[Biojava-l] SCF: support for ambiguities

[community at struck.lu]

Thank you,

Daniel

"Richard Holland" <holland at eaglegenomics.com> wrote:

> This has now been applied to the trunk of biojava-live.
> 
> cheers,
> Richard
> 
> 2008/11/3 Richard Holland <holland at eaglegenomics.com>:
> > Thanks for the fix. I'll review this and get back to you in a couple of
> days.
> >
> > cheers,
> > Richard
> >
> > 2008/11/3 community at struck.lu <community at struck.lu>:
> >> I have added the missing ambiguities to DNATools.java and then used these
> in
> >> SCF.java.
> >> The two patches are appended to this email.
> >>
> >> Greetings,
> >> Daniel
> >>
> >>
> >> "Richard Holland" <holland at eaglegenomics.com> wrote:
> >>
> >>> A patch would be much appreciated!
> >>>
> >>> cheers,
> >>> Richard
> >>>
> >>> 2008/10/31 community at struck.lu <community at struck.lu>:
> >>> > True. It was a first quick and dirty hack to get the rest of my
project
> >>> going.
> >>> >
> >>> > I think adding support of the IUPAC ambiguities to DNATools would be
the
> >>> most
> >>> > approbate solution. The SCF class can then easily be adapted.
> >>> >
> >>> > Are there any plans to do so?
> >>> > If not, I could give it a try and submit a patch for DNATools and SCF.
> >>> >
> >>> > Greetings,
> >>> > Daniel
> >>> >
> >>> > "Richard Holland" <holland at eaglegenomics.com> wrote:
> >>> >
> >>> >> It is the correct method, yes.
> >>> >>
> >>> >> However your code constructs a new hash set every time it does the
> >>> >> check for W or S etc.. It would be much more efficient to create
> >>> >> class-static references to the ambiguity symbols you need, instead of
> >>> >> (re)creating them every time they're encountered. A class-static gap
> >>> >> symbol reference would also be good in this situation.
> >>> >>
> >>> >> cheers,
> >>> >> Richard
> >>> >>
> >>> >>
> >>> >>
> >>> >> 2008/10/31 community at struck.lu <community at struck.lu>:
> >>> >> > Hello,
> >>> >> >
> >>> >> >
> >>> >> > I am using the SCF class in the context of HIV-1 population
> sequencing.
> >>> In
> >>> >> > this context we do have sometimes ambiguous base calls. To support
> them
> >> I
> >>> >> > extended the SCF class to allow for IUPAC ambiguities up to 2
> >>> nucleotides.
> >>> >> >
> >>> >> > Therefore I simply added the following code to the "decode"
function:
> >>> >> >
> >>> >> > #########################
> >>> >> >        public Symbol decode(byte call) throws
IllegalSymbolException
> {
> >>> >> >
> >>> >> >            //get the DNA Alphabet
> >>> >> >            Alphabet dna = DNATools.getDNA();
> >>> >> >
> >>> >> >            char c = (char) call;
> >>> >> >            switch (c) {
> >>> >> >                case 'a':
> >>> >> >                case 'A':
> >>> >> >                    return DNATools.a();
> >>> >> >                case 'c':
> >>> >> >                case 'C':
> >>> >> >                    return DNATools.c();
> >>> >> >                case 'g':
> >>> >> >                case 'G':
> >>> >> >                    return DNATools.g();
> >>> >> >                case 't':
> >>> >> >                case 'T':
> >>> >> >                    return DNATools.t();
> >>> >> >                case 'n':
> >>> >> >                case 'N':
> >>> >> >                    return DNATools.n();
> >>> >> >                case '-':
> >>> >> >                    return DNATools.getDNA().getGapSymbol();
> >>> >> >                case 'w':
> >>> >> >                case 'W':
> >>> >> >                    //make the 'W' symbol
> >>> >> >                    Set symbolsThatMakeW = new HashSet();
> >>> >> >                    symbolsThatMakeW.add(DNATools.a());
> >>> >> >                    symbolsThatMakeW.add(DNATools.t());
> >>> >> >                    Symbol w = dna.getAmbiguity(symbolsThatMakeW);
> >>> >> >                    return w;
> >>> >> >                case 's':
> >>> >> >                case 'S':
> >>> >> >                    //make the 'S' symbol
> >>> >> >                    Set symbolsThatMakeS = new HashSet();
> >>> >> >                    symbolsThatMakeS.add(DNATools.c());
> >>> >> >                    symbolsThatMakeS.add(DNATools.g());
> >>> >> >                    Symbol s = dna.getAmbiguity(symbolsThatMakeS);
> >>> >> >                    return s;
> >>> >> > ... (and so on)
> >>> >> > #########################
> >>> >> >
> >>> >> > Is this the right way to do it? And if so, how can this code be
> >> submitted
> >>> > to
> >>> >> > the official biojava source code?
> >>> >> >
> >>> >> >
> >>> >> > Best regards,
> >>> >> > Daniel Struck
> >>> >> > _________________________________________________________
> >>> >> > Mail sent using root eSolutions Webmailer - www.root.lu
> >>> >> >
> >>> >> >
> >>> >> > _______________________________________________
> >>> >> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> >> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>> >> >
> >>> >>
> >>> >>
> >>> >
> >>> >
> >>> > _________________________________________________________
> >>> > Mail sent using root eSolutions Webmailer - www.root.lu
> >>> >
> >>> >
> >>> >
> >>>
> >>>
> >>
> >>
> >> _________________________________________________________
> >> Mail sent using root eSolutions Webmailer - www.root.lu
> >>
> >
> >
> >
> > --
> > Richard Holland, BSc MBCS
> > Finance Director, Eagle Genomics Ltd
> > M: +44 7500 438846 | E: holland at eaglegenomics.com
> > http://www.eaglegenomics.com/
> >
> 
> 


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