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Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@876 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-06-02 16:55:05 +00:00
parent 82aa0533b8
commit 587d07da00
3 changed files with 57 additions and 42 deletions
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67
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -49,12 +49,6 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
long counted_sites = 0; // number of sites used to count covariates long counted_sites = 0; // number of sites used to count covariates
long skipped_sites = 0; // number of sites skipped because of a dbSNP entry long skipped_sites = 0; // number of sites skipped because of a dbSNP entry
String dinuc_root = "dinuc";
ArrayList<PrintStream> dinuc_outs = new ArrayList<PrintStream>();
PrintStream ByQualFile; // = new PrintStream("quality_empirical_vs_observed.csv");
PrintStream ByCycleFile;
PrintStream ByDinucFile;
private class RecalData { private class RecalData {
long N; long N;
long B; long B;
@ -104,15 +98,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
} }
try {
ByQualFile = new PrintStream(OUTPUT_FILEROOT+".empirical_v_reported_quality.csv");
ByCycleFile = new PrintStream(OUTPUT_FILEROOT+".quality_difference_v_cycle.csv");
ByDinucFile = new PrintStream(OUTPUT_FILEROOT+".quality_difference_v_dinucleotide.csv");
} catch (FileNotFoundException e){
System.out.println("Could not open output files based on OUTPUT_FILEROOT option: " + OUTPUT_FILEROOT);
System.exit(1);
}
} }
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
@ -123,7 +109,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
for (int i =0; i < reads.size(); i++ ) { for (int i =0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
if ((READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) && if (//read.getHeader().getReadGroup((String)read.getAttribute("RG")).getAttribute("PL") == "ILLUMINA" &&
!read.getReadNegativeStrandFlag() &&
(READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) &&
(read.getMappingQuality() >= MIN_MAPPING_QUALITY) && (read.getMappingQuality() >= MIN_MAPPING_QUALITY) &&
(DOWNSAMPLE_FRACTION == 1.0 || random_genrator.nextFloat() < DOWNSAMPLE_FRACTION)) { (DOWNSAMPLE_FRACTION == 1.0 || random_genrator.nextFloat() < DOWNSAMPLE_FRACTION)) {
//(random_genrator.nextFloat() <= DOWNSAMPLE_FRACTION) //(random_genrator.nextFloat() <= DOWNSAMPLE_FRACTION)
@ -134,14 +122,15 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
if (qual > 0 && qual <= MAX_QUAL_SCORE) { if (qual > 0 && qual <= MAX_QUAL_SCORE) {
// previous base is the next base in terms of machine chemistry if this is a negative strand // previous base is the next base in terms of machine chemistry if this is a negative strand
char base = (char)read.getReadBases()[offset]; char base = (char)read.getReadBases()[offset];
char prevBase = (char)read.getReadBases()[offset + (read.getReadNegativeStrandFlag() ? 1 : -1)]; char prevBase = (char)read.getReadBases()[offset -1];
int dinuc_index = bases2dinucIndex(prevBase, base, read.getReadNegativeStrandFlag()); int dinuc_index = bases2dinucIndex(prevBase, base, false);
//char prevBase = (char)read.getReadBases()[offset + (read.getReadNegativeStrandFlag() ? 1 : -1)]; //char prevBase = (char)read.getReadBases()[offset + (read.getReadNegativeStrandFlag() ? 1 : -1)];
//int dinuc_index = bases2dinucIndex(prevBase, base, read.getReadNegativeStrandFlag()); //int dinuc_index = bases2dinucIndex(prevBase, base, read.getReadNegativeStrandFlag());
// Convert offset into cycle position which means reversing the position of reads on the negative strand // Convert offset into cycle position which means reversing the position of reads on the negative strand
int cycle = read.getReadNegativeStrandFlag() ? numBases - offset - 1 : offset; //int cycle = read.getReadNegativeStrandFlag() ? numBases - offset - 1 : offset;
data[cycle][qual][dinuc_index].inc(base,ref); //data[cycle][qual][dinuc_index].inc(base,ref);
data[offset][qual][dinuc_index].inc(base,ref);
} }
} }
} }
@ -149,6 +138,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
counted_sites += 1; counted_sites += 1;
}else{ }else{
skipped_sites += 1; skipped_sites += 1;
//System.out.println(dbsnp.toSimpleString()+" "+new ReadBackedPileup(ref, context).getPileupString());
} }
return 1; return 1;
} }
@ -174,19 +164,14 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
out.printf("Skipped sites: %d%n", skipped_sites); out.printf("Skipped sites: %d%n", skipped_sites);
out.printf("Fraction skipped: 1/%.0f%n", (double)counted_sites / skipped_sites); out.printf("Fraction skipped: 1/%.0f%n", (double)counted_sites / skipped_sites);
// Close dinuc filehandles
if (CREATE_TRAINING_DATA) writeTrainingData(); if (CREATE_TRAINING_DATA) writeTrainingData();
/*if (CREATE_TRAINING_DATA)
for ( PrintStream dinuc_stream : this.dinuc_outs)
dinuc_stream.close();*/
} }
void writeTrainingData() { void writeTrainingData() {
for ( int dinuc_index=0; dinuc_index<NDINUCS; dinuc_index++) { for ( int dinuc_index=0; dinuc_index<NDINUCS; dinuc_index++) {
PrintStream dinuc_out = null; PrintStream dinuc_out = null;
try { try {
dinuc_out = new PrintStream( dinuc_root+"."+dinucIndex2bases(dinuc_index)+".csv"); dinuc_out = new PrintStream( OUTPUT_FILEROOT+".covariate_counts."+dinucIndex2bases(dinuc_index)+".csv");
dinuc_out.println("logitQ,pos,indicator,count"); dinuc_out.println("logitQ,pos,indicator,count");
for ( RecalData datum: flattenData ) { for ( RecalData datum: flattenData ) {
@ -225,6 +210,13 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
public void qualityDiffVsCycle() { public void qualityDiffVsCycle() {
PrintStream ByCycleFile = null;
try {
ByCycleFile = new PrintStream(OUTPUT_FILEROOT+".quality_difference_v_cycle.csv");
} catch (FileNotFoundException e){
System.out.println("Could not open output files based on OUTPUT_FILEROOT option: " + OUTPUT_FILEROOT);
System.exit(1);
}
ArrayList<RecalData> ByCycle = new ArrayList<RecalData>(); ArrayList<RecalData> ByCycle = new ArrayList<RecalData>();
ArrayList<MeanReportedQuality> ByCycleReportedQ = new ArrayList<MeanReportedQuality>(); ArrayList<MeanReportedQuality> ByCycleReportedQ = new ArrayList<MeanReportedQuality>();
ByCycleFile.printf("cycle,Qemp-obs,Qemp,Qobs,B,N%n"); ByCycleFile.printf("cycle,Qemp-obs,Qemp,Qobs,B,N%n");
@ -252,6 +244,13 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
public void qualityDiffVsDinucleotide() { public void qualityDiffVsDinucleotide() {
PrintStream ByDinucFile = null;
try {
ByDinucFile = new PrintStream(OUTPUT_FILEROOT+".quality_difference_v_dinucleotide.csv");
} catch (FileNotFoundException e){
System.out.println("Could not open output files based on OUTPUT_FILEROOT option: " + OUTPUT_FILEROOT);
System.exit(1);
}
ArrayList<RecalData> ByCycle = new ArrayList<RecalData>(); ArrayList<RecalData> ByCycle = new ArrayList<RecalData>();
ArrayList<MeanReportedQuality> ByCycleReportedQ = new ArrayList<MeanReportedQuality>(); ArrayList<MeanReportedQuality> ByCycleReportedQ = new ArrayList<MeanReportedQuality>();
ByDinucFile.printf("dinuc,Qemp-obs,Qemp,Qobs,B,N%n"); ByDinucFile.printf("dinuc,Qemp-obs,Qemp,Qobs,B,N%n");
@ -280,7 +279,13 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
public void qualityEmpiricalObserved() { public void qualityEmpiricalObserved() {
PrintStream ByQualFile = null;
try {
ByQualFile = new PrintStream(OUTPUT_FILEROOT+".empirical_v_reported_quality.csv");
} catch (FileNotFoundException e){
System.out.println("Could not open output files based on OUTPUT_FILEROOT option: " + OUTPUT_FILEROOT);
System.exit(1);
}
ArrayList<RecalData> ByQ = new ArrayList<RecalData>(); ArrayList<RecalData> ByQ = new ArrayList<RecalData>();
ArrayList<MeanReportedQuality> ByQReportedQ = new ArrayList<MeanReportedQuality>(); ArrayList<MeanReportedQuality> ByQReportedQ = new ArrayList<MeanReportedQuality>();
ByQualFile.printf("Qrep,Qemp,Qrep_avg,B,N%n"); ByQualFile.printf("Qrep,Qemp,Qrep_avg,B,N%n");
@ -353,12 +358,6 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
Random random_genrator; Random random_genrator;
// Print out data for regression // Print out data for regression
public CovariateCounterWalker() throws FileNotFoundException { public CovariateCounterWalker() throws FileNotFoundException {
/*if (CREATE_TRAINING_DATA)
for ( int i=0; i<NDINUCS; i++) {
PrintStream next_dinuc = new PrintStream( dinuc_root+"."+dinucIndex2bases(i)+".csv");
next_dinuc.println("logitQ,pos,indicator");
dinuc_outs.add(next_dinuc);
} */
random_genrator = new Random(123454321); // keep same random seed while debugging random_genrator = new Random(123454321); // keep same random seed while debugging
} }
} }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
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@ -62,7 +62,7 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
ArrayList<Pair<Integer, Integer>> mapping = new ArrayList<Pair<Integer, Integer>>(); ArrayList<Pair<Integer, Integer>> mapping = new ArrayList<Pair<Integer, Integer>>();
String[] elts = headerLine.split("\\s+"); String[] elts = headerLine.split("\\s+");
if ( ! elts[0].toLowerCase().equals("dinuc") ) if ( ! elts[0].toLowerCase().startsWith("dinuc") ) // checking only start of first field because dinuc will be followed by a version number to be checekde later
Utils.scareUser("Badly formatted Logistic regression header, upper left keyword must be dinuc: " + elts[0] + " line: " + headerLine); Utils.scareUser("Badly formatted Logistic regression header, upper left keyword must be dinuc: " + elts[0] + " line: " + headerLine);
for ( int k = 1; k < elts.length; k++ ) { for ( int k = 1; k < elts.length; k++ ) {

30
python/LogRegression.py
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@ -1,19 +1,35 @@
#!/usr/bin/env python #!/usr/bin/env python
import sys import subprocess, time, sys
dinuc_root = sys.argv[1] dinucs = ("AA","AC","AG","AT","CA","CC","CG","CT","GA","GC","GG","GT","TA","TC","TG","TT")
fout = file(dinuc_root+".log_reg_params", "w")
fout.write("dinuc\t") #covar_work_dir = "/humgen/gsa-scr1/andrewk/recalibration_work"
#covar_table_dir = "/humgen/gsa-scr1/andrewk/recalibration_tables"
fileroot = sys.argv[1]
covar_counts_root = fileroot+".covariate_counts"
parameter_root = fileroot+".log_reg"
recal_table = fileroot+".recalibration_table"
# Run all R process to do regression and wait for completion
kids = []
for dinuc in dinucs:
kids.append(subprocess.Popen(["/home/radon01/andrewk/covariates/logistic_regression.R", covar_counts_root, parameter_root, dinuc]))
#kids.append(subprocess.Popen(["sleep", "8"]))
while any(kid.poll() is None for kid in kids):
time.sleep(0.25)
fout = file(recal_table, "w")
fout.write("dinuc_v.1\t")
for p in range(5): for p in range(5):
for q in range(5): for q in range(5):
fout.write("%d,%d\t" % (p,q)) fout.write("%d,%d\t" % (p,q))
fout.write("\n") fout.write("\n")
for dinuc in ("AA","AC","AG","AT","CA","CC","CG","CT","GA","GC","GG","GT","TA","TC","TG","TT"): for dinuc in dinucs:
dinin = open(dinuc_root+"."+dinuc+".parameters") dinin = open(parameter_root+"."+dinuc+".parameters")
#dinin.readline() #dinin.readline()
params = [] params = []
for line in dinin: for line in dinin: