Re: [Gmod-schema] no parent error

[Dino I. <ie...@di...>]

Hi Scott,
	my problem is the follows:
	I need to load 121 gff files in a chado DB.
	This files represent 44 different organism.
	I'm trying to load this file in the db with the perl program:  
gmod_bulk_load_gff3.pl
	Before I sort the file with the option indicate on the gmod site.
	It is very strange because if I change the order in which I load the  
data file, this change also the error.
	All the errors are about "no parent", but I check the files manually  
and I find the ID definition reported in the error.
	Then I try this solution
		for a fixed file that I need to load before I delete it with the -- 
delete option then I load it with the --recreation_cache option
	In this way I have less errors.

	How can I do to load all the files without these errors?
	If I have different gff files for the same organism, Is it possible  
that these files interact each other in the load process?
	Is it possible that the same feature for an organism is present in  
different gff files?

All the best

Dino	


On May 12, 2010, at 4:38 AM, Scott Cain wrote:

> Hi Dino,
>
> I don't know.  It is unlikely to get worse at any rate.  If you wanted
> to send an accession, we could try it to, to see what is going wrong.
>
> Scott
>
>
> On Tue, May 11, 2010 at 6:14 PM, Dino Ienco <ie...@di...> wrote:
>>
>> Hi Scott,
>>        thanks for the answer.
>> I have the Bioperl 1.006 version.
>> Is a prokaryotic data but I don't know if it is circular.
>> Do you think that If I change the BioPerl version the error  
>> disappear?
>>
>> All the best
>>
>> Dino
>>
>>
>> On May 11, 2010, at 4:30 PM, Scott Cain wrote:
>>
>>> Hi Dino,
>>>
>>> There is a problem with the file you are using and it isn't  
>>> generating
>>> the parent lines that have ID=acnA and ID=Bmul_6163.  What version  
>>> of
>>> bioperl are you using?  Can you send a sample of the generated GFF  
>>> to
>>> the mailing list?  Is this prokaryotic data with a circular genome?
>>> There were some modifications to the genbank2gff3 script a few month
>>> ago that might help.  Try getting an anonymous checkout of
>>> bioperl-live:
>>>
>>>  http://github.com/bioperl/bioperl-live/archives/master
>>>
>>> Scott
>>>
>>>
>>> On Tue, May 11, 2010 at 10:21 AM, Dino Ienco <ie...@di...>  
>>> wrote:
>>>>
>>>> Hi guys,
>>>>       I continue with my error.
>>>> When I load gff3 files I have
>>>>       no parent error.
>>>>
>>>> How can I deal with this error?
>>>> some of the error are the following:
>>>>       no parent acnA;
>>>>       no parent Bmul_6163;
>>>>
>>>>
>>>> Is there a way to insert the corresponding gff file?
>>>>
>>>> Best regards
>>>>
>>>> Dino
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at  
>>> scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research