gusdev-gusdev

[GUSDEV] Sugestion for the ISF plugin

[Ricardo B. <rb...@gm...>]

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 separat=
e
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 problem=
s
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

Re: [GUSDEV] Sugestion for the ISF plugin

[Steve F. <sfi...@pc...>]

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

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
>

Re: [GUSDEV] Sugestion for the ISF plugin

[Ricardo B. <rb...@gm...>]

Ok Chris,

  We'll see this.

thanks,
Ricardo

On 3/7/06, chris mungall <cj...@fr...> wrote:
>
>
> 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
> >
>
>

Re: [GUSDEV] Sugestion for the ISF plugin

[Steve F. <sfi...@pc...>]

the problem with deploying the increased error threshold as a solution 
in this case is that you have just pushed the problem to the downstream 
processes. 

steve

Ricardo Balbi wrote:

> Ok Chris,
>
>   We'll see this.
>
> thanks,
> Ricardo
>
> On 3/7/06, *chris mungall* <cj...@fr... 
> <mailto:cj...@fr...>> wrote:
>
>
>     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
>     >
>
>