public static void main(String[] args) {
File toParse = new File("/Users/nix/Desktop/repeatMasker.bed");
String line;
String[] tokens;
try {
BufferedReader in = new BufferedReader(new FileReader(toParse));
int counter = 0;
while ((line = in.readLine()) != null) {
tokens = line.split("\\t+");
StringBuilder sb = new StringBuilder(tokens[4]);
for (int i = 5; i < tokens.length; i++) {
sb.append("_");
sb.append(tokens[i]);
}
counter++;
// 0 1 2 3 4
// chr1 8388322 8388809 + Dr000331
System.out.println(
tokens[0]
+ "\tRepeatMasker\tRepeatMasker\t"
+ tokens[1]
+ "\t"
+ tokens[2]
+ "\t.\t"
+ tokens[3]
+ "\t.\t"
+ sb
+ "_"
+ counter);
}
in.close();
} catch (Exception 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);
}
private void buildXmlTemplate() {
StringBuilder sb = new StringBuilder();
sb.append("<Pipeline>\n\n");
sb.append(fetchFieldXml());
sb.append(fetchQCXml());
sb.append(fetchVariantPoolsXml());
sb.append(fetchAnnotatorXml());
if (uploadVarsToNGSWeb) sb.append(fetchVariantUploadXml());
sb.append(fetchVariantOutputXml());
sb.append(fetchCleanupReviewDirLinkGenXml());
if (webRootForLinks != null) fetchWebRootLinksXml();
sb.append("\n</Pipeline>\n");
xmlTemplate = sb.toString();
}