compbio.data.sequence
Class SequenceUtil

java.lang.Object
  compbio.data.sequence.SequenceUtil

public final class SequenceUtil
extends Object

Utility class for operations on sequences

Since:

1.0

Version:

2.0 June 2011

Author:

Peter Troshin

Field Summary

static Pattern	AA Valid Amino acids
static Pattern	AMBIGUOUS_AA Same as AA pattern but with two additional letters - XU
static Pattern	AMBIGUOUS_NUCLEOTIDE Ambiguous nucleotide
static Pattern	DIGIT A digit
static Pattern	NON_AA inversion of AA pattern
static Pattern	NON_NUCLEOTIDE Non nucleotide
static Pattern	NONWORD Non word
static Pattern	NUCLEOTIDE Nucleotides a, t, g, c, u
static Pattern	WHITE_SPACE A whitespace character: [\t\n\x0B\f\r]

Method Summary

static String	cleanProteinSequence(String sequence) Remove all non AA chars from the sequence
static String	cleanSequence(String sequence) Removes all whitespace chars in the sequence string
static void	closeSilently(Logger log, Closeable stream) Closes the Closable and logs the exception if any
static String	deepCleanSequence(String sequence) Removes all special characters and digits as well as whitespace chars from the sequence
static boolean	isAmbiguosProtein(String sequence) Check whether the sequence confirms to amboguous protein sequence
static boolean	isNonAmbNucleotideSequence(String sequence) Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
static boolean	isNucleotideSequence(FastaSequence s)
static boolean	isProteinSequence(String sequence)
static List<FastaSequence>	openInputStream(String inFilePath) Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects
static HashSet<Score>	readAAConResults(InputStream results) Read AACon result with no alignment files.
static HashMap<String,Set<Score>>	readDisembl(InputStream input) > Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
static List<FastaSequence>	readFasta(InputStream inStream) Reads fasta sequences from inStream into the list of FastaSequence objects
static HashMap<String,Set<Score>>	readGlobPlot(InputStream input) > Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
static Map<String,Score>	readIUPred(File result) Read IUPred output
static Map<String,Score>	readJRonn(File result)
static Map<String,Score>	readJRonn(InputStream inStream) Reader for JRonn horizontal file format
static void	writeFasta(OutputStream os, List<FastaSequence> sequences) Writes FastaSequence in the file, each sequence will take one line only
static void	writeFasta(OutputStream outstream, List<FastaSequence> sequences, int width) Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line
static void	writeFastaKeepTheStream(OutputStream outstream, List<FastaSequence> sequences, int width)

Methods inherited from class java.lang.Object

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

Field Detail

WHITE_SPACE

public static final Pattern WHITE_SPACE

A whitespace character: [\t\n\x0B\f\r]

DIGIT

public static final Pattern DIGIT

A digit

NONWORD

public static final Pattern NONWORD

Non word

AA

public static final Pattern AA

Valid Amino acids

NON_AA

public static final Pattern NON_AA

inversion of AA pattern

AMBIGUOUS_AA

public static final Pattern AMBIGUOUS_AA

Same as AA pattern but with two additional letters - XU

NUCLEOTIDE

public static final Pattern NUCLEOTIDE

Nucleotides a, t, g, c, u

AMBIGUOUS_NUCLEOTIDE

public static final Pattern AMBIGUOUS_NUCLEOTIDE

Ambiguous nucleotide

NON_NUCLEOTIDE

public static final Pattern NON_NUCLEOTIDE

Non nucleotide

Method Detail

isNucleotideSequence

public static boolean isNucleotideSequence(FastaSequence s)

Returns:

true is the sequence contains only letters a,c, t, g, u

isNonAmbNucleotideSequence

public static boolean isNonAmbNucleotideSequence(String sequence)

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char

cleanSequence

public static String cleanSequence(String sequence)

Removes all whitespace chars in the sequence string

Parameters:

sequence -

Returns:

cleaned up sequence

deepCleanSequence

public static String deepCleanSequence(String sequence)

Removes all special characters and digits as well as whitespace chars from the sequence

Parameters:

sequence -

Returns:

cleaned up sequence

cleanProteinSequence

public static String cleanProteinSequence(String sequence)

Remove all non AA chars from the sequence

Parameters:

sequence - the sequence to clean

Returns:

cleaned sequence

isProteinSequence

public static boolean isProteinSequence(String sequence)

Parameters:

sequence -

Returns:

true is the sequence is a protein sequence, false overwise

isAmbiguosProtein

public static boolean isAmbiguosProtein(String sequence)

Check whether the sequence confirms to amboguous protein sequence

Parameters:

sequence -

Returns:

return true only if the sequence if ambiguous protein sequence Return false otherwise. e.g. if the sequence is non-ambiguous protein or DNA

writeFasta

public static void writeFasta(OutputStream outstream,
                              List<FastaSequence> sequences,
                              int width)
                       throws IOException

Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Parameters:

outstream -

sequences -

width - - the maximum number of characters to write in one line

Throws:

IOException

writeFastaKeepTheStream

public static void writeFastaKeepTheStream(OutputStream outstream,
                                           List<FastaSequence> sequences,
                                           int width)
                                    throws IOException

Throws:

IOException

readFasta

public static List<FastaSequence> readFasta(InputStream inStream)
                                     throws IOException

Reads fasta sequences from inStream into the list of FastaSequence objects

Parameters:

inStream - from

Returns:

list of FastaSequence objects

Throws:

IOException

writeFasta

public static void writeFasta(OutputStream os,
                              List<FastaSequence> sequences)
                       throws IOException

Writes FastaSequence in the file, each sequence will take one line only

Parameters:

os -

sequences -

Throws:

IOException

readIUPred

public static Map<String,Score> readIUPred(File result)
                                    throws IOException,
                                           UnknownFileFormatException

Read IUPred output

Parameters:

result -

Returns:

Map key->sequence name, value->Score

Throws:

IOException

UnknownFileFormatException

readJRonn

public static Map<String,Score> readJRonn(File result)
                                   throws IOException,
                                          UnknownFileFormatException

Throws:

IOException

UnknownFileFormatException

readJRonn

public static Map<String,Score> readJRonn(InputStream inStream)
                                   throws IOException,
                                          UnknownFileFormatException

Reader for JRonn horizontal file format

 >Foobar M G D T T A G 0.48 0.42
 0.42 0.48 0.52 0.53 0.54
 
 
 Where all values are tab delimited


Parameters:
inStream - the InputStream connected to the JRonn output file
Returns:
Map key=sequence name value=Score
Throws:
IOException - is thrown if the inStream has problems accessing the data
UnknownFileFormatException - is thrown if the inStream represents an unknown source of
 data, i.e. not a JRonn output

closeSilently

public static final void closeSilently(Logger log,
                                       Closeable stream)

Closes the Closable and logs the exception if any

Parameters:

log -

stream -

readDisembl

public static HashMap<String,Set<Score>> readDisembl(InputStream input)
                                              throws IOException,
                                                     UnknownFileFormatException

> Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name

Parameters:

input - the InputStream

Returns:

Map key=sequence name, value=set of score

Throws:

IOException

UnknownFileFormatException

readGlobPlot

public static HashMap<String,Set<Score>> readGlobPlot(InputStream input)
                                               throws IOException,
                                                      UnknownFileFormatException

> Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name

Parameters:

input -

Returns:

Map key=sequence name, value=set of score

Throws:

IOException

UnknownFileFormatException

readAAConResults

public static HashSet<Score> readAAConResults(InputStream results)

Read AACon result with no alignment files. This method leaves incoming InputStream open!

Parameters:

results - output file of AAConservation

Returns:

Map with keys ConservationMethod -> float[]

openInputStream

public static List<FastaSequence> openInputStream(String inFilePath)
                                           throws IOException,
                                                  UnknownFileFormatException

Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects

Parameters:

inFilePath - the path to the input file

Returns:

the List of FastaSequence objects

Throws:

IOException - if the file denoted by inFilePath cannot be read

UnknownFileFormatException - if the inFilePath points to the file which format cannot be recognised