[Biopython] How to optimize ACE file alignment (from newbler)

[Martin Mokrejs]

Hi Peter,
  no I haven't played with gap5 yet, so far only with consed and tablet.
Thanks for noting biopython has no write support for ACE.
Martin

Peter Cock wrote:
> On Tue, May 3, 2011 at 1:22 PM, Martin Mokrejs
> <mmokrejs at fold.natur.cuni.cz> wrote:
>> Hi,
>>  I would like to ask you how can I optimize the ACE alignment with files
>> produced by newbler. I see only the high-quality region is aligned while
>> the rest is not. I typically ask newbler to place into the ace files untrimmed
>> reads so the low-quality sequence is present, you can see it could have been
>> included in the alignment and contribute the consensus quite well.
>>  I found a new feature of consed-20 being able to re-align the reads
>> but that seemed to be too slow for me and had to kill re-processing of one
>> contig.
>>  Is there a way to direct some program that I want to re-align just some
>> columns since some position? That should first align to the consensus already
>> defined and afterwards continue with de novo alignment as long as it is possible.
>>  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
>> move columns back and forth, re-order rows) and do you re-calculate the
>> consensus?
>>  This is some sort of a follow-up to "Newbler ACE file to SAM?"
>> posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
>> ;)
>> Martin
> 
> Hi Martin,
> 
> Biopython only has an ACE parser, with no support for writing ACE files.
> So, even if you did manipulate the parsed ACE file in Biopython, you'd
> have to write your own output code (or use a simpler file format).
> 
> Regarding assembly editors, have you looked at Gap4 or Gap5?
> 
> This might be a good question to ask on the http://seqanswers.com
> forum.
> 
> Peter
> 
>