Package org.biojava.bio.program.phred

Class PhredTools

java.lang.Object

org.biojava.bio.program.phred.PhredTools

public final class PhredTools
extends Object

PhredTools contains static methods for working with phred quality data.

Copyright (c) 2001

Company: AgResearch

Since:

1.1 Note that Phred is a copyright of CodonCode Corporation.

Author:

Mark Schreiber, Matthew Pocock

Constructor Summary

Constructors

Constructor	Description
PhredTools()

Method Summary

Modifier and Type	Method	Description
static SymbolList	createPhred(SymbolList dna, SymbolList quality)	Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
static Symbol	dnaSymbolFromPhred(Symbol phredSym)	Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
static FiniteAlphabet	getPhredAlphabet()	Retrieves the PHRED alphabet from the AlphabetManager.
static Symbol	getPhredSymbol(Symbol dna, Symbol integer)	Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
static IntegerAlphabet.IntegerSymbol	integerSymbolFromPhred(Symbol phredSym)	Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
static double	pFromQuality(double quality)	Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
static double	pFromQuality(int quality)	Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
static double	pFromQuality(IntegerAlphabet.IntegerSymbol quality)	Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
static Distribution[]	phredAlignmentToDistArray(Alignment a)	converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
static Distribution[]	phredToDistArray(PhredSequence s)	Converts a Phred sequence to an array of distributions.
static double	qualityFromP(double probOfError)	The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
static StreamReader	readPhredQuality(BufferedReader br)	Constructs a StreamReader to read in Phred quality data in FASTA format.
static StreamReader	readPhredSequence(BufferedReader br)	Calls SeqIOTools.readFastaDNA(br), added here for convinience.
static void	writePhredQuality(OutputStream qual, OutputStream seq, SequenceDB db)	Writes Phred quality data in a Fasta type format.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhredTools

public PhredTools()

Method Detail

getPhredAlphabet

public static final FiniteAlphabet getPhredAlphabet()

Retrieves the PHRED alphabet from the AlphabetManager. The Phred alphabet is a cross product of a subset of the IntegerAlphabet from 0...99 and the DNA alphabet. The Phred alphabet is finite. The Phred Alphabet contains 400 BasisSymbols named, for example, (guanine 47). The BasisSymbols can be fragmented into their component AtomicSymbols using the getSymbols() method of BasisSymbol.

dnaSymbolFromPhred

public static final Symbol dnaSymbolFromPhred(Symbol phredSym)
                                       throws IllegalSymbolException

Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.

Throws:

IllegalSymbolException - if the provided symbol is not from the PHRED alphabet.

integerSymbolFromPhred

public static final IntegerAlphabet.IntegerSymbol integerSymbolFromPhred(Symbol phredSym)
                                                                  throws IllegalSymbolException

Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.

Throws:

IllegalSymbolException - if the provided symbol is not from the PHRED alphabet.

createPhred

public static SymbolList createPhred(SymbolList dna,
                                     SymbolList quality)
                              throws IllegalArgumentException,
                                     IllegalAlphabetException,
                                     IllegalSymbolException

Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.

Throws:

IllegalAlphabetException - if the alphabets are not of the required alphabets

IllegalArgumentException - if the two SymbolLists are not of equal length.

IllegalSymbolException - if a combination of Symbols cannot be represented by the PHRED alphabet.

getPhredSymbol

public static final Symbol getPhredSymbol(Symbol dna,
                                          Symbol integer)
                                   throws IllegalSymbolException

Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).

Throws:

IllegalSymbolException - if there is no Symbol in the PHRED alphabet that represents the two arguments.

writePhredQuality

public static void writePhredQuality(OutputStream qual,
                                     OutputStream seq,
                                     SequenceDB db)
                              throws IOException,
                                     BioException

Writes Phred quality data in a Fasta type format.

Parameters:

db - a bunch of PhredSequence objects

qual - the OutputStream to write the quality data to.

seq - the OutputStream to write the sequence data to.

Throws:

IOException

BioException

Since:

1.2

readPhredQuality

public static StreamReader readPhredQuality(BufferedReader br)

Constructs a StreamReader to read in Phred quality data in FASTA format. The data is converted into sequences consisting of Symbols from the IntegerAlphabet.

readPhredSequence

public static StreamReader readPhredSequence(BufferedReader br)

Calls SeqIOTools.readFastaDNA(br), added here for convinience.

qualityFromP

public static double qualityFromP(double probOfError)

The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.

Returns:

a double value, note that for most Phred scores this will be rounded to the nearest int

pFromQuality

public static double pFromQuality(double quality)

Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

pFromQuality

public static double pFromQuality(int quality)

Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

pFromQuality

public static double pFromQuality(IntegerAlphabet.IntegerSymbol quality)

Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

phredToDistArray

public static Distribution[] phredToDistArray(PhredSequence s)

Converts a Phred sequence to an array of distributions. Essentially a fuzzy sequence Assumes that all of the non called bases are equiprobable

phredAlignmentToDistArray

public static Distribution[] phredAlignmentToDistArray(Alignment a)

converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.

Throws:

ClassCastException - if the sequences in the alignment are not instances of PhredSequence