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PSMFile.getColumnValues improve error message
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IterativeLocalizer.calculateFalseLocalizationRates add model q-values to PSM table
bump to RC5
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@danielgeiszler
danielgeiszler committed May 1, 2024
1 parent 85cee56 commit 9cd80f7
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Showing 4 changed files with 105 additions and 35 deletions.
2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -30,7 +30,7 @@ java {
targetCompatibility = JavaVersion.VERSION_1_9
}

version = '3.0.0-rc4'
version = '3.0.0-rc5'

application {
// Define the main class for the application
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4 changes: 2 additions & 2 deletions src/edu/umich/andykong/ptmshepherd/PSMFile.java
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Expand Up @@ -1027,8 +1027,8 @@ public ArrayList<String> getColumnValues(String header) { //TODO I think you can
int colIndx = getColumn(header);

if (colIndx < 0 || colIndx >= (this.headers.length)) {
throw new ArrayIndexOutOfBoundsException(String.format("Column index %d is out of bounds for a %d column" +
"wide table", colIndx, this.headers.length));
throw new ArrayIndexOutOfBoundsException(String.format("Cannot fetch %s column. Column index %d is out of bounds for a %d column" +
"wide table", header, colIndx, this.headers.length));
}

ArrayList<String> values = new ArrayList<>(this.data.size());
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2 changes: 1 addition & 1 deletion src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
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Expand Up @@ -69,7 +69,7 @@
public class PTMShepherd {

public static final String name = "PTM-Shepherd";
public static final String version = "3.0.0-rc4";
public static final String version = "3.0.0-rc5";

static HashMap<String,String> params;
static TreeMap<String,ArrayList<String []>> datasets;
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132 changes: 101 additions & 31 deletions src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
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Expand Up @@ -5,6 +5,7 @@
import edu.umich.andykong.ptmshepherd.core.MXMLReader;
import edu.umich.andykong.ptmshepherd.core.Spectrum;
import edu.umich.andykong.ptmshepherd.utils.Peptide;
import org.jetbrains.annotations.NotNull;

import java.io.File;
import java.text.DecimalFormat;
Expand Down Expand Up @@ -363,13 +364,13 @@ private void calculateLocalizationProbabilities() throws Exception {
if (finalPass) {
// Update PSM table with new columns
psmf.addColumn(psmf.getColumn("Observed Modifications") + 1,
"delta_mass_loc", specNames, strOutputProbs);
psmf.addColumn(psmf.getColumn("delta_mass_loc") + 1,
"delta_mass_maxloc", specNames, strMaxProbs);
psmf.addColumn(psmf.getColumn("delta_mass_maxloc") + 1,
"delta_mass_entropy", specNames, strEntropies);
psmf.addColumn(psmf.getColumn("delta_mass_entropy") + 1,
"delta_mass_maxprob", specNames, strMaxProbs2);
"PTM-Shepherd Localization", specNames, strOutputProbs);
psmf.addColumn(psmf.getColumn("PTM-Shepherd Localization") + 1,
"PTM-Shepherd Best Localization", specNames, strMaxProbs);
//psmf.addColumn(psmf.getColumn("delta_mass_maxloc") + 1,
// "delta_mass_entropy", specNames, strEntropies);
//psmf.addColumn(psmf.getColumn("PTM-Shepherd Best Localization") + 1,
// "PTM-Shepherd Max Probability", specNames, strMaxProbs2);
psmf.save(true); // Do not overwrite
complete = true;
}
Expand Down Expand Up @@ -478,6 +479,9 @@ public static boolean[] parseAllowedPositions(String seq, String allowedAAs, flo
* which may not be desirable under all circumstances. This is calculated using the unbiased estimator (d+1)/t
* from Levitsky J Proteome Res. (2017), but adjusted by the ratio of decoy AAs/target AAs.
*
* //TODO clean up
* //TODO figure out double-decoy system
*
* @return
*/
private void calculateFalseLocalizationRates() throws Exception { //TODO this needs to be modularized so it can be unit tested
Expand All @@ -495,6 +499,31 @@ private void calculateFalseLocalizationRates() throws Exception { //TODO this ne
int[] targetEntropies = new int[1000+1]; //4 digit accuracy, plus one bin for 1.0000
int[] decoyEntropies = new int[1000+1];


// Create container that will allow us to sort on probabilities while retaining PSM level mapping
class SpecProbQ implements Comparable<SpecProbQ> {
String spec;
double prob;
double q;

SpecProbQ(String spec, double prob) {
this.spec = spec;
this.prob = prob;
}

@Override
public int compareTo(SpecProbQ o) {
if (this.prob < o.prob) {
return -1; // Return -1 if this object's prob is less than the other object's prob
} else if (this.prob > o.prob) {
return 1; // Return 1 if this object's prob is greater than the other object's prob
}
return 0; // Return 0 if they are equal
}
}

ArrayList<SpecProbQ> spqs = new ArrayList<>();

// Loop through datasets
for (String ds : this.datasets.keySet()) {
ArrayList<String[]> dsData = this.datasets.get(ds);
Expand All @@ -503,9 +532,10 @@ private void calculateFalseLocalizationRates() throws Exception { //TODO this ne

// Get values we're working with on first pass
PSMFile psmf = new PSMFile(new File(dsData.get(i)[0]));
ArrayList<String> specs = psmf.getColumnValues("Spectrum");
ArrayList<String> peps = psmf.getColumnValues("Peptide");
ArrayList<String> maxProbs = psmf.getColumnValues("delta_mass_maxloc");
ArrayList<String> entropies = psmf.getColumnValues("delta_mass_entropy");
ArrayList<String> maxProbs = psmf.getColumnValues("PTM-Shepherd Best Localization");
//ArrayList<String> entropies = psmf.getColumnValues("delta_mass_entropy");

// Add probs to target and decoy histos and calculate nTarget and nDecoyAAs
for (int j = 0; j < peps.size(); j++) {
Expand All @@ -527,18 +557,57 @@ private void calculateFalseLocalizationRates() throws Exception { //TODO this ne

// Add max probability and entropy
float p = Float.parseFloat(subString(maxProb, "(", ")"));
float entropy = Float.parseFloat(entropies.get(j));
//float entropy = Float.parseFloat(entropies.get(j));
if (isDecoyAA(maxProb.charAt(0))) {
decoyProbs[(int) (p * 1000.0)]++;
decoyEntropies[(int) (entropy * 1000.0)]++;
// decoyEntropies[(int) (entropy * 1000.0)]++;
} else {
targetProbs[(int) (p * 1000.0)]++;
targetEntropies[(int) (entropy * 1000.0)]++;
// targetEntropies[(int) (entropy * 1000.0)]++;
}
}
for (int j = 0; j < specs.size(); j++) {
String maxProb = maxProbs.get(j);
if (maxProb.equals(""))
continue;
double prob = Double.parseDouble(subString(maxProb, "(", ")"));
spqs.add(new SpecProbQ(specs.get(j), prob));
}

}
}

// Sort in descending probability order
Collections.sort(spqs, Collections.reverseOrder());

// Calculate local q-val
double runningQSum = 0.0;
int runningCount = 0;
for (SpecProbQ spq : spqs) {
runningQSum += 1.0 - spq.prob;
runningCount++;
spq.q = runningQSum / runningCount;
}

// Ensure q-val monotonicity
double cMin = 10000.0;
for (int i = spqs.size() - 1; i >= 0; i--) {
double tQ = spqs.get(i).q;
if (spqs.get(i).q < cMin) {
cMin = tQ;
} else {
while ((i >= 0) && (spqs.get(i).q >= cMin)) {
spqs.get(i).q = cMin;
i--;
}
i++;
}
}
// Extract spectrum to q-val and probability mappings in matched order
HashMap<String, Double> qValsMap = new HashMap<>();
for (SpecProbQ spq : spqs)
qValsMap.put(spq.spec, spq.q);

// Calculate the FLRs of each type
// Three different FLRs to compute
double[] flrProb = new double[1000+1]; // Assumes model probabilities are valid, does not use decoys
Expand Down Expand Up @@ -610,6 +679,9 @@ private void calculateFalseLocalizationRates() throws Exception { //TODO this ne
qEntropyDecoyModel[i] = min;
}




/**
// Print to test
for (int i = flrProb.length-1; i >= 0; i--) {
Expand Down Expand Up @@ -645,46 +717,44 @@ private void calculateFalseLocalizationRates() throws Exception { //TODO this ne
// Get values to map to q-vals
PSMFile psmf = new PSMFile(new File(dsData.get(i)[0]));
ArrayList<String> specNames = psmf.getColumnValues("Spectrum");
ArrayList<String> maxProbs = psmf.getColumnValues("delta_mass_maxloc");
ArrayList<String> entropies = psmf.getColumnValues("delta_mass_entropy");
ArrayList<String> maxProbs = psmf.getColumnValues("PTM-Shepherd Best Localization");
//ArrayList<String> entropies = psmf.getColumnValues("delta_mass_entropy");

// Assign each q-Val
ArrayList<String> probModelVals = new ArrayList<>(specNames.size());
ArrayList<String> probDecoyModelVals = new ArrayList<>(specNames.size());
ArrayList<String> entropyDecoyModelVals = new ArrayList<>(specNames.size());
ArrayList<String> probModelQVals = new ArrayList<>(specNames.size());
//ArrayList<String> probDecoyModelVals = new ArrayList<>(specNames.size());
//ArrayList<String> entropyDecoyModelVals = new ArrayList<>(specNames.size());
for (int j = 0; j < specNames.size(); j++) {

// Check if peptide is unmod and deal with it if it is
boolean unmodFlag = maxProbs.get(i).equals("") ? true : false;
boolean unmodFlag = maxProbs.get(j).equals("") ? true : false;
if (unmodFlag) {
// prob model
probModelVals.add("");
probModelQVals.add("");
// prob model with decoys
probDecoyModelVals.add("");
//probDecoyModelVals.add("");
// entropy model
entropyDecoyModelVals.add("");
//entropyDecoyModelVals.add("");
} else {
// prob model
double maxProb = Double.parseDouble(subString(maxProbs.get(i), "(", ")"));
probModelVals.add(new DecimalFormat("0.0000").format(qProbModel[(int) (maxProb * 1000)]));
probModelQVals.add(new DecimalFormat("0.0000").format(qValsMap.get(specNames.get(j))));
// prob model with decoys
probDecoyModelVals.add(new DecimalFormat("0.0000").format(qProbDecoyModel[(int) (maxProb * 1000)]));
//probDecoyModelVals.add(new DecimalFormat("0.0000").format(qProbDecoyModel[(int) (maxProb * 1000)]));
// entropy model
double entropy = Double.parseDouble(entropies.get(i));
entropyDecoyModelVals.add(new DecimalFormat("0.0000").format(qEntropyDecoyModel[(int) (entropy * 1000)]));
//double entropy = Double.parseDouble(entropies.get(i));
//entropyDecoyModelVals.add(new DecimalFormat("0.0000").format(qEntropyDecoyModel[(int) (entropy * 1000)]));
}
}

// Send to PSM file
psmf.addColumn(psmf.getColumn("delta_mass_maxloc") + 1, "delta_mass_BH_loc_q",
specNames, probModelVals);
psmf.addColumn(psmf.getColumn("PTM-Shepherd Best Localization") + 1, "PTM-Shepherd q-val",
specNames, probModelQVals);
/** //TODO figure out what's going on with these before implementing them, assuming they're even worth doing
psmf.addColumn(psmf.getColumn("delta_mass_BH_loc_q") + 1, "delta_mass_prob_decoyAA_q",
specNames, probDecoyModelVals);
psmf.addColumn(psmf.getColumn("delta_mass_entropy") + 1, "delta_mass_entropy_decoyAA_q",
specNames, entropyDecoyModelVals);
psmf.save(true); //TODO this will add these columns
**/
**/
psmf.save(true); // add columns
}
}

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