[Biojava-l] SCF: support for ambiguities

[Richard Holland]

It would be fine to add them there too. You'd still need to modify the
SCF parser though in order for it to be able to know about them.

cheers,
Richard

2008/10/31 Ben Berman <benb at fruitfly.org>:
>
> 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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>



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/