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

[Hilmar Lapp]

After looking at Chris' fix, it appears to be wrong: it would set 
the sublocs' strand to -1. The problem lies elsewhere, I'm going to 
revoke that fix.

	-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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