[Bioperl-l] Proposal of GSoC 2012 >> ACEtoSAM and SAMtoACE

afia hayati afia.hayati at gmail.com
Sat Apr 14 20:15:11 EDT 2012


Peter, Florent, and all, thanks for the responses.
Ya.., the idea is more to support SAM assemblies within the existing
Bio::Assembly::IO. SAM or ACE  files once imported should have similar
handles and methods. Bio::Assembly::IO::SAM is a read only. I also will try
to add write support for that module.

In Bio::Assembly::ACE, there are write methods, completed with the quality
score, so it "looks like" we can do SAMtoACE converter. Anyway, the main
point is to add write support in Bio::Assembly::SAM.

Please CMIIW, I am open to corrections and suggestions.

best regards,
Afiahayati

On Fri, Apr 13, 2012 at 5:32 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Apr 13, 2012 at 3:41 AM, Florent Angly <florent.angly at gmail.com>
> wrote:
> > Bioperl has a module to read and write ACE files,
> Bio::Assembly::IO::ace. It
> > also has a module to read (but not write) SAM files,
> Bio::Assembly::IO::sam.
> > So, it looks like you can already do SAMtoACE within Bioperl.
> Implementing
> > ACEtoSAM would involve adding write support to the Bio::Assembly::sam
> > module. This can be helped by looking at how Bio::Assembly::IO::ace and
> > Bio::Assembly::tigr implement write support.
> > Regards,
> > Florent
>
> Does SAMtoACE within Bioperl using Bio::Assembly::IO actually work?
>
> Note that proper multiple sequence alignments in SAM/BAM format are
> relatively rare - the vast majority of SAM/BAM files are just pairwise
> alignments which are not a good fit for ACE.
>
> Peter


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