Package org.snpeff.util

Class GprSeq

java.lang.Object
org.snpeff.util.GprSeq
public class GprSeq extends Object

  • Field Details

    • FASTQ_SANGER_ZERO

      public static final char FASTQ_SANGER_ZERO
      See Also:

    • BASES

      public static final char[] BASES

    • AMINO_ACIDS

      public static final char[] AMINO_ACIDS

    • GAP_CODE

      public static final byte GAP_CODE
      See Also:

    • KNOWN_FILE_EXTENSIONS

      public static final String[] KNOWN_FILE_EXTENSIONS

    • AA_TO_CODE

      public static byte[] AA_TO_CODE

    • CODE_TO_AA

      public static char[] CODE_TO_AA

    • DNA_TO_CODE

      public static byte[] DNA_TO_CODE

    • CODE_TO_DNA

      public static char[] CODE_TO_DNA

  • Constructor Details

    • GprSeq

      public GprSeq()

  • Method Details

    • aa2Code

      public static byte aa2Code(char aa)
      Convert from AA char to code

    • aa2Code

      public static byte[] aa2Code(String aa)
      Convert from AA sequence to codes

    • aaPairCode

      public static int aaPairCode(byte aaCode1, byte aaCode2)
      Code an AA-pair

    • aaPairCode

      public static int aaPairCode(char aa1, char aa2)
      Code an AA-pair

    • changeQuality

      public static String changeQuality(String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant fqSrc, org.biojava.nbio.genome.io.fastq.FastqVariant fqDst)
      Change a fastQ encoding in a quality sequence

    • code2aa

      public static char code2aa(byte aacode)
      Convert from AA_code to AA letter

    • code2aa

      public static String code2aa(byte[] aacodes)
      Convert from AA_code to AA letter

    • code2aa

      public static String code2aa(int[] aacodes)
      Convert from AA_code to AA letter

    • code2aaPair

      public static String code2aaPair(int code)

    • code2dna

      public static char code2dna(byte dnacode)
      Convert from DNA_code to DNA letter

    • dna2Code

      public static byte dna2Code(char base)
      Convert from DNA letter to code

    • fastaSimpleRead

      public static String fastaSimpleRead(String fastaFile)
      Read a fasta file containing one (and only one) sequence

    • fastqId

      public static String fastqId(org.biojava.nbio.genome.io.fastq.Fastq fastq)
      Get an ID from a fastq
      Parameters:
      fastq -
      Returns:
      Fastq's id

    • isAmbiguous

      public static boolean isAmbiguous(String sequence)
      Are there any ambiguous bases in this sequence?

    • padN

      public static String padN(String seq, int size)

    • randBase

      public static char randBase(Random random)
      Random base

    • randSequence

      public static String randSequence(Random random, int len)
      Random sequence

    • readId

      public static String readId(String line)
      Create an ID: Remove everything after the first space char. Remove trailing '/1' or '/2' (if any)

    • removeExt

      public static String removeExt(String fileName)

    • reverse

      public static String reverse(String seq)
      Reverse of a string (sequence)

    • reverseWc

      public static String reverseWc(String seq)
      Reverse Watson-Cricks complement

    • showMismatch

      public static String showMismatch(String seq1, String seq2, String prefix)
      Show differences between two sequences

    • string2fasta

      public static String string2fasta(String name, String sequence)
      Transform into a FASTA formatted string

    • wc

      public static char wc(char base)
      Watson-Cricks complement

    • wc

      public static String wc(String seq)
      Watson-Cricks complement