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Update percolator to pepxml rewriting #917

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Update percolator to pepxml rewriting #917

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aaa0088
Bring some sanity to pin/pepxml rewriting
Dec 7, 2022
58de27b
Remove comet test dir from test
Dec 8, 2022
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1 change: 1 addition & 0 deletions MSFragger-GUI/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,7 @@ distributions {
dependencies {
implementation 'com.github.albfernandez:juniversalchardet:2.4.0'
compileOnly files('tools/batmass-io-1.28.8.jar')
implementation 'com.fasterxml.woodstox:woodstox-core:6.2.8'
implementation 'com.google.code.gson:gson:2.10'
implementation 'one.util:streamex:0.8.1'
implementation 'org.jooq:jool-java-8:0.9.14'
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2 changes: 1 addition & 1 deletion MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeRun.java
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Expand Up @@ -1137,7 +1137,7 @@ private static boolean configureTaskGraph(JComponent parent, Path wd, Path jarPa
addConfig.accept(cmdPercolator, () -> {
if (cmdPercolator.isRun()) {
final String percolatorCmd = percolatorPanel.getCmdOpts();
if (!cmdPercolator.configure(parent, jarPath, percolatorCmd, isCombinedPepxml_percolator, sharedPepxmlFilesBeforePeptideValidation, crystalcPanel.isRun(), percolatorPanel.getMinProb())) {
if (!cmdPercolator.configure(parent, jarPath, percolatorCmd, decoyTag, isCombinedPepxml_percolator, sharedPepxmlFilesBeforePeptideValidation, crystalcPanel.isRun(), percolatorPanel.getMinProb())) {
return false;
}
}
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60 changes: 29 additions & 31 deletions MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/CmdPercolator.java
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Expand Up @@ -44,6 +44,8 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import com.github.chhh.utils.PathUtils;
import org.apache.commons.io.FilenameUtils;
import org.jooq.lambda.Seq;
import org.slf4j.Logger;
Expand Down Expand Up @@ -113,7 +115,7 @@ private static String remove_rank_suffix(final String s) {
/**
* @param pepxmlFiles Either pepxml files after search or after Crystal-C.
*/
public boolean configure(Component comp, Path jarFragpipe, String percolatorCmd, boolean combine, Map<InputLcmsFile, List<Path>> pepxmlFiles, boolean hasCrystalC, double minProb) {
public boolean configure(Component comp, Path jarFragpipe, String percolatorCmd, String decoyPrefix, boolean combine, Map<InputLcmsFile, List<Path>> pepxmlFiles, boolean hasCrystalC, double minProb) {
PeptideProphetParams percolatorParams = new PeptideProphetParams();
percolatorParams.setCmdLineParams(percolatorCmd);

Expand All @@ -133,55 +135,60 @@ public boolean configure(Component comp, Path jarFragpipe, String percolatorCmd,
for (Entry<InputLcmsFile, List<Path>> e : pepxmlFiles.entrySet()) {
for (Path pepxmlPath : e.getValue()) {
final Path pepxmlDir = pepxmlPath.getParent();
final String nameWithoutExt = FilenameUtils.removeExtension(pepxmlPath.getFileName().toString());
final String basename = remove_rank_suffix(nameWithoutExt);
if(!basenames.add(basename))
//final String nameWithoutExt = FilenameUtils.removeExtension(pepxmlPath.getFileName().toString());
final String nameWithoutExt = PathUtils.removeExtension(pepxmlPath.getFileName().toString(), 2, 10);
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@chhh Why create a new PathUtils.removeExtension() to replace the existing FilenameUtils.removeExtension?

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This one has additional parameters - how many times to remove an extension (in case of files like file.raw.pep.xml) and a limit on the length of the extension, this catches cases when somebody puts a dot in the file name.
I didn't just replace it in order to replace it, there was a real life example where the original one from apache commons failed.

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This is why I forced MSFragger to always generate <file name>.pepXML. If you want to support <file name>.pep.xml, there will be a lot of places to change and test. I think many places, including the other tools used by FragPipe, assume that the extension is everything after the last dot.

Since your case will never happen if use MSFragger, I don't think it is necessary to implement this new function to make the things more complicated.

final String fnBase = remove_rank_suffix(nameWithoutExt);
if(!basenames.add(fnBase))
continue;
// Percolator
List<String> cmdPp = new ArrayList<>();
final String percolator_bin = OsUtils.isUnix() ? "percolator-305/percolator" :
OsUtils.isWindows() ? "percolator-305/percolator.exe" : null;
cmdPp.add(FragpipeLocations.checkToolsMissing(Seq.of(percolator_bin)).get(0).toString());

String strippedBaseName;
final String fnStripped;
if (hasCrystalC) {
strippedBaseName = basename.replaceFirst("_c$", "");
fnStripped = fnBase.replaceFirst("_c$", "");
} else {
strippedBaseName = basename;
fnStripped = fnBase;
}

addFreeCommandLineParams(percolatorParams, cmdPp);
TabWorkflow tabWorkflow = Fragpipe.getStickyStrict(TabWorkflow.class);
cmdPp.add("--num-threads");
cmdPp.add("" + tabWorkflow.getThreads());
cmdPp.add("--protein-decoy-pattern");
cmdPp.add(decoyPrefix);
cmdPp.add("--results-psms");
cmdPp.add(strippedBaseName + "_percolator_target_psms.tsv");
cmdPp.add(fnStripped + "_percolator_target_psms.tsv");
cmdPp.add("--decoy-results-psms");
cmdPp.add(strippedBaseName + "_percolator_decoy_psms.tsv");
cmdPp.add(fnStripped + "_percolator_decoy_psms.tsv");

if (msboosterPanel.isRun()) {
cmdPp.add(Paths.get(strippedBaseName + "_edited.pin").toString());
cmdPp.add(Paths.get(fnStripped + "_edited.pin").toString());
} else {
cmdPp.add(Paths.get(strippedBaseName + ".pin").toString());
cmdPp.add(Paths.get(fnStripped + ".pin").toString());
}

ProcessBuilder pbPp = new ProcessBuilder(cmdPp);
setupEnv(pepxmlDir, pbPp);
pbisParallel.add(new PbiBuilder()
.setPb(pbPp)
.setParallelGroup(basename).create());
.setParallelGroup(fnBase).create());

// convert the percolator output tsv to PeptideProphet's pep.xml format
ProcessBuilder pbRewrite = pbConvertToPepxml(jarFragpipe, "interact-" + basename, strippedBaseName, basename, e.getKey().getDataType().contentEquals("DDA"), minProb);
final String fnOutBase = "interact-" + fnBase;
final boolean isDda = e.getKey().getDataType().contentEquals("DDA");
ProcessBuilder pbRewrite = pbConvertToPepxml(jarFragpipe, fnOutBase, fnStripped, fnBase, isDda, minProb);
pbRewrite.directory(pepxmlPath.getParent().toFile());
pbisPostParallel.add(new PbiBuilder().setName("Percolator: Convert to pepxml").setPb(pbRewrite).setParallelGroup(ProcessBuilderInfo.GROUP_SEQUENTIAL).create());

// delete intermediate files
PercolatorPanel percolatorPanel = Fragpipe.getStickyStrict(PercolatorPanel.class);
if (!percolatorPanel.isKeepTsvFiles()) {
final List<Path> temp = new ArrayList<>();
temp.add(pepxmlDir.resolve(strippedBaseName + "_percolator_target_psms.tsv"));
temp.add(pepxmlDir.resolve(strippedBaseName + "_percolator_decoy_psms.tsv"));
temp.add(pepxmlDir.resolve(fnStripped + "_percolator_target_psms.tsv"));
temp.add(pepxmlDir.resolve(fnStripped + "_percolator_decoy_psms.tsv"));
List<ProcessBuilder> pbsDeleteTemp = ToolingUtils
.pbsDeleteFiles(jarFragpipe, temp);
pbisPostParallel.addAll(pbsDeleteTemp.stream()
Expand Down Expand Up @@ -221,26 +228,17 @@ public ProcessBuildersDescriptor getBuilderDescriptor() {
return b;
}

private static ProcessBuilder pbConvertToPepxml(Path jarFragpipe, String outBaseName, String stripedBasename, String basename, boolean isDDA, double minProb) {
private static ProcessBuilder pbConvertToPepxml(Path jarFragpipe, String fnOutBase, String fnStripped, String fnBase, boolean isDDA, double minProb) {
if (jarFragpipe == null) {
throw new IllegalArgumentException("jar can't be null");
}
final List<String> cmd = new ArrayList<>();
cmd.add(Fragpipe.getBinJava());
cmd.add("-cp");
Path root = FragpipeLocations.get().getDirFragpipeRoot();
String libsDir = root.resolve("lib") + "/*";
if (Files.isDirectory(jarFragpipe)) {
libsDir = jarFragpipe.getParent().getParent().getParent().getParent().resolve("build/install/fragpipe/lib") + "/*";
log.debug("Dev message: Looks like FragPipe was run from IDE, changing libs directory to: {}", libsDir);
}
cmd.add(libsDir);
final List<String> cmd = ToolingUtils.cmdStubForJar(jarFragpipe);
cmd.add(PercolatorOutputToPepXML.class.getCanonicalName());
cmd.add(stripedBasename + ".pin");
cmd.add(basename);
cmd.add(stripedBasename + "_percolator_target_psms.tsv");
cmd.add(stripedBasename + "_percolator_decoy_psms.tsv");
cmd.add(outBaseName);
cmd.add(fnStripped + ".pin");
cmd.add(fnBase);
cmd.add(fnStripped + "_percolator_target_psms.tsv");
cmd.add(fnStripped + "_percolator_decoy_psms.tsv");
cmd.add(fnOutBase);
cmd.add(isDDA ? "DDA" : "DIA");
cmd.add(minProb + "");
return new ProcessBuilder(cmd);
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