I get the same error message, it looks like a bug in BioJava parsing comments from SCF files. My SCF files load fine, but they don't have comments inside.
Has anyone else seen this problem before? - Nick On 18 February 2013 19:48, Janier J. Ramírez <[email protected]>wrote: > Traying to read this SCF file, I get the following errors and warnings, > the fail is at: > > Chromatogram scf = ChromatogramFactory.create(stream); > > Warning: the code set (2) is not specifically supported. (It may still > work, though.) > Exception in thread "main" java.lang.IllegalArgumentException: Can't skip > backwards: (newOffset==0) < (offset==128) > at org.biojava.bio.program.scf.SCF$Parser.skipTo(SCF.java:424) > at > org.biojava.bio.program.scf.SCF$Parser.parseComments(SCF.java:384) > at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:372) > at > org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) > at org.biojava.bio.program.scf.SCF.load(SCF.java:149) > at org.biojava.bio.program.scf.SCF.create(SCF.java:133) > at > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:117) > at javaapplication1.NewClass.main(NewClass.java:44) > > > And this is my code > > public class NewClass { > > public static void main(String[] args) > throws Exception { > JFileChooser fileChooser = new JFileChooser(); > fileChooser.setDialogTitle("Abrir"); > fileChooser.setMultiSelectionEnabled(true); > > int a = JFileChooser.APPROVE_OPTION; > > fileChooser.setFileFilter(new Filtro("scf", "")); > if (a == fileChooser.showOpenDialog(null)) { > > File file = fileChooser.getSelectedFile(); > InputStream stream = new FileInputStream(file); > > Chromatogram scf = ChromatogramFactory.create(stream); > /***Here is the fail***/ > > stream.close(); > Alignment data = scf.getBaseCalls(); > String seq = data.symbolListForLabel("dna").seqString(); > } > > } > } > > Thanks > > ----- Mensaje original ----- > De: "Nick England" <[email protected]> > Para: "Janier J. Ramírez" <[email protected]> > CC: [email protected] > Enviados: Lunes, 18 de Febrero 2013 5:13:12 > Asunto: Re: [Biojava-l] Reading SCF files > > 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 < > [email protected] > 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 > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
