[Bioperl-l] How can I edit a sequence?

[Heikki Lehvaslaiho]

I could not resist coding the mutate function into SeqUtils.

It's in the CVS.

	-Heikki 

On Sun, 2003-06-01 at 11:08, Heikki Lehvaslaiho wrote:
> Yee Man,
> 
> There is nothing that would do inplace edit of the basic sequence
> object for you. There are Bio::LiveSeq sequence classes but they are
> definitely an overkill for this.
> 
> I suggest that you put the sequence into a string variable, do the
> modifications and put it back into the sequence object.
> 
> More object oriented alternatives:
> 
> 1. Add a method mutate() into Bio::SeqUtils using substr arguments.
> 2. Use Bio::LiveSeq::Mutation to describe your changes
> 
> # $seq->isa('Bio::PrimarySeq');
> # $mutation->isa('Bio::LiveSeq::Mutation');
> Bio::SeqUtils->mutate($seq, $mutation);
> 
> If you do not feel like writing it, I think I will at some point.
> Let me know.
> 
> -Heikki
> 
> On Fri, 2003-05-30 at 21:10, Yee Man Chan wrote:
> > Hi,
> > 
> > 	I want to change some residues in my Seq object. How can I do
> > that? I looked at this page:
> > 
> > http://doc.bioperl.org/releases/bioperl-1.2/Bio/Seq.html
> > 
> > but I still haven't figured out how to do that. For normal strings, I can
> > do
> > 
> > substr($str, $index, 1, "r");
> > 
> > if I want to replace the character at $index by "r". Is there a similar
> > function in Seq?
> > 
> > Thanks
> > Yee Man
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 

______________________________________________________________________
      
      Heikki Lehväslaiho     -     heikki/at/bioperl.org
______________________________________________________________________