feature tag

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feature tag

Sofia Robb
Hi,

I am trying to use the feature tag and am having a little problem.  If I
use the following format in my gff that is bulkloaded:

Contig_6_12849_1        NCBI_blastx:proteinMatch2GFF.pl protein_match  
9880    10557   3e-60   +       0      
ID=Protein:CAG09381;Target=CAG09381+547+750

I get this error:

BD::Pg::db commit failed: ERROR:  insert or update on table "featureloc"
violates foreign key constraint "featureloc_feature_id_fkey"
DETAIL:  Key (feature_id)=(1593) is not present in table "feature".
commit failed: ERROR:  insert or update on table "featureloc" violates
foreign key constraint "featureloc_feature_id_fkey"
DETAIL:  Key (feature_id)=(1593) is not present in table "feature".    

this feature_id does not exist, and I cannot determine why it is being
queried.

if I use this format in my gff:

Contig_6_12849_1        NCBI_blastx:proteinMatch2GFF.pl protein_match  
9880    10557   3e-60   .       .      
ID=Protein:CAG09381;Target=CAG09381 547 750 +

I get the following error:

Can't locate object method "value" via package "Bio::Annotation::Target"
at /usr/bin/gmod_bulk_load_gff3.pl line 1104, <GEN0> line 8.      

Any ideas?

-Sofia


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Re: feature tag

Scott Cain-2
Hi Sofia,

Is there a GFF line that identifies what Contig_6_12849_1 is?  Like:

Contig_6_12849_1 . contig 1 <seqlen> . . . ID=Contig_6_12849_1

or is there a feature in the database already that has Contig_6_12849_1
as a uniquename?

That is probably the problem.

Scott


On Mon, 2006-02-27 at 10:27 -0700, Sofia Robb wrote:

> Hi,
>
> I am trying to use the feature tag and am having a little problem.  If I
> use the following format in my gff that is bulkloaded:
>
> Contig_6_12849_1        NCBI_blastx:proteinMatch2GFF.pl protein_match  
> 9880    10557   3e-60   +       0      
> ID=Protein:CAG09381;Target=CAG09381+547+750
>
> I get this error:
>
> BD::Pg::db commit failed: ERROR:  insert or update on table "featureloc"
> violates foreign key constraint "featureloc_feature_id_fkey"
> DETAIL:  Key (feature_id)=(1593) is not present in table "feature".
> commit failed: ERROR:  insert or update on table "featureloc" violates
> foreign key constraint "featureloc_feature_id_fkey"
> DETAIL:  Key (feature_id)=(1593) is not present in table "feature".    
>
> this feature_id does not exist, and I cannot determine why it is being
> queried.
>
> if I use this format in my gff:
>
> Contig_6_12849_1        NCBI_blastx:proteinMatch2GFF.pl protein_match  
> 9880    10557   3e-60   .       .      
> ID=Protein:CAG09381;Target=CAG09381 547 750 +
>
> I get the following error:
>
> Can't locate object method "value" via package "Bio::Annotation::Target"
> at /usr/bin/gmod_bulk_load_gff3.pl line 1104, <GEN0> line 8.      
>
> Any ideas?
>
> -Sofia
>
>
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> that extends applications into web and mobile media. Attend the live webcast
> and join the prime developer group breaking into this new coding territory!
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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