
> Mikel
> 
> Brian Osborne(e)k dio:
>> 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-0
>>> 1.
>>> 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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>>   
> 





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