public static Map<String, SnpFrequencyData> getSnpFrequencies(
String filename, Collection<String> snpIDs) {
Map<String, SnpFrequencyData> freqs = new LinkedHashMap<String, SnpFrequencyData>();
for (String snpID : snpIDs) {
SnpFrequencyData freq = new SnpFrequencyData();
freqs.put(snpID, freq);
}
Scanner scanner = CFileHelper.createScanner(filename, "\n");
scanner.nextLine(); // skip the header line
while (scanner.hasNext()) {
String line = scanner.nextLine();
String[] tabs = line.split("\\s+");
String snpID = tabs[2];
if (!freqs.containsKey(snpID)) continue;
SnpFrequencyData snp = (SnpFrequencyData) freqs.get(snpID);
snp.setData(tabs);
}
CFileHelper.closeScanner(scanner);
return freqs;
}
public static void writeDataFile(String filename, CDataFrame dataframe) {
String output = dataframe.toString();
output = PlinkHelper.stripMissingValueToken(output);
CFileHelper.writeFile(filename, output);
}