public static HashMap<String, Double> getOneWayAnovaPValues(ENode root) throws Exception {
HashMap<String, Double> returnMap = new HashMap<String, Double>();
HashMap<Float, List<ENode>> map = ReadCluster.getMapByLevel(root);
System.out.println(map.size());
for (Float f : map.keySet()) {
File outFile =
new File(
ConfigReader.getETreeTestDir()
+ File.separator
+ "Mel74ColumnsAsTaxaFor"
+ f
+ ".txt");
System.out.println(outFile.getAbsolutePath());
PivotOut.pivotOut(map.get(f), outFile.getAbsolutePath());
OtuWrapper wrapper = new OtuWrapper(outFile);
List<List<Double>> list = wrapper.getDataPointsNormalizedThenLogged();
for (int x = 0; x < wrapper.getOtuNames().size(); x++) {
double pValue = 1;
if (!wrapper.getOtuNames().get(x).equals(ETree.ROOT_NAME)) {
List<Number> data = new ArrayList<Number>();
List<String> factors = new ArrayList<String>();
for (int y = 0; y < wrapper.getSampleNames().size(); y++) {
if (!wrapper.getSampleNames().get(y).equals(ETree.ROOT_NAME)) {
data.add(list.get(y).get(x));
factors.add("" + stripSuffix(wrapper.getSampleNames().get(y)));
}
}
OneWayAnova owa = new OneWayAnova(data, factors);
if (map.containsKey(wrapper.getOtuNames().get(x))) throw new Exception("Duplicate");
pValue = owa.getPValue();
}
returnMap.put(wrapper.getOtuNames().get(x), pValue);
}
}
return returnMap;
}
public static void main(String[] args) throws Exception {
File topDir = new File(ConfigReader.getVanderbiltDir() + File.separator + "krakenOut");
for (int x = 0; x < KRAKEN_LEVELS.length; x++) {
HashMap<String, HashMap<String, Integer>> map =
new HashMap<String, HashMap<String, Integer>>();
System.out.println(KRAKEN_LEVELS[x]);
for (String s : topDir.list())
if (s.startsWith("standardReport_for_Sample_") && s.indexOf("16S") == -1) {
// System.out.println("NON 16S " + s);
addToMap(new File(topDir.getAbsolutePath() + File.separator + s), map, KRAKEN_LEVELS[x]);
}
File outFile =
new File(
ConfigReader.getVanderbiltDir()
+ File.separator
+ "spreadsheets"
+ File.separator
+ "kraken_"
+ RDP_LEVELS[x]
+ "_taxaAsColumns.txt");
PivotOTUs.writeResults(map, outFile.getAbsolutePath());
OtuWrapper wrapper = new OtuWrapper(outFile);
wrapper.writeNormalizedLoggedDataToFile(
ConfigReader.getVanderbiltDir()
+ File.separator
+ "spreadsheets"
+ File.separator
+ "kraken_"
+ RDP_LEVELS[x]
+ "_taxaAsColumnsLogNorm.txt");
}
for (int x = 0; x < KRAKEN_LEVELS.length; x++) {
HashMap<String, HashMap<String, Integer>> map =
new HashMap<String, HashMap<String, Integer>>();
System.out.println(KRAKEN_LEVELS[x]);
for (String s : topDir.list()) {
// System.out.println(s);
if (s.startsWith("standardReport_for_") && s.indexOf("16S") != -1) {
// System.out.println("For 16S " + s);
addToMap(new File(topDir.getAbsolutePath() + File.separator + s), map, KRAKEN_LEVELS[x]);
}
}
File outFile =
new File(
ConfigReader.getVanderbiltDir()
+ File.separator
+ "spreadsheets"
+ File.separator
+ "kraken_"
+ RDP_LEVELS[x]
+ "_taxaAsColumnsFor16S.txt");
PivotOTUs.writeResults(map, outFile.getAbsolutePath());
OtuWrapper wrapper = new OtuWrapper(outFile);
wrapper.writeNormalizedLoggedDataToFile(
ConfigReader.getVanderbiltDir()
+ File.separator
+ "spreadsheets"
+ File.separator
+ "kraken_"
+ RDP_LEVELS[x]
+ "_taxaAsColumnsLogNormFor16S.txt");
}
}