[Biojava-l] [Biojava-dev] Problem converting ab1 to fastq files in Biojava 1.8

[Nick England]

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
<deltadedirac at gmail.com> 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:        deltadedirac at gmail.com
>                  sgarcialop at unal.edu.co
> Skype:       sebastiang55
> Mobile:      +57 3147569794
>
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