BulkUploader Question

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BulkUploader Question

Andrew Oberlin
Hi all,

I was wondering how the bulkuploader Perl script acts when it is run twice on the same organism. For instance, if I have used it once to upload the GFF of an organism and then information in the genbank files (and thus the GFF file) changes (i.e. a gene's use is discovered and it changes from the locus tag to having a new name). I was wondering how the bulkuploader would behave if I ran it on the new organism's GFF. Would it delete all the old entries for that organism and replace it with the new? Or does it do minimal changes?

I wish to add information related to the features table and we would not wish to lose this information upon update of the database.

Thanks,

Andrew Oberlin

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Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


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Re: BulkUploader Question

Scott Cain
Hi Andrew,

My recollection (since I haven't done this in a long time) is that the bulk loader assumes that these are new features, and so will create brand new features for everything in the GFF file on the second load.  This means it will give it the same name as the first time, but will "uniquify" the uniquename by appending the feature_id.  The bulk loader does have a delete option, where it will delete the features for a supplied GFF, so you could feed it the original GFF with the --delete option and then load the new GFF after, though you should definitely test how the delete option works in your environment, since I don't think it's been heavily tested (that is, I tested it, but I don't think it gets much real world use).  See the POD for more info on that option.

One alternative you could check out would be Tripal: my recollection is that the GFF loader in Tripal has an "update" option.  That might be overkill for you though.

Scott

On Tue, Oct 30, 2012 at 2:12 PM, Andrew Oberlin <[hidden email]> wrote:
Hi all,

I was wondering how the bulkuploader Perl script acts when it is run twice on the same organism. For instance, if I have used it once to upload the GFF of an organism and then information in the genbank files (and thus the GFF file) changes (i.e. a gene's use is discovered and it changes from the locus tag to having a new name). I was wondering how the bulkuploader would behave if I ran it on the new organism's GFF. Would it delete all the old entries for that organism and replace it with the new? Or does it do minimal changes?

I wish to add information related to the features table and we would not wish to lose this information upon update of the database.

Thanks,

Andrew Oberlin

--
Andrew Oberlin
Miami University 2013
Computer Science & Mathematics
[hidden email]  (330) 998-1603


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_sfd2d_oct
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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