Re: [GUSDEV] Sugestion for the ISF plugin

[chris m. <cj...@fr...>]

You can increase the threshold at which the severity of a problem 
causes the unflattener to throw an error.

$unf->error_threshold(2);  # do not throw for problems of severity <2

see the docs for more details

The policy here is up to you. As we discovered the last time this came 
up, this particular genbank record has an inconsistency. It's up to you 
whether you want to load the exons from this file, or if you would 
prefer to reject the entire record



On Mar 7, 2006, at 10:36 AM, Steve Fischer wrote:

> in this case, i am not sure this is possible.  the problem is during 
> the bioperl parsing.   if you would like to do the work to investigate 
> whether the bioperl parser (and the unflattener) have options for 
> this, that would be a first step.
>
> steve
>
> Ricardo Balbi wrote:
>
>> Hi all,
>>
>>   Ahead of all the problems that we are facing to load a GenBank file 
>> using the InsertSequenceFeatures (we thougth in coming back to use 
>> the GBParser), we have one sugestion:
>>   Maybe modify the ISF to separate the GIs that present problems in 
>> separate files, as GBParser does, not interrupting the execution.  We 
>> believe that this could help solve many of the problems that we are 
>> finding (and I believe that other groups too) and would very easy to 
>> correct these problems without interrupting the work that we are 
>> carrying at the moment.   We believe that with this modification, the 
>> ISF would become much more flexible and easy to work.
>>
>> thanks in advance,
>> Ricardo
>