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

[Elia Stupka]

I was going to have a look at both the ACE issue as well as the more 
general issues which I have found not ideal such as:
-resetting LocatableSeq coordinates (why not keep useful coords?)
-Having both features and LocatableSeqs, when LocatableSeqs give you 
both the gapped sequence as well as the coordinates

Will write in about 24 hours (I hope) with a decent outcome (I hope)

Cheers,

Elia



On Mar 10, 2005, at 8:03 PM, Jordan Swanson wrote:

> 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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