--- /dev/null
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Scanner;
+
+import javax.swing.JOptionPane;
+
+public class HMMSearch extends HmmerCommand
+{
+ static final String HMMSEARCH = "hmmsearch";
+
+ /*
+ * constants for i18n lookup of passed parameter names
+ */
+ static final String DATABASE_KEY = "label.database";
+
+ static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+ static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+ static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+ static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+ static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+ static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+ static final String CUTOFF_NONE = "None";
+
+ static final String CUTOFF_SCORE = "Score";
+
+ static final String CUTOFF_EVALUE = "E-Value";
+
+ static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+ static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+ static final String SEQ_SCORE_KEY = "label.seq_score";
+
+ static final String DOM_SCORE_KEY = "label.dom_score";
+
+ boolean realign = false;
+
+ boolean trim = false;
+
+ int seqsToReturn = Integer.MAX_VALUE;
+
+ SequenceI[] seqs;
+
+ private String databaseName;
+
+ /**
+ * Constructor for the HMMSearchThread
+ *
+ * @param af
+ */
+ public HMMSearch(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ }
+
+ /**
+ * Runs the HMMSearchThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ HiddenMarkovModel hmm = getHmmProfile();
+ if (hmm == null)
+ {
+ // shouldn't happen if we got this far
+ Cache.log.error("Error: no hmm for hmmsearch");
+ return;
+ }
+
+ SequenceI hmmSeq = hmm.getConsensusSequence();
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ msgId);
+
+ try
+ {
+ File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+ File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
+ ".sto");
+ File searchOutputFile = FileUtils.createTempFile("searchOutput",
+ ".sto");
+
+ exportHmm(hmm, hmmFile.getAbsoluteFile());
+
+ boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmsearch"));
+ return;
+ }
+
+ importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
+ // TODO make realignment of search results a step at this level
+ // and make it conditional on this.realign
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ finally
+ {
+ af.setProgressBar("", msgId);
+ }
+ }
+
+ /**
+ * Executes an hmmsearch with the given hmm as input. The database to be
+ * searched is a local file as specified by the 'Database' parameter, or the
+ * current alignment (written to file) if none is specified.
+ *
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+ File hmmFile) throws IOException
+ {
+ String command = getCommandPath(HMMSEARCH);
+ if (command == null)
+ {
+ return false;
+ }
+
+ List<String> args = new ArrayList<>();
+ args.add(command);
+ buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile);
+
+ return runCommand(args);
+ }
+
+ /**
+ * Appends command line arguments to the given list, to specify input and
+ * output files for the search, and any additional options that may have been
+ * passed from the parameters dialog
+ *
+ * @param args
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
+ * @throws IOException
+ */
+ protected void buildArguments(List<String> args, File searchOutputFile,
+ File hitsAlignmentFile, File hmmFile) throws IOException
+ {
+ args.add("-o");
+ args.add(getFilePath(searchOutputFile));
+ args.add("-A");
+ args.add(getFilePath(hitsAlignmentFile));
+
+ boolean dbFound = false;
+ String dbPath = "";
+ File databaseFile = null;
+
+ boolean useEvalueCutoff = false;
+ boolean useScoreCutoff = false;
+ String seqEvalueCutoff = null;
+ String domEvalueCutoff = null;
+ String seqScoreCutoff = null;
+ String domScoreCutoff = null;
+ databaseName = "Alignment";
+ boolean searchAlignment = false;
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
+ .equals(name))
+ {
+ seqsToReturn = Integer.parseInt(arg.getValue());
+ }
+ else if (MessageManager.getString("action.search").equals(name))
+ {
+ searchAlignment = arg.getValue().equals(
+ MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbPath = arg.getValue();
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
+ else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
+ .equals(name))
+ {
+ realign = true;
+ }
+ else if (MessageManager.getString(USE_ACCESSIONS_KEY)
+ .equals(name))
+ {
+ args.add("--acc");
+ }
+ else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
+ .equals(name))
+ {
+ if (CUTOFF_EVALUE.equals(arg.getValue()))
+ {
+ useEvalueCutoff = true;
+ }
+ else if (CUTOFF_SCORE.equals(arg.getValue()))
+ {
+ useScoreCutoff = true;
+ }
+ }
+ else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
+ {
+ seqEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
+ {
+ seqScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DOM_EVALUE_KEY)
+ .equals(name))
+ {
+ domEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
+ {
+ domScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(TRIM_TERMINI_KEY)
+ .equals(name))
+ {
+ trim = true;
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbFound = true;
+ dbPath = arg.getValue();
+ if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
+ .equals(dbPath))
+ {
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
+ }
+ }
+ }
+
+ if (useEvalueCutoff)
+ {
+ args.add("-E");
+ args.add(seqEvalueCutoff);
+ args.add("--domE");
+ args.add(domEvalueCutoff);
+ }
+ else if (useScoreCutoff)
+ {
+ args.add("-T");
+ args.add(seqScoreCutoff);
+ args.add("--domT");
+ args.add(domScoreCutoff);
+ }
+
+// if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+// .equals(dbPath))
+ if (searchAlignment)
+ {
+ /*
+ * no external database specified for search, so
+ * export current alignment as 'database' to search,
+ * excluding any HMM consensus sequences it contains
+ */
+ databaseFile = FileUtils.createTempFile("database", ".sto");
+ AlignmentI al = af.getViewport().getAlignment();
+ AlignmentI copy = new Alignment(al);
+ List<SequenceI> hmms = copy.getHmmSequences();
+ for (SequenceI hmmSeq : hmms)
+ {
+ copy.deleteSequence(hmmSeq);
+ }
+ exportStockholm(copy.getSequencesArray(), databaseFile, null);
+ }
+
+ args.add(getFilePath(hmmFile));
+ args.add(getFilePath(databaseFile));
+ }
+
+ /**
+ * Imports the data from the temporary file to which the output of hmmsearch
+ * was directed. The results are optionally realigned using hmmalign.
+ *
+ * @param hmmSeq
+ */
+ private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
+ File hmmTemp, File searchOutputFile)
+ throws IOException, InterruptedException
+ {
+ BufferedReader br = new BufferedReader(
+ new FileReader(inputAlignmentTemp));
+ try
+ {
+ if (br.readLine() == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("label.no_sequences_found"));
+ return;
+ }
+ StockholmFile file = new StockholmFile(new FileParse(
+ inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+ seqs = file.getSeqsAsArray();
+
+ readTable(searchOutputFile);
+
+ int seqCount = Math.min(seqs.length, seqsToReturn);
+ SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+ hmmAndSeqs[0] = hmmSeq;
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
+
+ if (realign)
+ {
+ realignResults(hmmAndSeqs);
+ }
+ else
+ {
+ AlignmentI al = new Alignment(hmmAndSeqs);
+ AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ String ttl = "hmmSearch of " + databaseName + " using "
+ + hmmSeq.getName();
+ Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ hmmTemp.delete();
+ inputAlignmentTemp.delete();
+ searchOutputFile.delete();
+ } finally
+ {
+ if (br != null)
+ {
+ br.close();
+ }
+ }
+ }
+
+ /**
+ * Realigns the given sequences using hmmalign, to the HMM profile sequence
+ * which is the first in the array, and opens the results in a new frame
+ *
+ * @param hmmAndSeqs
+ */
+ protected void realignResults(SequenceI[] hmmAndSeqs)
+ {
+ /*
+ * and align the search results to the HMM profile
+ */
+ AlignmentI al = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(al, 1, 1);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ String alignTo = hmmAndSeqs[0].getName();
+ List<String> options = Collections.singletonList(alignTo);
+ Option option = new Option(MessageManager.getString("label.use_hmm"),
+ "", true, alignTo, alignTo, options, null);
+ alignArgs.add(option);
+ if (trim)
+ {
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString(TRIM_TERMINI_KEY),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
+ }
+ HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
+ hmmalign.run();
+ }
+
+ /**
+ * Reads in the scores table output by hmmsearch and adds annotation to
+ * sequences for E-value and bit score
+ *
+ * @param inputTableTemp
+ * @throws IOException
+ */
+ void readTable(File inputTableTemp) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+ String line = "";
+ while (!line.startsWith("Query:"))
+ {
+ line = br.readLine();
+ }
+ for (int i = 0; i < 5; i++)
+ {
+ line = br.readLine();
+ }
+
+ int index = 0;
+ while (!" ------ inclusion threshold ------".equals(line)
+ && !"".equals(line))
+ {
+ SequenceI seq = seqs[index];
+ Scanner scanner = new Scanner(line);
+ String str = scanner.next();
+ addScoreAnnotation(str, seq, "hmmsearch E-value",
+ "Full sequence E-value");
+ str = scanner.next();
+ addScoreAnnotation(str, seq, "hmmsearch Score",
+ "Full sequence bit score");
+ scanner.close();
+ line = br.readLine();
+ index++;
+ }
+
+ br.close();
+ }
+
+ /**
+ * A helper method that adds one score-only (non-positional) annotation to a
+ * sequence
+ *
+ * @param value
+ * @param seq
+ * @param label
+ * @param description
+ */
+ protected void addScoreAnnotation(String value, SequenceI seq,
+ String label, String description)
+ {
+ try
+ {
+ AlignmentAnnotation annot = new AlignmentAnnotation(label,
+ description, null);
+ annot.setCalcId(HMMSEARCH);
+ double eValue = Double.parseDouble(value);
+ annot.setScore(eValue);
+ annot.setSequenceRef(seq);
+ seq.addAlignmentAnnotation(annot);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Error parsing " + label + " from " + value);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff