[Bioperl-l] Proposal for bio-perl updates: ACE assembly file

Jordan Swanson jswanson at iastate.edu
Thu Mar 10 14:03:39 EST 2005

On Thursday 10 March 2005 07:48 am, Fernan Aguero wrote:
> +----[ Elia Stupka <elia at tigem.it> (01.Mar.2005 10:17):
> | Hi Jordan,
> |
> | I have been doing some work on Contig::Assembly myself recently, and
> | have also been in touch with the author (Robson) about it. Perhaps the
> | best thing would be for the three of us to have a chat about this
> | object, try to revamp it a little with our improvements, and then
> | Robson or I can check it in?
> |
> | regards,
> |
> | Elia
> +----]
> Hi!
> We have just got a need to produce .ace files and noticed
> that this functionality was lacking.
> I also saw the recent thread about this topic on the list.
> Question: has this moved forward since the last message was
> posted (March 1st)?
> If so, are the  proposed changes in a form that can be
> applied and tested by others (a recursive diff, perhaps
> against a recent CVS checkout or against the 1.5-release)

I sent a copy of the code I have written to Elia and Robson.  Robson mentioned 
that he was extremely busy this month, and that he would be willing to 
discuss it at a later time.  Later today, I can send you a zipped up file (my 
diff-skills are non-existant, so I can't do it that way without poring 
through the manual) of the code we have been using, which is working well for 
the features that our lab uses.  Of course, I would appreciate any feedback 
that you could offer, as well.

Jordan M Swanson   
Department of Ecology, Evolution, and Organismal Biology 
431 Bessey Hall 
Iowa State University 
Ames, IA 50011 
Lab 515 294-7098 
FAX: 515-294-1337 

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