net.maizegenetics.dna.map.PositionListIOUtils Maven / Gradle / Ivy
/**
*
*/
package net.maizegenetics.dna.map;
import java.io.BufferedReader;
import net.maizegenetics.util.Utils;
/**
* Utilities for reading and writing Position Lists
*
* @author lcj34
*
*/
public class PositionListIOUtils {
private PositionListIOUtils() {
}
/**
* Returns a PositionList from a tab-delimited text SNP Conserve file. The
* input file has 2 tab-delimited fields indicating Chromosome Number and
* Position A header row is the first line and looks like this: #CHROM POS
* The remaining rows contains integer values as below: 9 18234
*
* @param fileName with complete path
* @return PositionList
*/
public static PositionList readSNPConserveFile(String fileName) {
try {
BufferedReader fileIn = Utils.getBufferedReader(fileName, 1000000);
PositionListBuilder plb = new PositionListBuilder();
//parse SNP position rows
// First value is Chromosome number, second is position
String line = fileIn.readLine(); // read/skip header
while ((line = fileIn.readLine()) != null) {
String[] tokens = line.split("\\t");
if (tokens.length != 2) {
System.err.println("Error in SNP Conserve File format:" + fileName);
System.err.println("Expecting tab-delimited file with 2 integer values per row");
}
Chromosome chrom = new Chromosome(tokens[0]);
int pos = Integer.parseInt(tokens[1]);
Position position = new GeneralPosition.Builder(chrom, pos).build();
plb.add(position);
}
return plb.build();
} catch (Exception e) {
System.err.println("Error in Reading SNP Conserve File:" + fileName);
e.printStackTrace();
}
return null;
}
/**
* Returns a PositionList from a tab-delimited text SNP Quality Score file. The
* input file has 3 tab-delimited fields indicating Chromosome Number and Quality Score
* Position A header row is the first line and looks like this: CHROM POS QUALITYSCORE
* The remaining rows contains integer values as below: 9 18234 15.5
* NOTE: the CHROM field is a string.
*
* @param fileName with complete path
* @return PositionList
*/
public static PositionList readQualityScoreFile(String fileName) {
if (fileName == null) return null;
try {
BufferedReader fileIn = Utils.getBufferedReader(fileName, 1000000);
PositionListBuilder plb = new PositionListBuilder();
//parse SNP position rows
// First value is Chromosome string, second is position, third is qualityScore
String line = fileIn.readLine(); // read/skip header
while ((line = fileIn.readLine()) != null) {
String[] tokens = line.split("\\t");
if (tokens.length < 3) {
System.err.println("Error in SNP Position QualityScore file format:" + fileName);
System.err.println("Expecting tab-delimited file where first 3 values in each row are type: integer, integer, float "
+ " with header values CHROM POS QUALITYSCORE");
}
Chromosome chrom = new Chromosome(tokens[0]);
int pos = Integer.parseInt(tokens[1]);
double qscore = Double.parseDouble(tokens[2]);
Position position = new GeneralPosition.Builder(chrom, pos)
.addAnno("QualityScore",qscore).build();
plb.add(position);
}
return plb.build();
} catch (Exception e) {
System.err.println("Error in Reading Quality Score File:" + fileName);
e.printStackTrace();
}
return null;
}
}