umcg.genetica.text.parsing.Demographics Maven / Gradle / Ivy
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package umcg.genetica.text.parsing;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import umcg.genetica.io.text.TextFile;
/**
*
* @author juha
*/
public class Demographics {
private String annotationFile;
public Demographics(String annotationFile) {
this.annotationFile = annotationFile;
}
public static void main(String[] args) throws IOException {
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").checkColumns("age");
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").writeMatchingSamples("age", "/Data/Sasha/GPL96GPL570AgeSamples.txt");
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").writeAgesMethylation("/Data/Sasha/GPL96GPL570AgeSamplesFinal.txt", 27, true);
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").combineAgesAndRanges("/Data/Sasha/GPL96GPL570AgeSamplesFinal.txt", "/Data/Sasha/GPL96GPL570AgeSamplesFinalRanges.txt",
// "/Data/Sasha/GPL96GPL570AgeSamplesWithRangesAveraged.txt");
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").writeGenders("/Data/Sasha/GPL96GPL570FemaleSamples.txt", "/Data/Sasha/GPL96GPL570MaleSamples.txt", 27);
// new Demographics("/Data/GeneExpressionFinal/SampleAnnotation/GPL8490/GPL8490_family_annotation_mesh2012.txt").writeGenders("/Data/MJ/GPL8490FemaleSamples.txt", "/Data/MJ/GPL8490MaleSamples.txt", 27);
// new Demographics("/Data/GeneExpressionFinal/SampleAnnotation/GPL8490/GPL8490_family_annotation_mesh2012.txt").writeAges("/Data/MJ/GPL8490Ages.txt", 27);
// new Demographics("D:\\UMCG\\Methylation_GPL8490\\GPL8490_raw_3112012\\GPL8490_family_annotation.txt").writeAgesMethylation("D:\\UMCG\\Methylation_GPL8490\\GPL8490_raw_3112012\\GPL8490Ages_New.txt", 27, true);
new Demographics("D:\\UMCG\\Methylation_GPL8490\\GPL8490_raw_3112012\\GPL8490_family_annotation.txt").writeGenders("D:\\UMCG\\Methylation_GPL8490\\GPL8490_raw_3112012\\GPL8490FemaleSamples.txt", "D:\\UMCG\\Methylation_GPL8490\\GPL8490_raw_3112012\\GPL8490MaleSamples.txt", 27);
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").writeMatchingSamples("female", "male", new int[]{7, 11, 30, 31, 33, 34}, "/Data/Sasha/GPL96GPL570FemaleSamples.txt");
// new Demographics("/Data/GeneExpression/SampleAnnotation/GPL96GPL570/GPL96GPL570SampleAnnotation.txt").writeMatchingSamples("male", "female", new int[]{7, 11, 30, 31, 33, 34}, "/Data/Sasha/GPL96GPL570MaleSamples.txt");
}
private void writeGenders(String femaleFileName, String maleFileName, int gseCol) throws IOException {
Pattern femaleP = Pattern.compile("\\bfemale\\b", Pattern.CASE_INSENSITIVE);
Pattern femaleP2 = Pattern.compile("\\b(gender|sex)[ ]*[:=]?[ ]*f", Pattern.CASE_INSENSITIVE);
Pattern maleP = Pattern.compile("\\bmale\\b", Pattern.CASE_INSENSITIVE);
Pattern maleP2 = Pattern.compile("\\b(gender|sex)[ ]*[:=]?[ ]*m(?!atched)", Pattern.CASE_INSENSITIVE);
TextFile fOut = new TextFile(femaleFileName, true);
TextFile mOut = new TextFile(maleFileName, true);
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
for (int i = 0; i < split.length; i++) {
Matcher femaleM = femaleP.matcher(split[i]);
Matcher femaleM2 = femaleP2.matcher(split[i]);
Matcher maleM = maleP.matcher(split[i]);
Matcher maleM2 = maleP2.matcher(split[i]);
String gse = split[gseCol].trim().replace("\t", " ");
if (femaleM.find(0) && !maleM.find(0)) {
fOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
} else if (maleM.find(0) && !femaleM.find(0)) {
mOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
} else if (femaleM2.find()) {
if (!split[i].toLowerCase().contains("gender: f/m")) {
fOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
}
} else if (maleM2.find()) {
if (!split[i].toLowerCase().contains("gender: m/f")) {
mOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
}
}
}
}
tf.close();
fOut.close();
mOut.close();
}
private void writeAges(String fileName, int gseCol) throws IOException {
Pattern ageP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern rangeP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[ ]*(to|-)[ ]*[0-9]+[ ]*(?!week))", Pattern.CASE_INSENSITIVE);
Pattern monthP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*[ ]*m(?!enopaus|iller))", Pattern.CASE_INSENSITIVE);
Pattern weekP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*[ ]*(week|gestational week))", Pattern.CASE_INSENSITIVE);
Pattern dayP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*[ ]*days(?! of symptoms))", Pattern.CASE_INSENSITIVE);
TextFile out = new TextFile(fileName, true);
TextFile rangeOut = new TextFile(fileName.replace(".txt", "") + "Ranges.txt", true);
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
for (int i = 0; i < split.length; i++) {
Matcher m1 = ageP.matcher(split[i]);
String gse = split[gseCol].trim().replace("\t", " ");
if (m1.find()) {
Matcher rangeM = rangeP.matcher(split[i]);
Matcher monthM = monthP.matcher(split[i]);
Matcher weekM = weekP.matcher(split[i]);
Matcher dayM = dayP.matcher(split[i]);
if (rangeM.find()) {
rangeOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + rangeM.group(1) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
} else if (!monthM.find() && !weekM.find() && !dayM.find()) {
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + m1.group(1) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
break;
}
}
}
}
tf.close();
out.close();
rangeOut.close();
}
private void writeAgesMethylation(String fileName, int gseCol, boolean specialSelection) throws IOException {
Pattern agePatern = Pattern.compile("\\bage[ ]*\\(*(y|yrs|years|months|[0-9]{4})*\\)*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern monthPatern1 = Pattern.compile("\\bage[ ]+\\(*(months|m)+\\)*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern monthPatern2 = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)[ ]*\\(*(month|m(?!enopaus|iller))+\\)*", Pattern.CASE_INSENSITIVE);
Pattern rangeP = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[ ]*(to|-)[ ]*[0-9]+[ ]*(?!week))", Pattern.CASE_INSENSITIVE);
Pattern weekPatern = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)[ ]*\\(*week[s]*\\)*", Pattern.CASE_INSENSITIVE);
Pattern dayPatern = Pattern.compile("\\bage[ ]*[:=]?[ ]*([0-9]+[\\.]?[0-9]*)[ ]*\\(*day[s]*\\)*", Pattern.CASE_INSENSITIVE);
Pattern ageSpecial1Patern = Pattern.compile("\\bageatdraw[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern ageSpecial2Patern = Pattern.compile("\\bageatdiagnosis[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern ageSpecial3Patern = Pattern.compile("\\bdurationt1d[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern ageSpecial4Patern = Pattern.compile(".*age at collection \\(months\\): ([0-9]+[\\.]?[0-9]*).*", Pattern.CASE_INSENSITIVE);
Pattern ageSpecial5Patern = Pattern.compile("\\bageatrecruitment[:=]?[ ]*([0-9]+[\\.]?[0-9]*)", Pattern.CASE_INSENSITIVE);
Pattern maternalAgePatern = Pattern.compile("\\bmaternal age", Pattern.CASE_INSENSITIVE);
TextFile out = new TextFile(fileName, true);
TextFile rangeOut = new TextFile(fileName.replace(".txt", "Ranges.txt"), true);
int numberMatches = 0;
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
for (int i = 0; i < split.length; i++) {
Matcher m1 = agePatern.matcher(split[i]);
String gse = split[gseCol].trim().replace("\t", " ");
if (m1.find()) {
Matcher monthM = monthPatern1.matcher(split[i]);
Matcher monthM2 = monthPatern2.matcher(split[i]);
Matcher maternalM = maternalAgePatern.matcher(split[i]);
Matcher weekM = weekPatern.matcher(split[i]);
Matcher dayM = dayPatern.matcher(split[i]);
Matcher rangeM = rangeP.matcher(split[i]);
if (rangeM.find(0)) {
rangeOut.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + rangeM.group(1) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
continue;
}
if (dayM.find(0) || weekM.find(0) || maternalM.find(0)) {
continue;
}
if (!monthM.find(0) && !monthM2.find(0) && Double.parseDouble(m1.group(2)) > 125) {
continue;
}
if (!monthM.find(0) && !monthM2.find(0)) {
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + m1.group(2) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
} else if (monthM.find(0) || monthM2.find(0)) {
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + Double.parseDouble(m1.group(2)) / 12 + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
}
}
if (specialSelection) {
Matcher special = ageSpecial1Patern.matcher(split[i]);
Matcher special0 = ageSpecial4Patern.matcher(split[i]);
Matcher special1 = ageSpecial2Patern.matcher(split[i]);
Matcher special2 = ageSpecial3Patern.matcher(split[i]);
Matcher special3 = ageSpecial5Patern.matcher(split[i]);
if (special.find(0)) {
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + special.group(1) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
} else if(special3.find(0)){
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + special3.group(1) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
} else if(special0.find(0)){
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + Double.parseDouble(special0.group(1)) / 12 + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
} else if (special1.find(0) && special2.find(0)) {
out.writeln(split[12] + "\t" + gse + "\t" + split[0] + "\t" + (Double.parseDouble(special1.group(1)) + Double.parseDouble(special2.group(1))) + "\t" + split[3] + "\t" + split[13] + "\t" + split[i]);
numberMatches++;
break;
}
}
}
}
System.out.println(numberMatches);
tf.close();
out.close();
rangeOut.close();
}
private void writeMatchingSamples(String matchThisWord, String fileName) throws IOException {
Pattern p1 = Pattern.compile("\\b" + matchThisWord + "\\b", Pattern.CASE_INSENSITIVE);
TextFile out = new TextFile(fileName, true);
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
for (int i = 0; i < split.length; i++) {
Matcher m1 = p1.matcher(split[i]);
if (m1.find()) {
out.writeln(split[0] + "\t" + split[i]);
}
}
}
tf.close();
out.close();
}
private void writeMatchingSamples(String matchThisWord, String dontMatchThisWord, int[] colsToSearch, String fileName) throws IOException {
Pattern p1 = Pattern.compile("\\b" + matchThisWord + "\\b", Pattern.CASE_INSENSITIVE);
Pattern p2 = Pattern.compile("\\b" + dontMatchThisWord + "\\b", Pattern.CASE_INSENSITIVE);
TextFile out = new TextFile(fileName, true);
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
boolean matches = false;
for (int col : colsToSearch) {
if (split.length > col) {
Matcher m1 = p1.matcher(split[col]);
Matcher m2 = p2.matcher(split[col]);
if (m1.find() && !m2.find()) {
matches = true;
break;
}
}
}
if (matches) {
out.writeln(split[0]);
}
}
tf.close();
out.close();
}
private void checkColumns(String query) throws IOException {
TextFile tf = new TextFile(annotationFile, false);
String line = tf.readLine();
int[] counts = new int[line.split("\t").length];
while ((line = tf.readLine()) != null) {
String[] split = line.split("\t");
for (int col = 0; col < split.length; col++) {
if (col < counts.length && split[col].contains(query)) {
counts[col]++;
}
}
}
for (int col = 0; col < counts.length; col++) {
if (counts[col] > 0) {
System.out.println(col + "\t" + counts[col]);
}
}
}
private void combineAgesAndRanges(String agefile, String rangefile, String outfile) throws IOException {
TextFile in = new TextFile(agefile, false);
TextFile out = new TextFile(outfile, true);
String line = null;
while ((line = in.readLine()) != null) {
out.writeln(line);
}
in.close();
in = new TextFile(rangefile, false);
while ((line = in.readLine()) != null) {
String[] split = line.split("\t");
String range = split[3].trim();
int indexOf = range.indexOf("-");
double age = -1;
if (indexOf > 0) {
int age1 = Integer.parseInt(range.substring(0, indexOf));
int age2 = Integer.parseInt(range.substring(indexOf + 1));
if (age2 - age1 < 19) {
age = (age2 + age1) / 2d;
}
} else {
indexOf = range.indexOf(" to ");
if (indexOf > 0) {
int age1 = Integer.parseInt(range.substring(0, indexOf));
int age2 = Integer.parseInt(range.substring(indexOf + 4));
if (age2 - age1 < 19) {
age = (age2 + age1) / 2d;
}
}
}
if (age > 0) {
String delim = "";
for (int i = 0; i < 3; i++) {
out.write(delim + split[i]);
delim = "\t";
}
out.write(delim + age);
for (int i = 4; i < split.length; i++) {
out.write(delim + split[i]);
}
out.writeln();
}
}
in.close();
out.close();
}
}
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