[Bioperl-l] *major* error in genbank parser or am i just insane?

[Hilmar Lapp]

Just a remark in addition, judged from looking at the code, I'm 
pretty sure we do not handle the difference between the two examples 
below ...

Anyone who feels up to it is welcome to fix this ... but FTHelper.pm 
may be too intimidating ... Generally, genbank/embl parsing needs a 
complete overhaul as we all know. Volunteers wholeheartedly welcome.

	-hilmar

On Wednesday, August 7, 2002, at 10:10  AM, Hilmar Lapp wrote:

> I have no idea what the present status on that is, but my reply was 
> generally not about a long-term/high-level/design/it would
> be much better if/ discussion. I basically asked the question what 
> complement(join(1..100,201..300)) exactly means, and whether it has 
> been decided how exactly it shall be translated into strand() 
> attributes of the parent and sub-locations. This hasn't been 
> answered yet ...
>
> Quoting from the FT definition:
>
> complement(join(2691..4571,4918..5163))
>                           Joins regions 2691 to 4571 and 4918 to 
> 5163, then 
>                           complements the joined segments (the 
> feature is 
>                           on the strand complementary to the 
> presented strand)
>  
> join(complement(4918..5163),complement(2691..4571))
>                           Complements regions 4918 to 5163 and 2691 
> to 4571, then 
>                           joins the complemented segments (the 
> feature is 
>                           on the strand complementary to the 
> presented strand)
>
> The case in question is the first example. To translate this 
> properly to Bioperl locations, this means the parent SplitLoc is 
> strand -1, whereas the subs are strand +1. Right?
>
> 	-hilmar
>
>
> On Tuesday, August 6, 2002, at 10:24  PM, Chris Mungall wrote:
>
>> ok, committed - it seems to have had some weird knock on effect 
>> breaking
>> other tests - i can uncommit if this is bad
>>
>> On Wed, 7 Aug 2002, Elia Stupka wrote:
>>
>>>> we need a short term fix for the standard situation even more - 
>>>> shall i
>>>> commit my chnange or will this mess things up more?
>>>
>>> Please commit it, I cannot stand when long-term/high-
>>> level/design/it would
>>> be much better if/ discussions get in the way of production
>>> improvement fixes.
>>>
>>> Once it's committed I can set off a script for the diffing of in/out
>>> genbank so you can be comfortable that it's not screwing up the 
>>> rest of
>>> genkank parsing ;)
>>>
>>> Elia
>>>
>>> ********************************
>>> * http://www.fugu-sg.org/~elia *
>>> * tel:    +65 6874 1467        *
>>> * mobile: +65 9030 7613        *
>>> * fax:    +65 6777 0402        *
>>> ********************************
>>>
>>>
>>>
>>
>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
--
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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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