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

[Jason Stajich]

Answer is there is a small bit of code in Bio::Location::Split that was
commented out because of a reported bug 1074, I cannot remember why now.
But that is what is breaking - the parsing is doing the job correctly
AFAIK but the only problem is the writing out of the file.  So in fact all
of Elia's db loads were working correctly.  So Chris we'll need to undo
your changes, and uncomment out the section in Split.pm.  Hilmar or I will
do this.

A little more discussion before jumping to changes for a module that a lot
of people use is a good idea here.

-jason


On Wed, 7 Aug 2002, 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
> -------------------------------------------------------------
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu