Package org.biojava.nbio.sequencing.io.fastq

Class FastqTools

java.lang.Object
org.biojava.nbio.sequencing.io.fastq.FastqTools
public final class FastqTools extends Object
Utility methods for FASTQ formatted sequences.
Since:
3.0.3

  • Method Details

    • createDNASequence

      public static DNASequence createDNASequence(Fastq fastq) throws CompoundNotFoundException
      Create and return a new DNASequence from the specified FASTQ formatted sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new DNASequence from the specified FASTQ formatted sequence
      Throws:
      CompoundNotFoundException - if DNA sequence in fastq contains unrecognised compounds

    • createDNASequenceWithQualityScores

      public static DNASequence createDNASequenceWithQualityScores(Fastq fastq) throws CompoundNotFoundException
      Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence. The quality scores are stored in a QualityFeature with a type "qualityScores" the same length as the sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new DNASequence with quality scores from the specified FASTQ formatted sequence
      Throws:
      CompoundNotFoundException - if DNA sequence in fastq contains unrecognised compounds

    • createDNASequenceWithErrorProbabilities

      public static DNASequence createDNASequenceWithErrorProbabilities(Fastq fastq) throws CompoundNotFoundException
      Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence. The error probabilities are stored in a QuantityFeature with a type "errorProbabilities" the same length as the sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new DNASequence with error probabilities from the specified FASTQ formatted sequence
      Throws:
      CompoundNotFoundException - if DNA sequence in fastq contains unrecognised compounds

    • createDNASequenceWithQualityScoresAndErrorProbabilities

      public static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq) throws CompoundNotFoundException
      Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence. The quality scores are stored in a QualityFeature with a type "qualityScores" the same length as the sequence and the error probabilities are stored in a QuantityFeature with a type "errorProbabilities" the same length as the sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence
      Throws:
      CompoundNotFoundException - if DNA sequence in fastq contains unrecognised compounds

    • createQualityScores

      public static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createQualityScores(Fastq fastq)
      Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence. The quality scores feature has a type "qualityScores" and will be the same length as the sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new QualityFeature from the quality scores of the specified FASTQ formatted sequence

    • createErrorProbabilities

      public static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound> createErrorProbabilities(Fastq fastq)
      Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence. The error probabilities feature has a type "errorProbabilities" and will be the same length as the sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      a new QualityFeature from the error probabilities of the specified FASTQ formatted sequence

    • qualityScores

      public static Iterable<Number> qualityScores(Fastq fastq)
      Return the quality scores from the specified FASTQ formatted sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      the quality scores from the specified FASTQ formatted sequence

    • qualityScores

      public static int[] qualityScores(Fastq fastq, int[] qualityScores)
      Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      qualityScores - int array of quality scores, must not be null and must be the same length as the FASTQ formatted sequence quality
      Returns:
      the specified int array of quality scores

    • errorProbabilities

      public static Iterable<Number> errorProbabilities(Fastq fastq)
      Return the error probabilities from the specified FASTQ formatted sequence.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      Returns:
      the error probabilities from the specified FASTQ formatted sequence

    • errorProbabilities

      public static double[] errorProbabilities(Fastq fastq, double[] errorProbabilities)
      Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      errorProbabilities - double array of error probabilities, must not be null and must be the same length as the FASTQ formatted sequence quality
      Returns:
      the specified double array of error probabilities

    • convert

      public static Fastq convert(Fastq fastq, FastqVariant variant)
      Convert the specified FASTQ formatted sequence to the specified FASTQ sequence format variant.
      Parameters:
      fastq - FASTQ formatted sequence, must not be null
      variant - FASTQ sequence format variant, must not be null
      Returns:
      the specified FASTQ formatted sequence converted to the specified FASTQ sequence format variant
      Since:
      4.2