public static void main(String[] args) {
File column = new File(args[0]);
try {
// how many different dbs are present
LinkedHashMap dbs = new LinkedHashMap();
BufferedReader in = new BufferedReader(new FileReader(column));
String line;
int index = 0;
while ((line = in.readLine()) != null) {
if (line.trim().length() == 0) continue;
String[] tokens = line.split("\\|");
for (int i = 0; i < tokens.length; i += 2) {
if (dbs.containsKey(tokens[i]) == false) {
dbs.put(tokens[i], new Integer(index++));
}
}
}
in.close();
// print header
Iterator it = dbs.keySet().iterator();
while (it.hasNext()) {
String c = (String) it.next();
System.out.print("Reporter BioSequence DatabaseEntry [" + c + "]\t");
}
System.out.println();
// print lines
in = new BufferedReader(new FileReader(column));
int numColumns = dbs.size();
while ((line = in.readLine()) != null) {
if (line.trim().length() == 0) {
System.out.println();
} else {
String[] columns = new String[numColumns];
String[] tokens = line.split("\\|");
for (int i = 0; i < tokens.length; i += 2) {
// System.out.println(line+"Tok"+tokens[i]);
int columnIndex = ((Integer) dbs.get(tokens[i])).intValue();
if (columns[columnIndex] == null) columns[columnIndex] = tokens[i + 1];
else columns[columnIndex] = columns[columnIndex] + ";" + tokens[i + 1];
}
// print it
for (int i = 0; i < numColumns; i++) {
if (columns[i] == null) columns[i] = "";
}
System.out.println(Misc.stringArrayToString(columns, "\t"));
}
}
in.close();
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* 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();
}