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();
}
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
File file = null;
Pattern pat = Pattern.compile("-[a-z]");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
file = new File(args[i + 1]);
i++;
break;
case 'v':
genomeVersion = args[i + 1];
i++;
break;
case 's':
sumScores = true;
break;
case 't':
threshold = Float.parseFloat(args[++i]);
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError, unknown option! " + mat.group());
}
} catch (Exception e) {
System.out.print("\nSorry, something doesn't look right with this parameter: -" + test);
System.out.println();
System.exit(0);
}
}
}
if (file == null || file.exists() == false)
Misc.printErrAndExit("Problem finding your bed files!\n");
// pull files
File[][] tot = new File[3][];
tot[0] = IO.extractFiles(file, ".bed");
tot[1] = IO.extractFiles(file, ".bed.zip");
tot[2] = IO.extractFiles(file, ".bed.gz");
bedFiles = IO.collapseFileArray(tot);
if (bedFiles == null || bedFiles.length == 0)
Misc.printErrAndExit("Problem finding your xxx.bed(.zip/.gz OK) files!\n");
// genome version
if (genomeVersion == null)
Misc.printErrAndExit(
"Please enter a genome version (e.g. H_sapiens_Mar_2006, see http://genome.ucsc.edu/FAQ/FAQreleases\n");
}