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

Florent Angly florent.angly at gmail.com
Thu Apr 12 22:41:54 EDT 2012

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.

On 12/04/12 22:47, Peter Cock wrote:
> On Thu, Apr 5, 2012 at 5:52 AM, afia hayati<afia.hayati at gmail.com>  wrote:
>> Dear all,
>> I am afia, a PhD student in Bioinformatics.  I am so interested to
>> participate GSoC and would like to apply for project Bio::Assembly, Ace2Sam
>> and Sam2Ace converter. I have written a proposal based on the guidance for
>> prospective GSoC student. I paste my proposal in here.
>> If you have time, please give me suggestions.
>> Thank you very much.
>> Sincerely,
>> Afiahayati
> Hello Afiahayati,
> What would you use this converter for?
> I can see it is useful to convert ACE to SAM/BAM for downstream analysis
> and visualization. At the moment the only assemblers I regularly use which
> produce ACE are the Roche 'Newbler' gsAssember, and MIRA.
> For MIRA, Bastien is working on native SAM output, but for the moment
> I wrote and maintain a converter from MIRA's alignment format (MAF) to
> SAM: https://github.com/peterjc/maf2sam
> Or is the idea more to support SAM (and BAM) assemblies within the
> existing BioPerl Bio::Assembly::IO: framework to allow easier
> manipulation from Perl?
> Peter
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