public Bed2Bar(String[] args) {
try {
processArgs(args);
// load Window[]
for (int i = 0; i < bedFiles.length; i++) {
bedFile = bedFiles[i];
System.out.println("Parsing " + bedFile.getName());
bedLinesHash = Bed.parseBedFile(bedFile, true, false);
if (bedLinesHash == null || bedLinesHash.size() == 0) {
System.out.println("Problem parsing bed file, skipping!");
continue;
}
barDirectory = IO.makeDirectory(bedFile, "");
File bedOutFile =
new File(Misc.removeExtension(bedFile.toString()) + "_" + threshold + "_Filt.bed");
bedOut = new PrintWriter(new FileWriter(bedOutFile));
makeStairStepBarFiles();
}
bedOut.close();
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
}
}
private void buildXmlPropertiesFile() {
System.out.println(
"\nBuilding and checking your pipeline properties file -> " + truncPipePropFile);
StringBuilder toPrint = new StringBuilder();
// walk through the prop file
String[] prop = IO.loadFileIntoStringArray(truncPipePropFile);
Pattern val = Pattern.compile("(<entry key.+>)([D|A|B].*)</entry>");
boolean missingFile = false;
for (String s : prop) {
// does it match a file needing prepending? Data/, Apps/, Bed/
Matcher mat = val.matcher(s);
if (mat.matches()) {
File test = new File(referenceDir, mat.group(2));
if (test.exists()) {
System.out.println("Found\t" + test);
toPrint.append(mat.group(1));
toPrint.append(test.toString());
toPrint.append("</entry>");
} else {
System.out.println("Misssing\t" + test);
missingFile = true;
}
}
// threads?
else if (s.contains("threads"))
toPrint.append("<entry key=\"threads\">" + threads + "</entry>");
// nope just save it and add a line return
else toPrint.append(s);
toPrint.append("\n");
}
// anything missing? if so exit
if (missingFile)
Misc.printErrAndExit(
"\nFailed to find all of the files in your properties file, see above.\n");
// OK, write it out
completePipelinePropFile = new File(outputDirectory, "pipelineProperties.xml");
if (IO.writeString(toPrint.toString(), completePipelinePropFile) == false)
Misc.printErrAndExit("Problem writing -> " + truncPipePropFile);
}
/**
* Makes a stair step heat map from an array of windows in bar format. One per chromosome. Don't
* forget to set the barDirectory and score Index!!!!!!!
*/
public void makeStairStepBarFiles() {
// make bar parser
BarParser bp = new BarParser();
bp.setZipCompress(true);
HashMap<String, String> tagVals = new HashMap<String, String>();
tagVals.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
tagVals.put(BarParser.GRAPH_TYPE_COLOR_TAG, "#FF00FF"); // fusha
tagVals.put(BarParser.SOURCE_TAG, bedFile.toString());
// for each chromosome
System.out.print("Printing... ");
Iterator<String> it = bedLinesHash.keySet().iterator();
while (it.hasNext()) {
chromosome = it.next();
System.out.print(chromosome + " ");
windows = bedLinesHash.get(chromosome);
// add blocks
assembleBlocks();
// balance by adding max or min at zero base
balanceValues();
// write bar file
File barFile = new File(barDirectory, chromosome + ".bar");
bp.writeBarFile(
barFile,
chromosome,
genomeVersion,
'.',
Num.arrayListOfIntegerToInts(bases),
Num.arrayListOfFloatToArray(values),
tagVals);
// clear ArrayLists
bases.clear();
values.clear();
}
System.out.println();
}