[Bioperl-l] More general Bio::Assembly::Contig question (was Bio::Tools::Run::Cap3 usage question)

Florent Angly florent.angly at gmail.com
Sat Nov 28 22:47:45 EST 2009

Hi Paolo,

The aligned reads of a contig are stored in 
Bio::Assembly::Contigs->{_elem}{READ_NAME}{_seq}. To implement a slice() 
method, you could retrieve the reads using get_seq_ids(), 
get_seq_by_name() or get_seq_by_pos(). To retrieve the position of an 
aligned read in the contig, use get_seq_coord() which returns a 
Bio::SeqFeature::Generic object (from 
on which you can call the start() and end() methods.

I'm not entirely sure what 
and {_quality_clipping:READ_NAME} are. I believe that they represent the 
clear range of the read/contig.

Hope it helps,


Paolo Pavan wrote:
> Dear Florent,
> Thank you for your kind answer and for your efforts spent in this module.
> Since you are working on these topics I would like to seize the day 
> and put you some questions about some doubts I have in mind, if you 
> agree, of course :-)
> Some times ago I tried to work with bioperl, loading the data from an 
> ACE file originated by Newbler; my need was to extract part of the 
> contig like an alignment of reads and I tought to do it with a slice() 
> method, since I saw Bio::Assembly::Contig implements Bio::AlignI 
> interface. Unfortunately I realize that this interface is inherited 
> but not implemented.
> I tried to hack it by adding a slice method which would act on a 
> Bio::Alignment created from the array of LocatableSeqs representing 
> the reads.
> This is the question:
> If I'm not wrong (please correct me if yes), Bio::Assembly::Contig 
> class stores reads informations in:
> Bio::Assembly::Contigs->{_elem}{READ_NAME}{_feat}{
>      _align_clipping:READ_NAME}
>      _aligned_coord:READ_NAME}
>      _quality_clipping:READ_NAME}
> Anyone of these 3 features _align_clipping, _aligned_coord, 
> _quality_clipping, contains a Bio::SeqFeature::Generic, which of them 
> is more suitable to the purpose expressed before, the slice method?
> And more, If you apologize me for being too long, is consequently to 
> the previous: I don't have perfectly clear the purpose of this 3 
> feature per read, can you explain it?
> Really thanks you for the time you would spend.
> Bye bye,
> Paolo

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