[Bioperl-l] Re: load_gff.pl question

[Scott Cain]

On Wed, 2003-08-06 at 23:52, Shin Enomoto wrote:
> Thank you.
> After a good night's sleep I modified the GFF table  one column at a  
> time and found that (ref, source, method, start, end, gclass, name)  
> mattered. What does fbin come from?

fbin is a value calculated at the time of the load to make searching
ranges faster, it is derived from the start and end values, so any
feature with the same start and end will have the same fbin value.
> 
> I have a different question?
> When I load the following:
> VI_3	nelson	cdna	404988	405465	.	+	.	EST "gi|2099810|"; Note "CpEST.323  
> uniZAPCpIOWAsporoLib3 Cryptosporidium parvum cDNA 5' similar to C.  
> elegans ORF M28.5 and H. sapiens nuclear protein-NHP2-like protein.,  
> mRNA sequence"
> 
> with a
> [EST]
> glyph	      = generic
> 
> in the configuration file.
> gbrowse script fails "glyph genric new not available".
> 
> My work around was either to change the word EST to something else or  
> use another glyph. What do you think is  the conflict?

The '[EST]' part is just the name of the block, and so it shouldn't
cause anything related to glyph drawing to fail.  Could you send the
whole EST configuration block?  (I assume the 'genric' is a typo on your
part, right?)

Thanks,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory