/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.feature.genome;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ParsingUtils;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.*;
import java.util.HashSet;
import java.util.Set;
import java.util.regex.Pattern;
/**
* @author Jim Robinson
* @date 5/1/12
*/
public class FastaUtils {
private static Logger log = Logger.getLogger(FastaUtils.class);
static Pattern WHITE_SPACE = Pattern.compile("\\s+");
/**
* Creates an index for the provided fasta file
* inputPath can be a URL, outputPath must point to a file.
*
* @param inputPath
* @param outputPath
* @return
* @throws org.broad.igv.exceptions.DataLoadException If the fasta file cannot be indexed, for instance
* because the lines are of an uneven length
*/
public static void createIndexFile(String inputPath, String outputPath) throws DataLoadException, IOException {
AsciiLineReader reader = null;
BufferedWriter writer = null;
try {
log.info("Creating index file at " + outputPath);
reader = new AsciiLineReader(ParsingUtils.openInputStream(inputPath));
writer = new BufferedWriter(new FileWriter(outputPath));
String line = null;
String curContig = null;
Set<String> allContigs = new HashSet<String>();
int basesPerLine = -1, bytesPerLine = -1;
long location = 0, size = 0, lastPosition = 0;
int basesThisLine, bytesThisLine;
int numInconsistentLines = -1;
boolean haveTasks = true;
//Number of blank lines in the current contig.
//-1 for not set
int numBlanks = -1;
int lastBlankLineNum = -1;
int curLineNum = 0;
//We loop through, generating a new FastaSequenceIndexEntry
//every time we see a new header line, or when the file ends.
while (haveTasks) {
line = reader.readLine();
curLineNum++;
if (line == null || line.startsWith(">")) {
//The last line can have a different number of bases/bytes
if (numInconsistentLines >= 2) {
throw new DataLoadException("Fasta file has uneven line lengths in contig " + curContig, inputPath);
}
//Done with old contig
if (curContig != null) {
writeLine(writer, curContig, size, location, basesPerLine, bytesPerLine);
}
if (line == null) {
haveTasks = false;
break;
}
//Header line
curContig = WHITE_SPACE.split(line)[0];
curContig = curContig.substring(1);
if (allContigs.contains(curContig)) {
throw new DataLoadException("Contig '" + curContig + "' found multiple times in file.", inputPath);
} else {
allContigs.add(curContig);
}
//Should be starting position of next line
location = reader.getPosition();
size = 0;
basesPerLine = -1;
bytesPerLine = -1;
numInconsistentLines = -1;
} else {
basesThisLine = line.length();
bytesThisLine = (int) (reader.getPosition() - lastPosition);
//Calculate stats per line if first line, otherwise
//check for consistency
if (numInconsistentLines < 0) {
basesPerLine = basesThisLine;
bytesPerLine = bytesThisLine;
numInconsistentLines = 0;
numBlanks = 0;
} else {
if ((basesPerLine != basesThisLine || bytesPerLine != bytesThisLine) && basesThisLine > 0) {
numInconsistentLines++;
}
}
//Empty line. This is allowed if it's at the end of the contig);
if (basesThisLine == 0) {
numBlanks++;
lastBlankLineNum = curLineNum;
} else if (numBlanks >= 1) {
throw new DataLoadException(String.format("Blank line at line number %d, followed by data line at %d, in contig %s\nBlank lines are only allowed at the end of a contig", lastBlankLineNum, curLineNum, curContig), inputPath);
}
size += basesThisLine;
}
lastPosition = reader.getPosition();
}
} catch (Exception e) {
MessageUtils.showErrorMessage("Could not create index file: " + outputPath, e);
if( Globals.isTesting()) throw e;
} finally {
if (reader != null) reader.close();
if (writer != null) writer.close();
}
}
static void writeLine(Writer writer, String contig, long size, long location, int basesPerLine, int bytesPerLine) throws IOException {
String delim = "\t";
String line = contig + delim + size + delim + location + delim + basesPerLine + delim + bytesPerLine;
writer.write(line);
//We infer the newline character based on bytesPerLine - basesPerLine
//Fasta file may not have been created on this platform, want to keep the index and fasta file consistent
String newline = "\n";
if (bytesPerLine - basesPerLine == 2) {
newline = "\r\n";
}
writer.write(newline);
}
public static void regularizeFastaFile(File inputFile, File outputFile) throws IOException {
int basesPerLine = 80;
BufferedReader br = null;
PrintWriter pw = null;
try {
br = new BufferedReader(new FileReader(inputFile));
pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
String nextLine;
int count = 0;
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith(">")) {
if (count != 0) {
pw.println();
}
pw.println(nextLine);
count = 0;
} else {
char[] characters = nextLine.toCharArray();
for (int i = 0; i < characters.length; i++) {
pw.print(characters[i]);
count++;
if (count == basesPerLine) {
pw.println();
count = 0;
}
}
}
}
} finally {
if (br != null) br.close();
if (pw != null) pw.close();
}
}
public static boolean isFastaPath(String absolutePath) {
String pth = absolutePath.toLowerCase();
return pth.endsWith(".fa") || pth.endsWith(".fasta") || pth.endsWith(".fna");
}
}