[Biojava-l] Sequence Iteration in BioJava(x)

[Richard HOLLAND]

Mark's comments earlier make my sample code redundant. I had the two
different window thingies confused.

See his post for more details!

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Mark Fortner
> Sent: Friday, December 16, 2005 10:36 AM
> To: biojava-list
> Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
> 
> 
> Richard,
> Thanks for the example.  Your approach is very similar to a 
> non-BioJava 
> approach that I had worked out earlier.  I was wondering if the 
> BioJava(x) API provides any performance benefit over simply running a 
> window along a character stream? 
> 
> The work that we're doing involves iterating through the 
> human genome, 
> (and in a number of cases, metagenomic sequences) and we're trying to 
> squeeze as much performance out of it as possible while 
> minimizing the 
> memory footprint.
> 
> Thanks,
> 
> Mark
> 
> Richard HOLLAND wrote:
> 
> >orderNSymbolList splits the sequence into non-overlapping 
> chunks. What
> >is required here is chunks that are only one base different 
> (further on)
> >than the previous chunk.
> >
> >The simplest way would be this:
> >
> >	SymbolList mySeq; // this is your sequence from somewhere else
> >	for (int i = 1 ; i <= mySeq.length()-2; i++) {
> >		SymbolList trimer = mySeq.subSeq(i,i+2); // coords are
> >inclusive so i to i+2 = 3 bases
> >		// do something with your trimer here
> >	}
> >
> >Note that the index starts at 1 and goes right up to and including
> >length(), as symbols in a SymbolList are 1-indexed, not 0-indexed.
> >	
> >cheers,
> >Richard
> >
> >Richard Holland
> >Bioinformatics Specialist
> >GIS extension 8199
> >---------------------------------------------
> >This email is confidential and may be privileged. If you are not the
> >intended recipient, please delete it and notify us 
> immediately. Please
> >do not copy or use it for any purpose, or disclose its content to any
> >other person. Thank you.
> >---------------------------------------------
> >
> >
> >  
> >
> >>-----Original Message-----
> >>From: biojava-l-bounces at portal.open-bio.org 
> >>[mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> David Huen
> >>Sent: Friday, December 16, 2005 7:34 AM
> >>To: m.fortner at sbcglobal.net
> >>Cc: biojava-list
> >>Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
> >>
> >>
> >>On Dec 15 2005, Mark Fortner wrote:
> >>I think what you want is the 
> SymbolListViews.orderNSymbolList method.
> >>
> >>It will take a SymbolList and turn it into another where it 
> >>is viewed in 
> >>another compound alphabet of the required order.
> >>
> >>
> >>    
> >>
> >>>I'm looking for the best way to iterate through all
> >>>nmers within a given sequence.  For example, given a
> >>>sequence that looks like this:
> >>>
> >>>ACTGACTGACTG
> >>>
> >>>If I extract all trimers from this I should get:
> >>>
> >>>ACT
> >>>CTG
> >>>TGA
> >>>GAC
> >>>ACT
> >>>CTG
> >>>TGA
> >>>GAC
> >>>ACT
> >>>CTG
> >>>
> >>>Is there an existing class that will allow me to
> >>>iterate through a sequence this way, or am I on my
> >>>own?
> >>>
> >>>      
> >>>
> >>_______________________________________________
> >>Biojava-l mailing list  -  Biojava-l at biojava.org
> >>http://biojava.org/mailman/listinfo/biojava-l
> >>
> >>    
> >>
> >
> >  
> >
> 
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