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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
package net.maizegenetics.dna.snp.io;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.Optional;
import java.util.regex.Pattern;
import net.maizegenetics.dna.map.Chromosome;
import net.maizegenetics.dna.map.GeneralPosition;
import net.maizegenetics.dna.map.PositionList;
import net.maizegenetics.dna.map.PositionListBuilder;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.GenotypeTableBuilder;
import net.maizegenetics.dna.snp.score.ReferenceProbability;
import net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.TaxaListBuilder;
import net.maizegenetics.util.Utils;
public class ReadNumericMarkerUtils {
//prevents instantiation
private ReadNumericMarkerUtils() {
}
/**
* @param inputFile the input file with TASSEL v3 annotations or with no
* input directives
* @return
* @throws IOException
*/
public static GenotypeTable readNumericMarkerFile(String inputFile) throws IOException {
BufferedReader br = Utils.getBufferedReader(inputFile);
String inputline = br.readLine();
Pattern sep = Pattern.compile("\\s+");
String[] markerName = null;
int numberOfColumns = 0;
//process header rows and count the non-blank rows
int numberOfDataLines = 0;
while (inputline != null) {
inputline = inputline.trim();
String[] parsedline = sep.split(inputline);
if (parsedline.length > 1 && !inputline.startsWith("<") && !inputline.startsWith("#")) {
numberOfDataLines++;
} else if (parsedline[0].toUpperCase().equals("")) {
markerName = processHeader(numberOfColumns, parsedline, inputFile);
numberOfColumns = markerName.length;
}
inputline = br.readLine();
}
br.close();
if (numberOfDataLines == 0) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(inputFile);
msg.append(": Missing taxa values.");
throw new IllegalArgumentException(msg.toString());
}
if (numberOfColumns == 0) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(inputFile);
msg.append(": Missing taxa data values.");
throw new IllegalArgumentException(msg.toString());
}
//process body of data: we needed numberOfColumns and numberOfDataLines from above
String[][] textdata = new String[numberOfColumns][numberOfDataLines];
String[] taxanames = new String[numberOfDataLines];
br = Utils.getBufferedReader(inputFile);
inputline = br.readLine();
int totallines = 0;
int linecount = 0;
while (inputline != null) {
totallines++;
inputline = inputline.trim();
String[] parsedline = sep.split(inputline);
if (parsedline.length > 1 && !inputline.startsWith("<") && !inputline.startsWith("#")) {
if (parsedline.length != numberOfColumns + 1) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(inputFile);
msg.append(" line ").append(totallines);
msg.append(": Incorrect number of data values.");
throw new IllegalArgumentException(msg.toString());
}
taxanames[linecount] = parsedline[0];
for (int c = 0; c < numberOfColumns; c++) {
textdata[c][linecount] = parsedline[c + 1];
}
linecount++;
}
inputline = br.readLine();
}
br.close();
TaxaList tL = new TaxaListBuilder().addAll(taxanames).build();
ReferenceProbabilityBuilder rpb = ReferenceProbabilityBuilder.getInstance(numberOfDataLines,
numberOfColumns, tL);
//Create a list of values for each taxon.
for (int indexR = 0; indexR < numberOfDataLines; indexR++) {
float[] fvalues = new float[numberOfColumns];
for (int indexC = 0; indexC < numberOfColumns; indexC++) {
// Create array of floats - these are values for each taxon
// Note when we read a line at a time when processing the file, the
// text array was defined as textData[columns][rows], sa access it thus
if (textdata[indexC][indexR].equalsIgnoreCase("NaN")
|| textdata[indexC][indexR].equalsIgnoreCase("NA")
|| textdata[indexC][indexR].equals(".")) {
fvalues[indexC] = Float.NaN;
} else {
try {
fvalues[indexC] = Float.parseFloat(textdata[indexC][indexR]);
} catch (Exception e) {
throw new IllegalArgumentException("ReadNumericMarkerUtils: readNumericMarkerFile: Can't convert: " + textdata[indexC][indexR] + " to a number on data line: " + indexR);
}
}
}
rpb.addTaxon(indexR, fvalues); // taxon is the row.
}
ReferenceProbability rp = rpb.build(); // build does the "new"
// Build PositionList for GenotypeTable
PositionListBuilder posBuilder = new PositionListBuilder();
for (int mNum = 0; mNum < numberOfColumns; mNum++) {
String snpname = markerName[mNum];
Optional info = decodeSnpName(snpname);
if (info.isPresent()) {
posBuilder.add(new GeneralPosition.Builder((Chromosome) info.get()[0], (Integer) info.get()[1]).snpName(snpname).build());
} else {
posBuilder.add(new GeneralPosition.Builder(Chromosome.UNKNOWN, mNum).snpName(snpname).build());
}
}
PositionList pl = posBuilder.build();
return GenotypeTableBuilder.getInstance(null, pl, tL, null, null, rp, null, null);
}
private static String[] processHeader(int numberOfColumns, String[] parsedline, String filename) {
if (parsedline[0].equalsIgnoreCase("\\s]")[1];
if (!parsedline[1].contains("name=") || headername.length() == 0) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(filename);
msg.append(": Improperly formatted line.");
throw new IllegalArgumentException(msg.toString());
}
int finalBracketPosition = 0;
while (!parsedline[finalBracketPosition].contains(">")) {
finalBracketPosition++;
}
if (numberOfColumns == 0) {
numberOfColumns = parsedline.length - finalBracketPosition - 1;
} else if (numberOfColumns != parsedline.length - finalBracketPosition - 1) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(filename);
msg.append(": The number of ");
msg.append(parsedline[0]).append(" ").append(parsedline[1]);
msg.append(" columns does not match the number of columns in previous header rows");
throw new IllegalArgumentException(msg.toString());
}
String[] contents = new String[numberOfColumns + 1];
contents[0] = headername;
for (int i = 0; i < numberOfColumns; i++) {
contents[i + 1] = parsedline[i + finalBracketPosition + 1];
}
return contents;
} else {
if (numberOfColumns == 0) {
numberOfColumns = parsedline.length - 1;
} else if (numberOfColumns != parsedline.length - 1) {
StringBuilder msg = new StringBuilder("Error in ");
msg.append(filename);
msg.append(": The number of ");
msg.append(parsedline[0]);
msg.append(" columns does not match the number of columns in previous header rows");
throw new IllegalArgumentException(msg.toString());
}
String[] contents = new String[numberOfColumns];
for (int i = 0; i < numberOfColumns; i++) {
contents[i] = parsedline[i + 1];
}
return contents;
}
}
public static Optional decodeSnpName(String name) {
if (!name.startsWith("S")) return Optional.empty();
try {
name = name.substring(1);
int ndx = name.indexOf('_');
return Optional.of(new Object[]{new Chromosome(name.substring(0, ndx)) ,Integer.parseInt(name.substring(ndx + 1))});
} catch (Exception e) {
return Optional.empty();
}
}
}