Hello all,
I need some help once again.
My situation is that I have already generated the following files from
phred: .scf, .qual, .seq. The goal is to create a Trace object for an
applet.
Now I want to get a Sequence file as my final output for displaying it onto a
SequencePanel.
I want to use the files generated from the phred tool to create a Sequence. I
have explored much of biojava but i could not find any suitable classes that
could be used to encapsulate the data obtained from the phred output.
The approach that I want to use is somehow get a SymbolList from the data that
I have.After that I want to Run the PhredSequence . After that I want to run
the PhredTools.create() method to generate the Sequence...
*************************************************
File ft = new File("C:/Documents and Settings/Abhi/apptest/src/3422_A01.ab1");
// I am currently using the ab1 file but I want to use the .phd or the .seq
file here.
SymbolList seq_sym = trace.getSequence();
PhredSequence temp = new PhredSequence(seq_sem , " " ," ",
Annotation.EMPTY_ANNOTATION);
SymbolList seq_qual = temp.getQuality();
Sequence final_seq = PhredTools.create(seq_sym,seq_qual);
***************************************************
When I run this particular code I get the exception that PhredSequence cannot
DNA symbolList as input. So that basically is the problem.
I wanted to make sure if the method that I am following is the correct one and
if not then what approach can be taken so that my Final output is a sequence
that can be rendered.
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