[Biojava-l] Reading SCF files

[Nick England]

Janier,

Here is a snippet which should read in SCF files for you, you will have to
have BioJava 1.0 for this to work.

File file = new File(String "your path here");
InputStream stream = new FileInputStream(file);
Chromatogram scf= ChromatogramFactory.create(stream);
stream.close();
Alignment data = scf.getBaseCalls();
String seq=data.symbolListForLabel("dna").seqString();

Cheers,

Nick


On 18 February 2013 05:09, Janier J. Ramírez
<jjramirez at estudiantes.uci.cu>wrote:

> Yes that's ok, Now I need an example of how given the path of the scf
> file, get the secuence, to them parse it to fasta, or if I can do it
> directly from scf to fasta.
>
> Thanks for your time
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