Re: [Biojava-dev] Problem converting ab1 to fastq files in Biojava 1.8
Andy Yates <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi, It's been about 7-8 years since I last looked into the ABIFChromatogram object and I all remember failing to extract quality scores. Can you convert the AB1 file into an SCF trace and then use biojava? The staden io package comes with a binary called convert_trace which will get you into SCF. No guarantee the scores will be converted as well but it's worth a try I guess. Andy On 20 Sep 2012, at 16:06, Nick England wrote: > 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l