[Bioperl-l] contig disassembly

Heikki Lehvaslaiho heikki at sanbi.ac.za
Wed Jan 17 03:38:22 EST 2007


Andrew,

The default interface to Bio::SeqI objects does not do it. The methods leave 
you to deal with feature table changes after sequence changes.

However, there are some attempts to provide this kind functionality in the 
Bio::SeqUtils class.

Bio::SeqUtils::cat
Bio::SeqUtils::revcom_with_features
Bio::SeqUtils::trunc_with_features

These could be expanded and made more complete, maybe even a class of its own 
if there is enough interest?

	-Heikki


On Tuesday 16 January 2007 23:11, Andrew Stewart wrote:
> If I want to take a Bio::Seq object representing a contig and
> disassemble it into the constituent sequences which originally lead
> to its formation, all the while preserving the feature annotation
> associated with each sub-sequence, and with the coordinates of these
> feature sets updated to reflect their position relative to these sub-
> sequences, what is the best way to go about this?  If I take a
> subsequence of a Seq object, will it carry over the relevant features
> as well?
>
>
> --
> Andrew Stewart
> Research Assistant, Genomics Team
> Navy Medical Research Center (NMRC)
> Biological Defense Research Directorate (BDRD)
> BDRD Annex
> 12300 Washington Avenue, 2nd Floor
> Rockville, MD 20852
>
> email: stewarta at nmrc.navy.mil
> phone: 301-231-6700 Ext 270
>
>
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-- 
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
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