GFF3 loader bugs

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GFF3 loader bugs

Scott Cain
Hi Stephen,

I just wanted to point out a few bugs:

1. When loading data into featureloc, the default rank should be 0, not 1.  You only get into ranks > 0 when storing alignment data.  This is a fairly big deal, as it breaks GBrowse with rank = 1 (GBrowse assumes it should ignore those because they are not on the "main" srcfeature, since their ranks are not 0).

2. When loading values from the ninth column, they should be URI-unescaped first.  I just loaded some data from SGD and they still URI escape the spaces in their values (which was originally required in the spec), and I get something like this when I look at the feature in Tripal:

  display     Protein%20that%20forms%20a%20heterotrimeric%20complex%20with%20Erp2p

Thanks,
Scott


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

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Re: GFF3 loader bugs

Stephen Ficklin-2
Hi Scott,

Thanks for pointing out the bugs!  I'll try to get this fixed in SVN for you as soon as I can.  It shouldn't be too hard to fix either of these.

Stephen

On 10/20/2011 4:00 PM, Scott Cain wrote:
Hi Stephen,

I just wanted to point out a few bugs:

1. When loading data into featureloc, the default rank should be 0, not 1.  You only get into ranks > 0 when storing alignment data.  This is a fairly big deal, as it breaks GBrowse with rank = 1 (GBrowse assumes it should ignore those because they are not on the "main" srcfeature, since their ranks are not 0).

2. When loading values from the ninth column, they should be URI-unescaped first.  I just loaded some data from SGD and they still URI escape the spaces in their values (which was originally required in the spec), and I get something like this when I look at the feature in Tripal:

  display     Protein%20that%20forms%20a%20heterotrimeric%20complex%20with%20Erp2p

Thanks,
Scott


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


------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn 
about Cisco certifications, training, and career opportunities. 
http://p.sf.net/sfu/cisco-dev2dev


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The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
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