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

[Hilmar Lapp]

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
-------------------------------------------------------------