[Biojava-l] SCF: support for ambiguities
Ben Berman
benb at fruitfly.org
Fri Oct 31 13:38:32 UTC 2008
Is there a reason why IUPAC ambiguity codes have never been added to
DNATools? Would it hurt the performance of symbol lookups?
On Oct 31, 2008, at 3:05 AM, community at struck.lu wrote:
> 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
> _________________________________________________________
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>
>
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>
----
Ben Berman, PhD
Research Associate, USC Epigenome Center
Harlyne J. Norris Research Tower
1450 Biggy St.
Room #G511, MC 9601
Los Angeles, CA 90033
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