--- /dev/null
+/**
+ * File written by Raphael Champeimont
+ * UMR 7238 Genomique des Microorganismes
+ */
+package fr.orsay.lri.varna.models.templates;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.exceptions.ExceptionXmlLoading;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+
+public class BatchBenchmark {
+ private VARNAConfig conf = new VARNAConfig();
+
+ final boolean DEFAULT_STRAIGHT_BULGES = false;
+
+ public static RNA loadRNA(File file) throws ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed {
+ Collection<RNA> rnas = RNAFactory.loadSecStr(file.getPath());
+ if (rnas.isEmpty()) {
+ throw new ExceptionFileFormatOrSyntax(
+ "No RNA could be parsed from that source.");
+ }
+ return rnas.iterator().next();
+ }
+
+ public void benchmarkRNA(File templatePath, File rnaPath, BufferedWriter outbuf) throws ExceptionXmlLoading, RNATemplateDrawingAlgorithmException, ExceptionFileFormatOrSyntax, ExceptionUnmatchedClosingParentheses, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionNAViewAlgorithm, IOException {
+ // load template
+ RNATemplate template = RNATemplate.fromXMLFile(templatePath);
+
+ // load RNA
+ RNA rna = loadRNA(rnaPath);
+
+ for (int algo=0; algo<=100; algo++) {
+ String algoname = "";
+
+ // draw RNA
+ switch (algo) {
+ //case 0:
+ // rna.drawRNALine(conf);
+ // algoname = "Linear";
+ // break;
+ //case 1:
+ // rna.drawRNACircle(conf);
+ // algoname = "Circular";
+ // break;
+ case 2:
+ rna.drawRNARadiate(conf);
+ algoname = "Radiate";
+ break;
+ case 3:
+ rna.drawRNANAView(conf);
+ algoname = "NAView";
+ break;
+ case 10:
+ algoname = "Template/noadj";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE, DEFAULT_STRAIGHT_BULGES);
+ break;
+ case 11:
+ algoname = "Template/noadj/ellipses";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES, DEFAULT_STRAIGHT_BULGES);
+ break;
+ case 12:
+ algoname = "Template/noadj/smart";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOADJUST, DrawRNATemplateCurveMethod.SMART, DEFAULT_STRAIGHT_BULGES);
+ break;
+ /*
+ case 5:
+ algoname = "Template/maxfactor";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.MAXSCALINGFACTOR, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE, DEFAULT_STRAIGHT_BULGES);
+ break;
+ */
+ case 6:
+ algoname = "Template/mininter";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.NOINTERSECT, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE, DEFAULT_STRAIGHT_BULGES);
+ break;
+ case 30:
+ algoname = "Template/translate";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.EXACTLY_AS_IN_TEMPLATE, DEFAULT_STRAIGHT_BULGES);
+ break;
+ case 31:
+ algoname = "Template/translate/ellipses";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.ALWAYS_REPLACE_BY_ELLIPSES, DEFAULT_STRAIGHT_BULGES);
+ break;
+ case 32:
+ algoname = "Template/translate/smart";
+ rna.drawRNATemplate(template, conf, DrawRNATemplateMethod.HELIXTRANSLATE, DrawRNATemplateCurveMethod.SMART, DEFAULT_STRAIGHT_BULGES);
+ break;
+ default:
+ continue;
+ }
+
+ // benchmark
+ Benchmark benchmark = new Benchmark(rna);
+
+ // print results
+ outbuf.write(
+ removeExt(rnaPath.getName())
+ + "\t" + algoname
+ + "\t" + benchmark.backboneCrossings
+ // averageUnpairedDistance % -> best is 100
+ + "\t" + (benchmark.averageUnpairedDistance / benchmark.targetConsecutiveBaseDistance *100)
+ + "\t" + benchmark.tooNearConsecutiveBases
+ + "\t" + benchmark.tooFarConsecutiveBases
+ + "\n");
+ }
+
+ }
+
+ public void runBenchmark(List<File> templates, List<File> rnas, File outfile) throws Exception {
+ if (templates.size() != rnas.size()) {
+ throw new Error("templates and rnas list size differ");
+ }
+
+ BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
+
+ outbuf.write("RNA\tAlgorithm\tBackbone crossings\tAverage unpaired distance %\tToo near\tToo far\n");
+
+ for (int i=0; i<templates.size(); i++) {
+ System.out.println("Benchmarking for RNA " + removeExt(rnas.get(i).getName()));
+ benchmarkRNA(templates.get(i), rnas.get(i), outbuf);
+ }
+
+ outbuf.close();
+
+ System.out.println("******* Benchmark finished. *******");
+ }
+
+ public void runExamples() throws Exception {
+ File templatesDir = new File("templates");
+ File root = new File(templatesDir, "examples");
+ File outfile = new File(new File(templatesDir, "benchmark"), "benchmark.txt");
+
+ String seqlist[] = {"RNase P E Coli.ct", "RNase P Synechocystis-PCC6803.ct", "RNase P M Musculus.ct"};
+
+ List<File> templates = new ArrayList<File>();
+ List<File> rnas = new ArrayList<File>();
+
+ for (String seq: seqlist) {
+ templates.add(new File(root, "RNase P E Coli.xml"));
+ rnas.add(new File(root, seq));
+ }
+
+ runBenchmark(templates, rnas, outfile);
+ }
+
+ public static void readFASTA(File file, List<String> seqnames, List<String> sequences) throws IOException {
+ BufferedReader buf = new BufferedReader(new FileReader(file));
+ String line = buf.readLine();
+ while (line != null) {
+ if (line.length() != 0) {
+ if (line.charAt(0) == '>') {
+ String id = line.substring(1); // remove the >
+ seqnames.add(id);
+ sequences.add("");
+ } else {
+ sequences.set(sequences.size()-1, sequences.get(sequences.size()-1) + line);
+ }
+ }
+ line = buf.readLine();
+ }
+ buf.close();
+ }
+
+
+ /**
+ * We assume given directory contains a alignemnt.fasta file,
+ * of which the first sequence is the consensus structure,
+ * and the other sequences are aligned nucleotides.
+ * The principle is to convert it to a set of secondary structure,
+ * using the following rule:
+ * - keep the same nucleotides as in original sequence
+ * - keep base pairs where both bases of the pair are non-gaps in our sequence
+ */
+ public void benchmarkAllDir(File rootdir) throws Exception {
+ File seqdir = new File(rootdir, "sequences");
+ File templateFile = new File(rootdir, "template.xml");
+ File sequenceFiles[] = seqdir.listFiles();
+ Arrays.sort(sequenceFiles);
+
+ List<File> templates = new ArrayList<File>();
+ List<File> rnas = new ArrayList<File>();
+ for (File seq: sequenceFiles) {
+ if (!seq.getPath().endsWith(".dbn")) continue;
+ rnas.add(seq);
+ templates.add(templateFile);
+ }
+
+ File outfile = new File(rootdir, "benchmark.txt");
+ runBenchmark(templates, rnas, outfile);
+
+ }
+
+
+ public static void main(String[] args) throws Exception {
+ File templatesDir = new File("templates");
+ if (args.length < 1) {
+ System.out.println("Command-line argument required: RNA");
+ System.out.println("Example: RNaseP_bact_a");
+ System.exit(1);
+ }
+ //new BatchBenchmark().runExamples();
+ for (String arg: args) {
+ new BatchBenchmark().benchmarkAllDir(new File(templatesDir, arg));
+ }
+ }
+
+ /**
+ * Return the given file path without the (last) extension.
+ */
+ public static String removeExt(String path) {
+ return path.substring(0, path.lastIndexOf('.'));
+ }
+
+ public static File removeExt(File path) {
+ return new File(removeExt(path.getPath()));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff