private static void writeFile(String tissue, boolean onlyOnePerCage) throws Exception {
BufferedReader reader =
new BufferedReader(
new FileReader(
new File(
ConfigReader.getRachSachReanalysisDir()
+ File.separator
+ "pcoa_otu_"
+ tissue
+ "_taxaAsColsLogNorm.txt")));
BufferedWriter writer =
new BufferedWriter(
new FileWriter(
new File(
ConfigReader.getRachSachReanalysisDir()
+ File.separator
+ (onlyOnePerCage
? "pcoa_otu_Colon Content_taxaAsColsLogNormWithMetadataOnePerCage.txt"
: "pcoa_otu_"
+ tissue
+ "_taxaAsColsLogNormWithMetadataAllMice.txt"))));
writer.write("sample\tcondition\ttissue\tcage\t");
writer.write(reader.readLine() + "\n");
HashMap<String, String> cageMap = getCageMap();
HashMap<String, MappingFileLine> map = MappingFileLine.getMap();
HashSet<String> cages = new HashSet<String>();
for (String s = reader.readLine(); s != null; s = reader.readLine()) {
String[] splits = s.split("\t");
MappingFileLine mfl = map.get(splits[0].replaceAll("\"", ""));
String cage = cageMap.get(mfl.getRatID());
if (!onlyOnePerCage || !cages.contains(cage)) {
writer.write(splits[0].replaceAll("\"", "") + "\t");
writer.write(mfl.getLine() + "\t");
writer.write(mfl.getTissue() + "\t");
writer.write(cage);
for (int x = 1; x < splits.length; x++) writer.write("\t" + splits[x]);
writer.write("\n");
cages.add(cage);
}
}
writer.flush();
writer.close();
}
public static HashMap<String, MetadataParserFileLine> parseMetadata() throws Exception {
HashMap<String, MetadataParserFileLine> map =
new LinkedHashMap<String, MetadataParserFileLine>();
BufferedReader reader =
new BufferedReader(
new FileReader(
new File(
ConfigReader.getBigDataScalingFactorsDir()
+ File.separator
+ "MouseDonors"
+ File.separator
+ "map.txt")));
reader.readLine();
for (String s = reader.readLine(); s != null; s = reader.readLine()) {
MetadataParserFileLine mpfl = new MetadataParserFileLine(s);
if (map.containsKey(mpfl.sample)) throw new Exception("Duplicate");
map.put(mpfl.sample, mpfl);
}
return map;
}
public static HashMap<String, String> getTaxaMap(int level) throws Exception {
HashMap<String, String> map = new HashMap<String, String>();
BufferedReader reader =
new BufferedReader(
new FileReader(
new File(
ConfigReader.getGoranTrialDir()
+ File.separator
+ "OTU_Front_DATA Serum Solar Sano 02-20-2015.txt")));
reader.readLine();
reader.readLine();
for (String s = reader.readLine(); s != null; s = reader.readLine()) {
String[] splits = s.split("\t");
// System.out.println(splits[2]);
if (splits[2].split(";").length - 1 >= level) {
String familyString = splits[2].split(";")[level];
familyString =
new StringTokenizer(familyString, "(").nextToken().replaceAll("\"", "").trim();
if (map.containsKey(splits[0])) throw new Exception("No");
map.put(splits[0], familyString);
}
}
return map;
}
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;
}
private static HashMap<String, String> getCageMap() throws Exception {
HashMap<String, String> cageMap = new HashMap<String, String>();
BufferedReader reader =
new BufferedReader(
new FileReader(
new File(
ConfigReader.getRachSachReanalysisDir()
+ File.separator
+ "TTULyteCages.txt")));
reader.readLine();
for (String s = reader.readLine(); s != null; s = reader.readLine()) {
String[] splits = s.split("\t");
if (cageMap.containsKey(splits[1])) throw new Exception("No");
cageMap.put(splits[1], splits[0]);
}
return cageMap;
}
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");
}
}