/**
* Load chromosomes from given ID or file name.
*
* @param idOrFile Genome ID or file name where chromosome lengths written
* @return Chromosome lengths
* @throws IOException if chromosome length file not found
*/
public static List<Chromosome> loadChromosomes(String idOrFile) throws IOException {
InputStream is = null;
try {
// Note: to get this to work, had to edit Intellij settings
// so that "?*.sizes" are considered sources to be copied to class path
is = HiCTools.class.getResourceAsStream(idOrFile + ".chrom.sizes");
if (is == null) {
// Not an ID, see if its a file
File file = new File(idOrFile);
if (file.exists()) {
is = new FileInputStream(file);
} else {
throw new FileNotFoundException("Could not find chromosome sizes file for: " + idOrFile);
}
}
List<Chromosome> chromosomes = new ArrayList();
chromosomes.add(0, null); // Index 0 reserved for "whole genome" psuedo-chromosome
Pattern pattern = Pattern.compile("\t");
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
String nextLine;
long genomeLength = 0;
int idx = 1;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = pattern.split(nextLine);
if (tokens.length == 2) {
String name = tokens[0];
int length = Integer.parseInt(tokens[1]);
genomeLength += length;
chromosomes.add(idx, new Chromosome(idx, name, length));
idx++;
} else {
System.out.println("Skipping " + nextLine);
}
}
// Add the "psuedo-chromosome" All, representing the whole genome. Units are in kilo-bases
chromosomes.set(0, new Chromosome(0, "All", (int) (genomeLength / 1000)));
return chromosomes;
} finally {
if (is != null) is.close();
}
}
public static void main(String[] argv)
throws IOException, CmdLineParser.UnknownOptionException,
CmdLineParser.IllegalOptionValueException {
if (argv.length < 4) {
System.out.println("Usage: hictools pre <options> <inputFile> <outputFile> <genomeID>");
System.out.println(" <options>: -d only calculate intra chromosome (diagonal) [false]");
System.out.println(
" : -o calculate densities (observed/expected), write to file [false]");
System.out.println(" : -t <int> only write cells with count above threshold t [0]");
System.out.println(
" : -c <chromosome ID> only calculate map on specific chromosome");
System.exit(0);
}
Globals.setHeadless(true);
CommandLineParser parser = new CommandLineParser();
parser.parse(argv);
String[] args = parser.getRemainingArgs();
if (args[0].equals("sort")) {
AlignmentsSorter.sort(args[1], args[2], null);
} else if (args[0].equals("pairsToBin")) {
String ifile = args[1];
String ofile = args[2];
String genomeId = args[3];
List<Chromosome> chromosomes = loadChromosomes(genomeId);
AsciiToBinConverter.convert(ifile, ofile, chromosomes);
} else if (args[0].equals("binToPairs")) {
String ifile = args[1];
String ofile = args[2];
AsciiToBinConverter.convertBack(ifile, ofile);
} else if (args[0].equals("printmatrix")) {
if (args.length < 5) {
System.err.println(
"Usage: hictools printmatrix <observed/oe/pearson> hicFile chr1 chr2 binsize");
System.exit(-1);
}
String type = args[1];
String file = args[2];
String chr1 = args[3];
String chr2 = args[4];
String binSizeSt = args[5];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
dumpMatrix(file, chr1, chr2, binSize, type);
} else if (args[0].equals("eigenvector")) {
if (args.length < 4) {
System.err.println("Usage: hictools eigenvector hicFile chr binsize");
}
String file = args[1];
String chr = args[2];
String binSizeSt = args[3];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
calculateEigenvector(file, chr, binSize);
} else if (args[0].equals("pre")) {
String genomeId = "";
try {
genomeId = args[3];
} catch (ArrayIndexOutOfBoundsException e) {
System.err.println("No genome ID given");
System.exit(0);
}
List<Chromosome> chromosomes = loadChromosomes(genomeId);
long genomeLength = 0;
for (Chromosome c : chromosomes) {
if (c != null) genomeLength += c.getSize();
}
chromosomes.set(0, new Chromosome(0, "All", (int) (genomeLength / 1000)));
String[] tokens = args[1].split(",");
List<String> files = new ArrayList<String>(tokens.length);
for (String f : tokens) {
files.add(f);
}
Preprocessor preprocessor = new Preprocessor(new File(args[2]), chromosomes);
preprocessor.setIncludedChromosomes(parser.getChromosomeOption());
preprocessor.setCountThreshold(parser.getCountThresholdOption());
preprocessor.setNumberOfThreads(parser.getThreadedOption());
preprocessor.setDiagonalsOnly(parser.getDiagonalsOption());
preprocessor.setLoadDensities(parser.getDensitiesOption());
preprocessor.preprocess(files);
}
}