/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
File dir = null;
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':
dir = new File(args[i + 1]);
i++;
break;
case 'v':
genomeVersion = args[i + 1];
i++;
break;
case 's':
strand = args[++i];
break;
case 't':
stairStep = true;
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError: unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
if (dir == null || dir.canRead() == false)
Misc.printExit("\nError: cannot find or read your sgr file/ directory.\n");
File[][] tot = new File[3][];
tot[0] = IO.extractFiles(dir, ".sgr");
tot[1] = IO.extractFiles(dir, ".sgr.zip");
tot[2] = IO.extractFiles(dir, ".sgr.gz");
sgrFiles = IO.collapseFileArray(tot);
if (sgrFiles == null || sgrFiles.length == 0)
Misc.printExit("\nError: cannot find your xxx.sgr.zip file(s)");
if (genomeVersion == null)
Misc.printExit(
"\nError: you must supply a genome version. Goto http://genome.ucsc.edu/cgi-"
+ "bin/hgGateway load your organism to find the associated genome version.\n");
}
// constructor
public Sgr2Bar(String[] args) {
try {
// check for args
processArgs(args);
System.out.println("Genome version -> " + genomeVersion);
System.out.println("Strand -> " + strand);
System.out.println("Stair Step? -> " + stairStep);
System.out.println();
// load tagValues
if (stairStep) tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
else tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_BAR);
for (int x = 0; x < sgrFiles.length; x++) {
System.out.println("\tLoading -> " + sgrFiles[x]);
GrGraph[] grs = GrGraph.loadSgrFile(sgrFiles[x]);
// make save directory
String dirName;
dirName = Misc.removeExtension(sgrFiles[x].getCanonicalPath());
File dir = new File(dirName);
dir.mkdir();
// print bar files
System.out.println("\tSaving...");
for (int i = 0; i < grs.length; i++) {
File barFile = new File(dir, grs[i].getChromosome() + ".bar");
barParser.writeBarFile(
barFile,
grs[i].getChromosome(),
genomeVersion,
strand.charAt(0),
grs[i].getBasePositions(),
grs[i].getValues(),
tagValues);
}
}
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nFailed to parse file!");
}
}
