util.bio.seq
Class Seq

java.lang.Object
  util.bio.seq.Seq

public class Seq

extends java.lang.Object

For manipulating nucleic acid sequences.

Field Summary

static java.lang.String[]	all4BaseCombinations All possible 4 base combinations.
static java.util.regex.Pattern	chrLetter
static java.util.regex.Pattern	chrNumber

Constructor Summary

Seq()

Method Summary

static java.lang.String	complementDNA(java.lang.String seq) Takes a DNA seq and complement it, ambiguous symbols OK.
static int[]	countBases(java.lang.String sequence) Given a sequence returns the number of G's,A's,T's,C's,N's as an int[5].
static java.lang.String	extractChromosomeName(java.lang.String x) Attempts to extract chr1,2,3...22 or chrX,Y,M,MT from the String.
static boolean[]	fetchGCContent(char[] chromosomeSequence) Converts a DNA sequence into a boolean[], everything not g or c is recorded as false.
static java.lang.String	fetchSubSequence(int start, int stop, int bpFirstBase, java.lang.String sequence) Returns a sub sequence given a relative start and stop, the bp for the first base.
static java.lang.String	filterDNASeqLeaveWS(java.lang.String seq) Deletes any non IUP characters but leaves whitespaces
static java.lang.String	filterDNASequence(java.lang.String seq) Deletes any non IUP characters
static java.lang.String	filterDNASequenceStrict(java.lang.String seq) Deletes any non GATCNX characters
static java.lang.String	genDashes(java.lang.String seq1, java.lang.String seq2) Generates identitiy dashes (ie"||| | |||") between two aligned sequences
static java.util.HashMap	makeByte4BaseMap() Makes a hash map of each 4bp combination in the all4BaseCombinations String[] and a unique Byte.
static java.util.HashMap	makeChromosomeNameFileHash(java.io.File[] files) Uses Seq.extractChromosomeName() to extract a chromosome name from each file.
static int[][]	makeFrequencyMatrix(java.lang.String[] hits) Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[].
static java.lang.String	readBinarySequence(java.io.File file) Reads a binary sequence file returning gatc or n, lower case.
static java.lang.String	reverseComplementDNA(java.lang.String seq) Takes a DNA seq and reverse comps it, ambiguous symbols OK.
static boolean	writeBinarySequence(java.lang.String seq, java.io.File file) Writes a binary sequence, gatc, anything else is assumed to be n.

Methods inherited from class java.lang.Object

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

Field Detail

chrNumber

public static final java.util.regex.Pattern chrNumber

chrLetter

public static final java.util.regex.Pattern chrLetter

all4BaseCombinations

public static final java.lang.String[] all4BaseCombinations

All possible 4 base combinations.

Constructor Detail

Seq

public Seq()

Method Detail

extractChromosomeName

public static java.lang.String extractChromosomeName(java.lang.String x)

Attempts to extract chr1,2,3...22 or chrX,Y,M,MT from the String. Returns chromosome or null.

makeChromosomeNameFileHash

public static java.util.HashMap makeChromosomeNameFileHash(java.io.File[] files)

Uses Seq.extractChromosomeName() to extract a chromosome name from each file. Adds this to a HashMap containing key: value, chrom name: File. Returns null if two files with the same chromosome name are found. Skips any files in which a chromosome name cannot be extracted.

fetchGCContent

public static boolean[] fetchGCContent(char[] chromosomeSequence)

Converts a DNA sequence into a boolean[], everything not g or c is recorded as false. Returns null if a fasta is not found.

writeBinarySequence

public static boolean writeBinarySequence(java.lang.String seq,
                                          java.io.File file)

Writes a binary sequence, gatc, anything else is assumed to be n.

Returns:

true if sucessful, false if something bad happened.

readBinarySequence

public static java.lang.String readBinarySequence(java.io.File file)

Reads a binary sequence file returning gatc or n, lower case.

Returns:

null if something bad happened.

makeByte4BaseMap

public static java.util.HashMap makeByte4BaseMap()

Makes a hash map of each 4bp combination in the all4BaseCombinations String[] and a unique Byte.

filterDNASequence

public static java.lang.String filterDNASequence(java.lang.String seq)

Deletes any non IUP characters

filterDNASequenceStrict

public static java.lang.String filterDNASequenceStrict(java.lang.String seq)

Deletes any non GATCNX characters

filterDNASeqLeaveWS

public static java.lang.String filterDNASeqLeaveWS(java.lang.String seq)

Deletes any non IUP characters but leaves whitespaces

fetchSubSequence

public static java.lang.String fetchSubSequence(int start,
                                                int stop,
                                                int bpFirstBase,
                                                java.lang.String sequence)

Returns a sub sequence given a relative start and stop, the bp for the first base. Stop is inclusive.

genDashes

public static java.lang.String genDashes(java.lang.String seq1,
                                         java.lang.String seq2)

Generates identitiy dashes (ie"||| | |||") between two aligned sequences

countBases

public static int[] countBases(java.lang.String sequence)

Given a sequence returns the number of G's,A's,T's,C's,N's as an int[5]. Any non word chars are deleted, afterward any non GATC chars are counted as Ns. Case, space insensitive.

makeFrequencyMatrix

public static int[][] makeFrequencyMatrix(java.lang.String[] hits)

Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[]. The String[] should contain equal length Strings, comprised entirely of GATC.

reverseComplementDNA

public static java.lang.String reverseComplementDNA(java.lang.String seq)

Takes a DNA seq and reverse comps it, ambiguous symbols OK. Will warn if it finds an unrecognized base. Works with ' GATCRYWSKMBDHVNX .- ' case and space insensitive.

complementDNA

public static java.lang.String complementDNA(java.lang.String seq)

Takes a DNA seq and complement it, ambiguous symbols OK. Will warn if it finds an unrecognized base. Works with ' GATCRYWSKMBDHVNX .- ' case and space insensitive.