Add script to filter mutations in MAF file

This script uses the same filters that are used during the load (except filter by gene that required connection to the database)

src/main/java/org/mskcc/cbio/portal/scripts/FilterMutationData.java

@@ -0,0 +1,137 @@
+/*
+ * Copyright (c) 2015 - 2022 Memorial Sloan Kettering Cancer Center.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
+ * is on an "as is" basis, and Memorial Sloan Kettering Cancer Center has no
+ * obligations to provide maintenance, support, updates, enhancements or
+ * modifications. In no event shall Memorial Sloan Kettering Cancer Center be
+ * liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if Memorial Sloan Kettering Cancer
+ * Center has been advised of the possibility of such damage.
+ */
+
+/*
+ * This file is part of cBioPortal.
+ *
+ * cBioPortal is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.mskcc.cbio.portal.scripts;
+
+import joptsimple.OptionException;
+import joptsimple.OptionParser;
+import joptsimple.OptionSet;
+import joptsimple.OptionSpec;
+import org.mskcc.cbio.maf.MafRecord;
+import org.mskcc.cbio.maf.MafUtil;
+import org.mskcc.cbio.portal.util.*;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * Read MAF records, filter records of interest and writes back to the file. The script backs up original file under {filename with extension}_backup.
+ *
+ * @author Ruslan Forostianov
+ */
+public class FilterMutationData extends ConsoleRunnable {
+
+    /**
+     * Instantiates a ConsoleRunnable to run with the given command line args.
+     *
+     * @param args the command line arguments to be used
+     * @see {@link #run()}
+     */
+    public FilterMutationData(String[] args) {
+        super(args);
+    }
+
+    public void run() {
+        String description = "Filter MAF file for records of interest and rewrites it with selected mutations.";
+        OptionParser parser = new OptionParser();
+        OptionSpec<String> data = parser.accepts( "data",
+                "MAF data file" ).withRequiredArg().describedAs( "data_mutations.txt" ).ofType( String.class );
+        OptionSpec<String> meta = parser.accepts( "meta",
+                "meta (description) file" ).withOptionalArg().describedAs( "meta_mutations.txt" ).ofType( String.class );
+
+        OptionSet options = null;
+        File originalMutationFile;
+        Set<String> namespaces = null;
+        Set<String> filteredMutations = null;
+
+        try {
+            options = parser.parse( args );
+            originalMutationFile = new File((String) options.valueOf("data"));
+            if (options.has("meta")) {
+                File descriptorFile = new File((String) options.valueOf( "meta" ) );
+                filteredMutations = GeneticProfileReader.getVariantClassificationFilter(descriptorFile);
+                namespaces = GeneticProfileReader.getNamespaces(descriptorFile);
+            }
+        } catch (OptionException e) {
+            throw new UsageException(
+                    this.getClass().getName(), description, parser,
+                    e.getMessage());
+        } catch (Exception e) {
+           throw new RuntimeException(e);
+        }
+        ProgressMonitor.setCurrentMessage("Start filtering mutation records in the MAF file ...");
+        File resultMutationFile = new File(originalMutationFile.getAbsolutePath() + "_filtered");
+        final MutationFilter mutationFilter = new MutationFilter();
+        try (
+                BufferedReader originalFileBufferedReader = new BufferedReader(new FileReader(originalMutationFile));
+                BufferedWriter resultFileBufferedWriter = new BufferedWriter(new FileWriter(resultMutationFile))
+        ) {
+            String line;
+            MafUtil mafUtil = null;
+            while ((line = originalFileBufferedReader.readLine()) != null) {
+                ProgressMonitor.incrementCurValue();
+                ConsoleUtil.showProgress();
+
+                if (TsvUtil.isDataLine(line)) {
+                    if (mafUtil == null) {
+                        mafUtil = new MafUtil(line, namespaces);
+                    } else {
+                        MafRecord record = mafUtil.parseRecord(line);
+                        if (!mutationFilter.acceptMutation(record, filteredMutations)) {
+                            continue;
+                        }
+                    }
+                }
+                resultFileBufferedWriter.write(line);
+                resultFileBufferedWriter.write(System.lineSeparator());
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+        File backupMutationFile = new File(originalMutationFile.getAbsolutePath() + "_backup");
+        if (originalMutationFile.renameTo(backupMutationFile)) {
+            ProgressMonitor.setCurrentMessage("The original file is backed up to:"
+                    + backupMutationFile.getAbsolutePath());
+            if (resultMutationFile.renameTo(originalMutationFile)) {
+                ProgressMonitor.setCurrentMessage("The MAF file has been overwritten with filtered records.");
+            } else {
+                throw new RuntimeException("Failed to rename the filtered MAF file ("
+                        + resultMutationFile.getAbsolutePath() + ") to the input MAF file ("
+                        + originalMutationFile.getAbsolutePath() + ").");
+            }
+        } else {
+            throw new RuntimeException("Failed to rename MAF file ("
+                    + originalMutationFile.getAbsolutePath() + ") for backup.");
+        }
+        ProgressMonitor.setCurrentMessage(mutationFilter.getStatistics());
+    }
+}

src/test/java/org/mskcc/cbio/portal/scripts/TestFilterMutationData.java

@@ -0,0 +1,100 @@
+/*
+ * Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
+ * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
+ * obligations to provide maintenance, support, updates, enhancements or
+ * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
+ * liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if Memorial Sloan-Kettering Cancer
+ * Center has been advised of the possibility of such damage.
+ */
+
+/*
+ * This file is part of cBioPortal.
+ *
+ * cBioPortal is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.mskcc.cbio.portal.scripts;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.BeforeEach;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.util.Comparator;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+/**
+ * JUnit tests for FilterMutationData step
+ */
+public class TestFilterMutationData {
+
+    public static final String SRC_MAF_DATA_FILE_PATH = "src/test/resources/data_mutations_extended.txt";
+    private Path tempDir;
+
+    @BeforeEach
+    public void setUp() throws IOException {
+        // Create a temporary directory for each test
+        tempDir = Files.createTempDirectory("tempTestDir");
+
+        // Copy files to the temporary directory
+        Path dataFile = Paths.get(SRC_MAF_DATA_FILE_PATH);
+        Path copiedDataFile = tempDir.resolve(dataFile.getFileName());
+        Files.copy(dataFile, copiedDataFile, StandardCopyOption.REPLACE_EXISTING);
+
+        Path metaFile = Paths.get("src/test/resources/meta_mutations_extended.txt");
+        Path copiedMetaFile = tempDir.resolve(metaFile.getFileName());
+        Files.copy(metaFile, copiedMetaFile, StandardCopyOption.REPLACE_EXISTING);
+    }
+
+  @AfterEach
+    public void tearDown() throws IOException {
+        // Delete the temporary directory and files after each test
+        Files.walk(tempDir)
+                .sorted(Comparator.reverseOrder())
+                .map(Path::toFile)
+                .forEach(File::delete);
+    }
+
+    @Test
+    public void testFilterMutationData() throws IOException {
+        String mafFile = tempDir + "/data_mutations_extended.txt";
+        String[] args = {
+                "--data", mafFile,
+                "--meta", tempDir + "/meta_mutations_extended.txt"
+        };
+        FilterMutationData runner = new FilterMutationData(args);
+        runner.run();
+
+        List<String> filteredDataFileLines = Files.readAllLines(Paths.get(mafFile));
+        List<String> backedUpDataFileLines = Files.readAllLines(Paths.get(mafFile + "_backup"));
+        List<String> originalDataFileLines = Files.readAllLines(Paths.get(SRC_MAF_DATA_FILE_PATH));
+        assertEquals(originalDataFileLines, backedUpDataFileLines);
+        assertFalse(filteredDataFileLines.isEmpty());
+        assertTrue(originalDataFileLines.size() > filteredDataFileLines.size());
+        assertTrue(originalDataFileLines.containsAll(filteredDataFileLines));
+    }
+}