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

[Andy Yates]

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
> <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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> 
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