{

public class Utils

{

//Reads data from tab-delimited file with header, last column is class

public static int[][] ReadDataFromFile(string filename)

{

StreamReader SR = File.OpenText(filename);

char delimiter = '\t';

//Count entries in the header line to get # of SNPs

int attributes = SR.ReadLine().Split(delimiter).Length-1;

//Count lines to get the # of samples

int samples = 0;

while (SR.ReadLine()!=null)

samples++;

Console.WriteLine("Reading "+samples+" samples with "+attributes+" SNPs from "+filename+"...");

SR.Close();

//Now make the array and read in data

int[][] R = new int[samples][];

for (int i=0;i<samples;i++)

R[i] = new int[attributes+1];

SR = File.OpenText(filename);

//Read off header line

SR.ReadLine();

int sampleNumber = 0;

while (sampleNumber < samples)

{

//Read SNP values

string[] parts = SR.ReadLine().Split(delimiter);

for (int i = 0; i < R[sampleNumber].Length - 1; i++)

R[sampleNumber][i] = Convert.ToInt32(parts[i]);

//Read class value

R[sampleNumber][R[sampleNumber].Length - 1] = Convert.ToInt32(parts[parts.Length - 1]);

sampleNumber++;

}

SR.Close();

Console.WriteLine("Finished reading...");

return R;

}

//Write the MoRF scores with a SNP ID and score on each line, separated by a tab

public static void WriteReliefOutput(string filename, double[] W)

{

StreamWriter output = new System.IO.StreamWriter(filename);

for (int i = 0; i < W.Length; i++)

output.WriteLine(i+"\t"+W[i]);

output.Close();

}

//Read the MoRF score output files (for power statistics)

public static List<ReliefUtils.SNP> ReadReliefOutput(string filename)

{

List<ReliefUtils.SNP> SNPs = new List<ReliefUtils.SNP> { };

StreamReader SR = File.OpenText(filename);

string line = SR.ReadLine();

while (line != null)

{

string[] parts = line.Split('\t');

SNPs.Add(new ReliefUtils.SNP(Convert.ToInt16(parts[0]),Convert.ToDouble(parts[1])));

line = SR.ReadLine();

}

return SNPs;

}

//Write the power output file

//Output is 100 numbers separated by tabs, representing the power at 1% threshold, 2%, 3%... 100%

public static void powerOutput(string filenameStub,int m, int startRep, int endRep)

{

int[] ranks = new int[endRep - startRep + 1];

double[] power = new double[100];

int attributes = 1000;

for (int rep = startRep; rep <= endRep; rep++)

{

string filename = filenameStub + rep + ".txt";

List<ReliefUtils.SNP> SNPs = FileUtilities.Utils.ReadReliefOutput(filename);

attributes = SNPs.Count;

//Sort SNPs by descending score

SNPs.Sort(delegate(ReliefUtils.SNP S1, ReliefUtils.SNP S2) { return S2.W.CompareTo(S1.W); });

//Find the lower ranked of the 2 informative SNPs (0 and 1)

int rank0 = SNPs.FindIndex(delegate(ReliefUtils.SNP s) { return s.ID == 0; });

int rank1 = SNPs.FindIndex(delegate(ReliefUtils.SNP s) { return s.ID == 1; });

ranks[rep-startRep] = Math.Max(rank0, rank1);

}

string powerFilename = filenameStub + startRep + "to" + endRep + ".power.txt";

StreamWriter powerOutput = new StreamWriter(powerFilename);

//Find the power by percentiles (% of reps with both SNPs above threshold)

for (int percentile = 1; percentile <= 100; percentile++)

{

int passed = 0;

for (int rep = 0; rep <= endRep - startRep; rep++)

{

if (ranks[rep] <= (attributes * percentile / 100.0))

passed++;

}

power[percentile - 1] = passed / (endRep - startRep + 1.0);

Console.WriteLine("Power at " + percentile + "%: " + power[percentile - 1]);

powerOutput.Write(power[percentile - 1]);

if (percentile != 100) powerOutput.Write("\t");

}

powerOutput.Close();

}

}