[Bioperl-l] Re: load_gff.pl question

[Shin Enomoto]

It was a typo in the configuration file also that was causing the  
script to abort.


On Thursday, August 7, 2003, at 11:07 AM, Scott Cain wrote:

> 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
>
>
Shin Enomoto
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