Hello Tony, The javadoc here
http://www.biojava.org/docs/api/org/biojava3/sequencing/io/fastq/FastqTools.html#createDNASequenceWithQualityScores%28org.biojava3.sequencing.io.fastq.Fastq%29 says "The quality scores are stored in a QualityFeature with a type "qualityScores" the same length as the sequence." QualityFeature has several different methods to access the quality scores, List<Number> getQualities, Number getQualitiesAt(int index), etc. http://www.biojava.org/docs/api/org/biojava3/core/sequence/features/QualityFeature.html Alternatively, it may be more efficient to not create DNASequence objects, something like FastqReader fastqReader = new SangerFastqReader(); InputSupplier inputSupplier = Files.newReaderSupplier(new File("sanger.fastq")); fastqReader.stream(inputSupplier, new StreamListener() { @Override public void fastq(final Fastq fastq) { int size = fastq.getSequence().length(); double[] qualityScores = FastqTools.qualityScores(fastq, new double[size]); .... } }); michael On Thu, Nov 15, 2012 at 9:03 AM, Tony Power <[email protected]> wrote: > Thanks for the feedback. > So, from the example I provided, how would you print the quality features? > > > On Thu, Nov 15, 2012 at 2:46 PM, Scooter Willis <[email protected]> wrote: > >> Tony >> >> The features get added as a named string to support any number of feature >> types. If you look in the FastqTools code should be able to find the >> string that is used to denote the quality score and then use the >> corresponding get method to return the value. >> >> Scooter >> >> On 11/15/12 9:23 AM, "Tony Power" <[email protected]> wrote: >> >> >Sorry, the message went before I finish it. >> > >> >How can I access the qualities of each sequence? >> > >> >I am trying like this: >> >List<FeatureInterface<AbstractSequence<NucleotideCompound>, >> >NucleotideCompound>> features = s.getFeaturesByType("qualityScores"); >> >for (int i = 0; i < features.size(); i++){ >> > System.out.println(": " + features.get(i).toString()); >> >} >> > >> >How can I access the qualities? >> > >> >Thanks for your help, >> >Tony >> > >> > >> >On Thu, Nov 15, 2012 at 2:15 PM, Tony Power <[email protected]> wrote: >> > >> >> Hi, >> >> >> >> I am trying to access to the qualities created with the example: >> >> >> >> FastqReader fastqReader = new SangerFastqReader(); >> >> List<DNASequence> sequences = new LinkedList<DNASequence>(); >> >> for (Fastq fastq : fastqReader.read(new File >> >>< >> http://www.google.com/search?hl=en&q=allinurl%3Afile+java.sun.com&btnI=I >> >>%27m%20Feeling%20Lucky>("sanger.fastq"))){ >> >> sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));} >> >> >> >> >> >_______________________________________________ >> >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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
