[Biojava-dev] [Biojava-l] access to qualities

[Andreas Prlic]

Perhaps might be good to also add this as a cookbook recipe on the wiki?

Andreas


On Fri, Nov 16, 2012 at 2:03 AM, Tony Power <power3d at gmail.com> wrote:

> This is what I really needed as suggested by Michael:
> List features = sequence.getFeaturesByType("qualityScores");
>
> Instead what I was doing:
> List<FeatureInterface<AbstractSequence<NucleotideCompound>,
> NucleotideCompound>> features = s.getFeaturesByType("qualityScores");
>
> Thanks you all guys for your feedback,
> Tony
>
>
> On Thu, Nov 15, 2012 at 4:37 PM, Michael Heuer <heuermh at gmail.com> wrote:
>
> > Hello Tony,
> >
> > This unit test shows how to access the qualities in a QualityFeature
> >
> >     public void testCreateDNASequenceWithQualityScores()
> >     {
> >         DNASequence sequence =
> > FastqTools.createDNASequenceWithQualityScores(builder.build());
> >         assertNotNull(sequence);
> >
> >         List features = sequence.getFeaturesByType("qualityScores");
> >         assertNotNull(features);
> >         assertEquals(1, features.size());
> >         QualityFeature qualityScores = (QualityFeature) features.get(0);
> >         assertEquals(sequence.getLength(),
> > qualityScores.getQualities().size());
> >         assertEquals(sequence.getLength(),
> > qualityScores.getLocations().getLength());
> >     }
> >
> >
> >
> http://code.open-bio.org/biojava-live/trunk/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqToolsTest.java?revision=9583&root=biojava&view=markup
> >
> >    michael
> >
> >
> > On Thu, Nov 15, 2012 at 10:34 AM, Michael Heuer <heuermh at gmail.com>
> wrote:
> > > 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 <power3d at gmail.com> 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 <HWillis at scripps.edu>
> > 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" <power3d at gmail.com> 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 <power3d at gmail.com>
> > 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));}
> > >>> >>
> > >>> >>
> > >>> >_______________________________________________
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> > >>> >http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >>>
> > >>>
> > >> _______________________________________________
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> >
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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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