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, [EMAIL PROTECTED] 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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----
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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