Package org.snpeff.util
Class GprSeq
java.lang.Object
org.snpeff.util.GprSeq
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic byte[]
static final char[]
static final char[]
static char[]
static char[]
static byte[]
static final char
static final byte
static final String[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic byte
aa2Code
(char aa) Convert from AA char to codestatic byte[]
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 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 sequencestatic char
code2aa
(byte aacode) Convert from AA_code to AA letterstatic String
code2aa
(byte[] aacodes) Convert from AA_code to AA letterstatic String
code2aa
(int[] aacodes) Convert from AA_code to AA letterstatic 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 String
fastaSimpleRead
(String fastaFile) Read a fasta file containing one (and only one) sequencestatic String
fastqId
(org.biojava.nbio.genome.io.fastq.Fastq fastq) Get an ID from a fastqstatic boolean
isAmbiguous
(String sequence) Are there any ambiguous bases in this sequence?static String
static char
Random basestatic String
randSequence
(Random random, int len) Random sequencestatic String
Create an ID: Remove everything after the first space char.static String
static String
Reverse of a string (sequence)static String
Reverse Watson-Cricks complementstatic String
showMismatch
(String seq1, String seq2, String prefix) Show differences between two sequencesstatic String
string2fasta
(String name, String sequence) Transform into a FASTA formatted stringstatic char
wc
(char base) Watson-Cricks complementstatic String
Watson-Cricks complement
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Field Details
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FASTQ_SANGER_ZERO
public static final char FASTQ_SANGER_ZERO- See Also:
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BASES
public static final char[] BASES -
AMINO_ACIDS
public static final char[] AMINO_ACIDS -
GAP_CODE
public static final byte GAP_CODE- See Also:
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KNOWN_FILE_EXTENSIONS
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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
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Constructor Details
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GprSeq
public GprSeq()
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Method Details
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aa2Code
public static byte aa2Code(char aa) Convert from AA char to code -
aa2Code
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
Convert from AA_code to AA letter -
code2aa
Convert from AA_code to AA letter -
code2aaPair
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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
Read a fasta file containing one (and only one) sequence -
fastqId
Get an ID from a fastq- Parameters:
fastq
-- Returns:
- Fastq's id
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isAmbiguous
Are there any ambiguous bases in this sequence? -
padN
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randBase
Random base -
randSequence
Random sequence -
readId
Create an ID: Remove everything after the first space char. Remove trailing '/1' or '/2' (if any) -
removeExt
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reverse
Reverse of a string (sequence) -
reverseWc
Reverse Watson-Cricks complement -
showMismatch
Show differences between two sequences -
string2fasta
Transform into a FASTA formatted string -
wc
public static char wc(char base) Watson-Cricks complement -
wc
Watson-Cricks complement
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