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/*
* @(#)SequenceUtil.java 1.0 September 2009
*
* Copyright (c) 2009 Peter Troshin
*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.data.sequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Utility class for operations on sequences
*
* @author Peter Troshin
* @version 1.0
* @since 3.0.2
*/
public final class SequenceUtil {
private static final Logger logger = LoggerFactory.getLogger(SequenceUtil.class);
/**
* A whitespace character: [\t\n\x0B\f\r]
*/
public static final Pattern WHITE_SPACE = Pattern.compile("\\s");
/**
* A digit
*/
public static final Pattern DIGIT = Pattern.compile("\\d");
/**
* Non word
*/
public static final Pattern NONWORD = Pattern.compile("\\W");
/**
* Valid Amino acids
*/
public static final Pattern AA = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUO]+",
Pattern.CASE_INSENSITIVE);
/**
* inversion of AA pattern
*/
public static final Pattern NON_AA = Pattern.compile(
"[^ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
/**
* Same as AA pattern but with one additional letters - X
*/
public static final Pattern AMBIGUOUS_AA = Pattern.compile(
"[ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
/**
* Nucleotides a, t, g, c, u
*/
public static final Pattern NUCLEOTIDE = Pattern.compile("[AGTCU]+",
Pattern.CASE_INSENSITIVE);
/**
* Ambiguous nucleotide
*/
public static final Pattern AMBIGUOUS_NUCLEOTIDE = Pattern.compile(
"[AGTCRYMKSWHBVDNU]+", Pattern.CASE_INSENSITIVE); // see IUPAC
/**
* Non nucleotide
*/
public static final Pattern NON_NUCLEOTIDE = Pattern.compile("[^AGTCU]+",
Pattern.CASE_INSENSITIVE);
private SequenceUtil() {
} // utility class, no instantiation
/*
* public static void write_PirSeq(OutputStream os, FastaSequence seq)
* throws IOException { BufferedWriter pir_out = new BufferedWriter(new
* OutputStreamWriter(os)); pir_out.write(">P1;" + seq.getId() +
* SysPrefs.newlinechar); pir_out.write(seq.getSequence() +
* SysPrefs.newlinechar); pir_out.close(); }
*
* public static void write_FastaSeq(OutputStream os, FastaSequence seq)
* throws IOException { BufferedWriter fasta_out = new BufferedWriter( new
* OutputStreamWriter(os)); fasta_out.write(">" + seq.getId() +
* SysPrefs.newlinechar); fasta_out.write(seq.getSequence() +
* SysPrefs.newlinechar); fasta_out.close(); }
*/
/**
* @return true is the sequence contains only letters a,c, t, g, u
*/
public static boolean isNucleotideSequence(final FastaSequence s) {
return SequenceUtil.isNonAmbNucleotideSequence(s.getSequence());
}
/**
* Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
* (!) - B char
*/
public static boolean isNonAmbNucleotideSequence(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
if (SequenceUtil.DIGIT.matcher(sequence).find()) {
return false;
}
if (SequenceUtil.NON_NUCLEOTIDE.matcher(sequence).find()) {
return false;
/*
* System.out.format("I found the text starting at " +
* "index %d and ending at index %d.%n", nonDNAmatcher .start(),
* nonDNAmatcher.end());
*/
}
final Matcher DNAmatcher = SequenceUtil.NUCLEOTIDE.matcher(sequence);
return DNAmatcher.find();
}
/**
* Removes all whitespace chars in the sequence string
*
* @param sequence
* @return cleaned up sequence
*/
public static String cleanSequence(String sequence) {
assert sequence != null;
final Matcher m = SequenceUtil.WHITE_SPACE.matcher(sequence);
sequence = m.replaceAll("").toUpperCase();
return sequence;
}
/**
* Removes all special characters and digits as well as whitespace chars
* from the sequence
*
* @param sequence
* @return cleaned up sequence
*/
public static String deepCleanSequence(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
sequence = SequenceUtil.DIGIT.matcher(sequence).replaceAll("");
sequence = SequenceUtil.NONWORD.matcher(sequence).replaceAll("");
final Pattern othernonSeqChars = Pattern.compile("[_-]+");
sequence = othernonSeqChars.matcher(sequence).replaceAll("");
return sequence;
}
/**
*
* @param sequence
* @return true is the sequence is a protein sequence, false overwise
*/
public static boolean isProteinSequence(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
return false;
}
if (SequenceUtil.DIGIT.matcher(sequence).find()) {
return false;
}
if (SequenceUtil.NON_AA.matcher(sequence).find()) {
logger.info("Found non aa: {}", sequence);
return false;
}
final Matcher protmatcher = SequenceUtil.AA.matcher(sequence);
return protmatcher.find();
}
/**
* Check whether the sequence confirms to amboguous protein sequence
*
* @param sequence
* @return return true only if the sequence if ambiguous protein sequence
* Return false otherwise. e.g. if the sequence is non-ambiguous
* protein or DNA
*/
public static boolean isAmbiguosProtein(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
if (SequenceUtil.isNonAmbNucleotideSequence(sequence)) {
return false;
}
if (SequenceUtil.DIGIT.matcher(sequence).find()) {
return false;
}
if (SequenceUtil.NON_AA.matcher(sequence).find()) {
return false;
}
if (SequenceUtil.AA.matcher(sequence).find()) {
return false;
}
final Matcher amb_prot = SequenceUtil.AMBIGUOUS_AA.matcher(sequence);
return amb_prot.find();
}
/**
* Writes list of FastaSequeces into the outstream formatting the sequence
* so that it contains width chars on each line
*
* @param outstream
* @param sequences
* @param width
* - the maximum number of characters to write in one line
* @throws IOException
*/
public static void writeFasta(final OutputStream outstream,
final List sequences, final int width)
throws IOException {
final OutputStreamWriter writer = new OutputStreamWriter(outstream);
final BufferedWriter fastawriter = new BufferedWriter(writer);
for (final FastaSequence fs : sequences) {
fastawriter.write(fs.getFormatedSequence(width));
}
outstream.flush();
fastawriter.close();
writer.close();
}
/**
* Reads fasta sequences from inStream into the list of FastaSequence
* objects
*
* @param inStream
* from
* @return list of FastaSequence objects
* @throws IOException
*/
public static List readFasta(final InputStream inStream)
throws IOException {
final List seqs = new ArrayList();
final BufferedReader infasta = new BufferedReader(
new InputStreamReader(inStream, "UTF8"), 16000);
final Pattern pattern = Pattern.compile("//s+");
String line;
String sname = "", seqstr = null;
do {
line = infasta.readLine();
if ((line == null) || line.startsWith(">")) {
if (seqstr != null) {
seqs.add(new FastaSequence(sname.substring(1), seqstr));
}
sname = line; // remove >
seqstr = "";
} else {
final String subseq = pattern.matcher(line).replaceAll("");
seqstr += subseq;
}
} while (line != null);
infasta.close();
return seqs;
}
/**
* Writes FastaSequence in the file, each sequence will take one line only
*
* @param os
* @param sequences
* @throws IOException
*/
public static void writeFasta(final OutputStream os,
final List sequences) throws IOException {
final OutputStreamWriter outWriter = new OutputStreamWriter(os);
final BufferedWriter fasta_out = new BufferedWriter(outWriter);
for (final FastaSequence fs : sequences) {
fasta_out.write(fs.getOnelineFasta());
}
fasta_out.close();
outWriter.close();
}
}
