[Bioperl-l] module for unflattening GenBank/EMBL/DDBJ records

[Hilmar Lapp]

On Wednesday, June 18, 2003, at 09:37  AM, Chris Mungall wrote:

>>>
>>> It is called Bio::Tools::GenBankCollector - is this the correct 
>>> namespace?
>>> good name?
>>
>> Bio::Tools::GenBankFeatureCollector ???
>
> now's the time for a name change if required
>
> the idea is that it 'collects' features together, into groups then
> hierarchies.
>
> perhaps 'GenBank' should be removed form the name; though i think the
> primary use will be GenBank/EMBL/DDBJ sourced data
>
> Bio::Tools::Unflattener
> Bio::Tools::HierarchyBuilder
> Bio::Tools::NestedFeatureBuilder
>

Is this related to the ideas behind Lincoln's aggregators? Yes? Please?

what about <...>::FeatureGraphBuilder?

I'd actually put it into the Bio::SeqFeature namespace. Bio::Tools is 
for when you're parsing somebody's output.


> ?
>
>>>
>>> Should I commit this? Main trunk or branch?
>>>
>>
>> Main trunk.
>

Right.

> ok
>
>>> What is an acceptable size for a t/data file? Is ~400kb fine? 
>>> Presumably I
>>> should do a "cvs add -kb" (it is a genbank record).
>>>
>>
>> Fine.
>

Actually I've seen my cvs (on Mac OSX) crash numerous times on large 
binary files of that size. You have to restart and then it passes, but 
sort of annoying. Is it possible to compress it and then read it piped 
through gunzip?

	-hilmar

> ok
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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