Sebastian, I have also tried to obtain the AB1 quality scores using BioJava, but was not successful. I can obtain them from scf files, but not AB1. Looking at the API it appears that they are not available, but I would be happy to be shown wrong!
Nick On 20 September 2012 15:49, Sebastian garcia lopez <[email protected]> wrote: > Good day to all, > > Excuse me for my english, I wil try to explain in a better way my problem: > I need to parser ab1 file into fastq file, the problem is that I do not > know the form to obtain the quality scores from ab1. to obtain the > sequence, I use ABIFChromatogram, and in fact, I can obtain the sequence, > yet I do not know how I can obtain the quality scores to build my fastq > file. The problem is that the "trace-offsets" do not correspond with > quality scores. If it is helpful, I put a fragment of the code that I am > using > > > ABIFChromatogram y = new ABIFChromatogram();//ya casi lo logro, falta ver > como leer esos alignment > y=ABIFChromatogram.create(new File(Path)); > Alignment to=y.getBaseCalls(); > SymbolList dnaSeq=to.symbolListForLabel("dna"); > SymbolList trace=to.symbolListForLabel("trace-offsets"); > > System.out.println(dnaSeq.seqString()); > System.out.println(trace.seqString()); > > Please, if somebody know the mode to obtain the scores from ab1 files in > Biojava, please let me know. > > Thank you. > > -- > Sebastián García López > Electronic Engineer > Universidad Nacional de Colombia at Manizales > > Ms.Eng. Industrial Automation Student > Control and Digital Signal Processing Research Group (GC&PDS) > Universidad Nacional de Colombia at Manizales > MCP-Microsoft Certified Professional > > Email: [email protected] > [email protected] > Skype: sebastiang55 > Mobile: +57 3147569794 > > _______________________________________________ > biojava-dev mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
