[Biojava-l] converting fastq format

[Michael Heuer]

Hello Daniel,

The whole point of the FASTQ APIs in biojava is to support conversions as
you are trying to do, so you shouldn't have to do it yourself.

I would also be interested in seeing (some of) your input data.  If you've
found a historical edge case, or something that otherwise bends the rules,
we could add it to the repo as another test case.

   michael


On Wed, Sep 16, 2015 at 2:22 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Daniel,
>
> I can't help you on the BioJava specifics, but do your input files really
> have Illumina's old FASTQ quality encoding? Can you show use the
> first couple of records which is usually enough to guess.
>
> http://dx.doi.org/10.1093/nar/gkp1137
>
> Peter
>
> On Wed, Sep 16, 2015 at 4:28 AM, Daniel Katzel <dkatzel at gmail.com> wrote:
> > Sorry if this has been asked many times, but I couldn't find it when
> > searching the mailing list or popular forums. When I follow the BioJava
> > cookbook to convert a Sanger fastq file into an illumina fastq I get
> > validation errors.
> >
> > The cookbook
> >
> >
> http://biojava.org/wiki/BioJava:CookBook3:FASTQ#Convert_between_FASTQ_variants_using_streaming_API
> >
> > says this will work:
> >
> > FastqReader fastqReader = new IlluminaFastqReader();
> > final FastqWriter fastqWriter = new SangerFastqWriter();
> > final FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
> > InputStream in = ...
> >
> > fastqReader.stream(in, new StreamListener()
> >   {
> >     @Override
> >     public void fastq(final Fastq fastq)
> >     {
> >       fastqWriter.append(fileWriter, fastq);
> >     }
> >   });
> >
> >
> > But instead it throws this error:
> >
> > Caused by: java.io.IOException: sequence SRR062634.1
> > HWI-EAS110_103327062:6:1:1092:8469/1 not fastq-illumina format, was
> > fastq-sanger
> >         at
> >
> org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter.validate(IlluminaFastqWriter.java:43)
> >         at
> >
> org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:62)
> >         at
> >
> org.biojava.nbio.sequencing.io.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:46)
> >
> >
> > My workaround was to create a new Fastq instance inside the
> > StreamListener#fastq() method to manually convert the quality chars
> >
> >
> >  char[] oldQual = fastq.getQuality().toCharArray();
> >                     char[] newQual = new char[oldQual.length];
> >                     for(int i=0; i< oldQual.length; i++){
> >                         newQual[i] =
> >
> FastqVariant.FASTQ_ILLUMINA.quality(FastqVariant.FASTQ_SANGER.qualityScore(oldQual[i]));
> >                     }
> >
> >                     Fastq newFastq = new
> > FastqBuilder().withDescription(fastq.getDescription())
> >                                     .withSequence(fastq.getSequence())
> >                                     .withQuality(new String(newQual))
> >
> > .withVariant(FastqVariant.FASTQ_ILLUMINA)
> >                                     .build();
> >                     try {
> >                         fastqWriter.append(writer, newFastq);
> >                     } catch (IOException e) {
> >                        throw new UncheckedIOException(e);
> >                     }
> >
> >
> > Is that the correct way to do it? Is there a better way?
> >
> > Thanks
> >
> > _______________________________________________
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> > http://mailman.open-bio.org/mailman/listinfo/biojava-l
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