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BioJava_CookBook3_FASTQ.md

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title BioJava:CookBook3:FASTQ
permalink wiki/BioJava%3ACookBook3%3AFASTQ

How do I work with nextgen sequencing reads in FASTQ format?

The org.biojava.nbio.genome.io.fastq package provides support for reading and writing nextgen sequencing reads in FASTQ format (FastqReader and FastqWriter, respectively) and for converting FASTQ sequences into proper biojava3 DNASequences for analysis purposes (FastqTools).

The following code snippets demonstrate how to use the APIs for common use cases.

Convert between FASTQ variants

FastqReader fastqReader = new IlluminaFastqReader();
FastqWriter fastqWriter = new SangerFastqWriter();

fastqWriter.write(new File("sanger.fastq"),
  fastqReader.read(new File("illumina.fastq")));

Convert only long sequences

FastqReader fastqReader = new IlluminaFastqReader();
FastqWriter fastqWriter = new SangerFastqWriter();
FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));

for (Fastq fastq : fastqReader.read(new File("illumina.fastq"))) {
  if (fastq.getSequence().length() > 16) {
    fastqWriter.append(fileWriter, fastq);`  
  }
}

Convert between FASTQ variants using streaming API

FastqReader fastqReader = new IlluminaFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
final FastqWriter fastqWriter = new SangerFastqWriter();
final FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    fastqWriter.append(fileWriter, fastq);
  }
});

Convert only long sequences using streaming API

FastqReader fastqReader = new IlluminaFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
FastqWriter fastqWriter = new SangerFastqWriter();
FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    if (fastq.getSequence().length() > 16) {
      fastqWriter.append(fileWriter, fastq);
    }
  }
});

Count sequences

FastqReader fastqReader = new IlluminaFastqReader();

int count = 0;
for (Fastq fastq : fastqReader.read(new File("illumina.fastq"))) {
  count++:
}
System.out.println(count);

Count sequences using streaming API

FastqReader fastqReader = new IlluminaFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));

final AtomicInteger count = new AtomicInteger();
fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    count.incrementAndGet();
  }
});

System.out.println(count.get());

Count sequences using low-level API

FastqReader fastqReader = new IlluminaFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));

final AtomicInteger count = new AtomicInteger();
fastqReader.parse(reader, new ParseAdapter() {
  @Override
  public void complete() throws IOException {
    count.incrementAndGet();
  }
});

System.out.println(count.get());

Pattern match description lines using low-level API

final Pattern pattern = Pattern.compile("^HWUSI-EAS100R:.\*$");
FastqReader fastqReader = new IlluminaFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));

fastqReader.parse(reader, new ParseAdapter() {
  @Override
  public void description(final String description) throws IOException {
    if (pattern.matches(description)) {
      System.out.println(description);
    }
  }
});

Create DNASequences from FASTQ sequences

FastqReader fastqReader = new SangerFastqReader();
List<DNASequence> sequences = new ArrayList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
  sequences.add(FastqTools.createDNASequence(fastq));
}

Create DNASequences with quality scores in QualityFeature from FASTQ sequences

FastqReader fastqReader = new SangerFastqReader();
List<DNASequence> sequences = new ArrayList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
  sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));
}

Create DNASequences with quality scores in QualityFeature and error probabilities in QuantityFeature from FASTQ sequences

FastqReader fastqReader = new SangerFastqReader();
List<DNASequence> sequences = new ArrayList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {
  sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));
}

Create DNASequences with streaming API

FastqReader fastqReader = new SangerFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
List<DNASequence> sequences = new ArrayList<DNASequence>();

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    sequences.add(FastqTools.createDNASequence(fastq));
  }
});

Create DNASequences with quality scores in QualityFeature from FASTQ sequences with streaming API

FastqReader fastqReader = new SangerFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
List<DNASequence> sequences = new ArrayList<DNASequence>();

fastqReader.stream(inputSupplier, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));
  }
});

Create DNASequences with quality scores in QualityFeature and error probabilities in QuantityFeature from FASTQ sequences with streaming API

FastqReader fastqReader = new SangerFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
List<DNASequence> sequences = new ArrayList<DNASequence>();

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));
  }
});

Calculate mean p scores using streaming API

FastqReader fastqReader = new SangerFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
SummaryStatistics stats = new SummaryStatistics();
StringBuilder sb = new StringBuilder(512);

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    stats.clear();
    for (Double errorProbability : FastqTools.errorProbabilities(fastq)) {
      stats.addValue(errorProbability);
    }
    sb.delete(0, sb.length());
    sb.append(fastq.getDescription());
    sb.append("\t");
    sb.append(stats.getMean());
    sb.append("\t");
    sb.append(stats.getStandardDeviation());
    System.out.println(sb.toString());
  }
});

Calculate mean p scores using streaming API and double array

FastqReader fastqReader = new SangerFastqReader();
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
SummaryStatistics stats = new SummaryStatistics();
StringBuilder sb = new StringBuilder(512);

fastqReader.stream(reader, new StreamListener() {
  @Override
  public void fastq(final Fastq fastq) {
    stats.clear();
    int size = fastq.getSequence().length();
    double[] errorProbabilities = FastqTools.errorProbabilties(fastq, new double[size]);
    for (int i = 0; i < size; i++) {
      stats.addValue(errorProbabilities[i]);
    }
    sb.delete(0, sb.length());
    sb.append(fastq.getDescription());
    sb.append("\t");
    sb.append(stats.getMean());
    sb.append("\t");
    sb.append(stats.getStandardDeviation());
    System.out.println(sb.toString());
  }
});