Package org.snpeff.util
Class GprSeq
- java.lang.Object
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- org.snpeff.util.GprSeq
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public class GprSeq extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static byte[]
AA_TO_CODE
static char[]
AMINO_ACIDS
static char[]
BASES
static char[]
CODE_TO_AA
static char[]
CODE_TO_DNA
static byte[]
DNA_TO_CODE
static char
FASTQ_SANGER_ZERO
static byte
GAP_CODE
static java.lang.String[]
KNOWN_FILE_EXTENSIONS
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Constructor Summary
Constructors Constructor Description GprSeq()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static byte
aa2Code(char aa)
Convert from AA char to codestatic byte[]
aa2Code(java.lang.String aa)
Convert from AA sequence to codesstatic int
aaPairCode(byte aaCode1, byte aaCode2)
Code an AA-pairstatic int
aaPairCode(char aa1, char aa2)
Code an AA-pairstatic java.lang.String
changeQuality(java.lang.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 sequencestatic char
code2aa(byte aacode)
Convert from AA_code to AA letterstatic java.lang.String
code2aa(byte[] aacodes)
Convert from AA_code to AA letterstatic java.lang.String
code2aa(int[] aacodes)
Convert from AA_code to AA letterstatic java.lang.String
code2aaPair(int code)
static char
code2dna(byte dnacode)
Convert from DNA_code to DNA letterstatic byte
dna2Code(char base)
Convert from DNA letter to codestatic java.lang.String
fastaSimpleRead(java.lang.String fastaFile)
Read a fasta file containing one (and only one) sequencestatic java.lang.String
fastqId(org.biojava.nbio.genome.io.fastq.Fastq fastq)
Get an ID from a fastqstatic boolean
isAmbiguous(java.lang.String sequence)
Are there any ambiguous bases in this sequence?static java.lang.String
padN(java.lang.String seq, int size)
static char
randBase(java.util.Random random)
Random basestatic java.lang.String
randSequence(java.util.Random random, int len)
Random sequencestatic java.lang.String
readId(java.lang.String line)
Create an ID: Remove everything after the first space char.static java.lang.String
removeExt(java.lang.String fileName)
static java.lang.String
reverse(java.lang.String seq)
Reverse of a string (sequence)static java.lang.String
reverseWc(java.lang.String seq)
Reverse Watson-Cricks complementstatic java.lang.String
showMismatch(java.lang.String seq1, java.lang.String seq2, java.lang.String prefix)
Show differences between two sequencesstatic java.lang.String
string2fasta(java.lang.String name, java.lang.String sequence)
Transform into a FASTA formatted stringstatic char
wc(char base)
Watson-Cricks complementstatic java.lang.String
wc(java.lang.String seq)
Watson-Cricks complement
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Field Detail
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FASTQ_SANGER_ZERO
public static final char FASTQ_SANGER_ZERO
- See Also:
- Constant Field Values
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BASES
public static final char[] BASES
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AMINO_ACIDS
public static final char[] AMINO_ACIDS
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GAP_CODE
public static final byte GAP_CODE
- See Also:
- Constant Field Values
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KNOWN_FILE_EXTENSIONS
public static final java.lang.String[] KNOWN_FILE_EXTENSIONS
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AA_TO_CODE
public static byte[] AA_TO_CODE
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CODE_TO_AA
public static char[] CODE_TO_AA
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DNA_TO_CODE
public static byte[] DNA_TO_CODE
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CODE_TO_DNA
public static char[] CODE_TO_DNA
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Method Detail
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aa2Code
public static byte aa2Code(char aa)
Convert from AA char to code
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aa2Code
public static byte[] aa2Code(java.lang.String aa)
Convert from AA sequence to codes
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aaPairCode
public static int aaPairCode(byte aaCode1, byte aaCode2)
Code an AA-pair
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aaPairCode
public static int aaPairCode(char aa1, char aa2)
Code an AA-pair
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changeQuality
public static java.lang.String changeQuality(java.lang.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
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code2aa
public static char code2aa(byte aacode)
Convert from AA_code to AA letter
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code2aa
public static java.lang.String code2aa(byte[] aacodes)
Convert from AA_code to AA letter
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code2aa
public static java.lang.String code2aa(int[] aacodes)
Convert from AA_code to AA letter
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code2aaPair
public static java.lang.String code2aaPair(int code)
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code2dna
public static char code2dna(byte dnacode)
Convert from DNA_code to DNA letter
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dna2Code
public static byte dna2Code(char base)
Convert from DNA letter to code
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fastaSimpleRead
public static java.lang.String fastaSimpleRead(java.lang.String fastaFile)
Read a fasta file containing one (and only one) sequence
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fastqId
public static java.lang.String fastqId(org.biojava.nbio.genome.io.fastq.Fastq fastq)
Get an ID from a fastq- Parameters:
fastq
-- Returns:
- Fastq's id
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isAmbiguous
public static boolean isAmbiguous(java.lang.String sequence)
Are there any ambiguous bases in this sequence?
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padN
public static java.lang.String padN(java.lang.String seq, int size)
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randBase
public static char randBase(java.util.Random random)
Random base
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randSequence
public static java.lang.String randSequence(java.util.Random random, int len)
Random sequence
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readId
public static java.lang.String readId(java.lang.String line)
Create an ID: Remove everything after the first space char. Remove trailing '/1' or '/2' (if any)
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removeExt
public static java.lang.String removeExt(java.lang.String fileName)
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reverse
public static java.lang.String reverse(java.lang.String seq)
Reverse of a string (sequence)
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reverseWc
public static java.lang.String reverseWc(java.lang.String seq)
Reverse Watson-Cricks complement
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showMismatch
public static java.lang.String showMismatch(java.lang.String seq1, java.lang.String seq2, java.lang.String prefix)
Show differences between two sequences
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string2fasta
public static java.lang.String string2fasta(java.lang.String name, java.lang.String sequence)
Transform into a FASTA formatted string
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wc
public static char wc(char base)
Watson-Cricks complement
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wc
public static java.lang.String wc(java.lang.String seq)
Watson-Cricks complement
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