Bioperl: Re: Bioperl-guts: Notification: incoming/236

[Ewan Birney]

[cc'ing this back to bioperl list]

> 
> Hi,
> 
> I've just installed bioperl and tried to step through the example script
> simplealign.pl; however, it doesn't work because the function
> sort_alphabetically messes up the object.  There seems to be a
> discrepancy over whether whether seq ids are stored internally as
> GBP2_YEAST-124-193 or GBP2_YEAST/124-193.


Hmmm. Ok something to look up.

> 
> In general, I'm curious whether this module is being actively worked on
> (and will soon become cooler), or if it's waiting around as a low
> priority.  I've been following the vsns-bcd-perl list for a while and
> haven't noticed it mentioned.


Alignments are officially 'challenging'. I have not seen a decent object
model for them every - I have had about 4/5 aborted attempts at decent
object models for alignments (my piece de resistance was the OMG BSA
alignment object which was pretty close to my ideal alignment object but
sadly only understandable by me and michele. I'm not sure if michele
agrees with this or not either!).

Alignment objects are waiting for someone to take them over and make them
work nicely. Feel free to do this yourself if you like. If anyone else
wants to give them a stab, let me know. 


It is certainly something I'd like to see a good, motivated person work
on.


> 
> thanks,
> -Lisa
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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