[Gmod-help] deleting features via gff file

[Scott Cain]

Hi Anne,

It is possible to delete by GFF file, if you provide a --delete flag  
to the gmod_bulk_load_gff3.pl script.  While I tested it at the time I  
wrote it (a few years ago), I haven't tested much since, so definitely  
make a back up of the database before you do anything.  Also, it is  
slow relative to SQL commands issued in the database, so if there is a  
lot of data to delete, you might want to figure out if there is a SQL  
command you can issue to delete the features.

As for deletes in general, the database is designed with cascading  
deletes on most tables.  That is, if you delete a row in the feature  
table, the rows that refer to it in the featureloc, featureprop,  
feature_dbxref, etc will be deleted as well.

Scott


On Oct 27, 2009, at 1:25 PM, Anne Descour wrote:

> Hello,
>
> I've been told I can delete features previously loaded to a chado  
> database by using the gmod_bulk_load_gff3.pl script with the  
> original gff file used for loading. However this page:
>
> http://gmod.org/wiki/Chado_Update_via_GFF
>
> suggests that this capability was only on a wish list. If there is  
> not an existing delete script, I presume I can just delete by name  
> from the feature table. Might the bulk_load influence any other  
> tables besides the feature table?  Thanks,
>
> Anne
>
> ------------------------------------------------------------
> Anne Descour
> AGCoL (Arizona Genomics Computational Laboratory)
> BIO5 Institute
>
> Email:  anne at agcol.arizona.edu  http://www.agcol.arizona.edu
> Phone:  (520) 626-9598  FAX: (520) 626-4824
> Mail:   Thomas W. Keating Bioresearch Building        1657 E. Helen  
> Street
>       University of Arizona, Tucson AZ 85721
>

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research