Usefull tools for working with Unigene.
* *This class is the main port-of-call for users of the Unigene package. It * provides the core APIs for finding a Unigene database as well as registering * your own Unigene drivers. Additionaly, it contains methods to return parsers * for each of the main Unigene flat-file types. If you wish to bypass the * biojava object model entirely, you can choose to use these parsers instead. *
* *Creating a Unigene instance from your local Unigene directory (assuming * that you have read/write privileges to the directory)
* *
* UnigeneDB unigene = UnigeneTools.createUnigene(
* new URL("file:///usr/local/biodata/unigene") );
*
*
* Fetch a unigene cluster
* *
* UnigeneDB unigene = UnigeneTools.loadUnigene(
* new URL("file:///usr/local/biodata/unigene") );
* UnigeneCluster cluster = unigenge.getCluster("Aga001");
* System.out.println("Title: " + cluster.getTitle());
*
*
* Parse a data file yourself
* *
* BufferedReader br = new BufferedReader(new FileReader(unigeneFile));
* Parser = new Parser();
* TagValueListener echo = new Echo();
* ParserListener pl = UnigeneTools.buildDataParser(echo);
*
* while(parser.read(br, pl.getParser(), pl.getListener())) {
* // read an entry
* }
*
*
* @author Matthew Pocock
*/
public class UnigeneTools {
/**
* * Annotation schema for all UnigeneCluster instances. This states what * propperties can be expected to be associated with a cluster and how many * values they may have. *
*/ public static final AnnotationType UNIGENE_ANNOTATION; /** ** Annotation schema for all Unigene libraries. This states what propperties * can be expected to be associated with a library and how many values they * may have. *
*/ public static final AnnotationType LIBRARY_ANNOTATION; private static final List factories; private static final Map shortName2SpeciesName; static { factories = new ArrayList(); registerFactory(new FlatFileUnigeneFactory()); shortName2SpeciesName = new HashMap(); shortName2SpeciesName.put("Aga", "Anophelese gambiae"); shortName2SpeciesName.put("Hs", "Homo sapiens"); shortName2SpeciesName.put("Aga", "Anopheles gambiae"); shortName2SpeciesName.put("Bt", "Bos taurus"); shortName2SpeciesName.put("Dm", "Drosophila melanogaster"); shortName2SpeciesName.put("Dr", "Danio rario"); shortName2SpeciesName.put("Mm", "Mus musculus"); shortName2SpeciesName.put("Rn", "Rattus norvegicus"); shortName2SpeciesName.put("Xl", "Xenopus laevis"); shortName2SpeciesName.put("At", "Arabidopsis thaliana"); shortName2SpeciesName.put("Gma", "Glycine max"); shortName2SpeciesName.put("Hv", "Hordeum vulgare"); shortName2SpeciesName.put("Les", "Lycopersicon esculentum"); shortName2SpeciesName.put("Mtr", "Medicago truncatula"); shortName2SpeciesName.put("Os", "Oryza sativa"); shortName2SpeciesName.put("Ta", "Triticum aestivum"); shortName2SpeciesName.put("Zm", "Zea mays"); // start to build this annotation type for .data files & UnigeneCluster // annotation bundles PropertyConstraint pc_string = new PropertyConstraint.ByClass(String.class); PropertyConstraint pc_int = new PropertyConstraint.ByClass(Integer.class); AnnotationType.Impl at_sts = new AnnotationType.Impl(); at_sts.setConstraints("NAME", pc_string, CardinalityConstraint.ONE); at_sts.setConstraints("ACC", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sts.setConstraints("DSEG", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sts.setConstraints("UNISTS", pc_string, CardinalityConstraint.ONE); PropertyConstraint pc_sts = new PropertyConstraint.ByAnnotationType(at_sts); AnnotationType.Impl at_txmap = new AnnotationType.Impl(); at_txmap.setConstraints("MARKER", pc_string, CardinalityConstraint.ONE); at_txmap.setConstraints("RHPANEL", pc_string, CardinalityConstraint.ONE); PropertyConstraint pc_txmap = new PropertyConstraint.ByAnnotationType(at_txmap); AnnotationType.Impl at_protsim = new AnnotationType.Impl(); at_protsim.setConstraints("ORG", pc_string, CardinalityConstraint.ONE); at_protsim.setConstraints("PROTGI", pc_string, CardinalityConstraint.ONE); at_protsim.setConstraints("PROTID", pc_string, CardinalityConstraint.ONE); at_protsim.setConstraints("PCT", pc_string, CardinalityConstraint.ONE); at_protsim.setConstraints("ALN", pc_int, CardinalityConstraint.ONE); PropertyConstraint pc_prosim = new PropertyConstraint.ByAnnotationType(at_protsim); AnnotationType.Impl at_sequence = new AnnotationType.Impl(); at_sequence.setConstraints("ACC", pc_string, CardinalityConstraint.ONE); at_sequence.setConstraints("NID", pc_string, CardinalityConstraint.ONE); at_sequence.setConstraints("PID", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sequence.setConstraints("CLONE", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sequence.setConstraints("END", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sequence.setConstraints("LID", pc_string, CardinalityConstraint.ZERO_OR_ONE); at_sequence.setConstraints("MGC", pc_string, CardinalityConstraint.ZERO_OR_ONE); PropertyConstraint pc_sequence = new PropertyConstraint.ByAnnotationType(at_sequence); AnnotationType.Impl unigene = new AnnotationType.Impl(); unigene.setConstraints("ID", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("TITLE", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("GENE", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("CYTOBAND", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("EXPRESS", pc_string, CardinalityConstraint.ONE); unigene.setConstraints( "GNM_TERMINUS", new PropertyConstraint.Enumeration(new Object[] { "T", "I", "S" } ), CardinalityConstraint.ONE); unigene.setConstraints("LOCUSLINK", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("CHROMOSOME", pc_string, CardinalityConstraint.ONE); unigene.setConstraints("STS", pc_sts, CardinalityConstraint.ANY); unigene.setConstraints("TXMAP", pc_txmap, CardinalityConstraint.ANY); unigene.setConstraints("PROSIM", pc_prosim, CardinalityConstraint.ANY); unigene.setConstraints("SCOUNT", pc_int, CardinalityConstraint.ONE); unigene.setConstraints("SEQUENCE", pc_sequence, CardinalityConstraint.ANY); UNIGENE_ANNOTATION = unigene; AnnotationType.Impl library = new AnnotationType.Impl(); library.setConstraints("ID", pc_string, CardinalityConstraint.ONE); library.setConstraints("TITLE", pc_string, CardinalityConstraint.ONE); library.setConstraints("TISSUE", pc_string, CardinalityConstraint.ONE); library.setConstraints("VECTOR", pc_string, CardinalityConstraint.ONE); LIBRARY_ANNOTATION = library; } /** * Converts short species names (like Hs) to long species names (like Homo * Sapiens). * * @param name the short name * @return the long name */ public static String getSpeciesForShortName(String name) { return (String) shortName2SpeciesName.get(name); } /** * Generate a tag-value parser for unigene data files that will pass all * parsing events on to your listener. * * @param listener the TagValueListener to pass events onto * @return a ParserListener that is ready to consume unigene data documents */ public static ParserListener buildDataParser(TagValueListener listener) throws ParserException { try { LineSplitParser entryParser = (LineSplitParser) LineSplitParser.GENBANK.clone(); entryParser.setTrimValue(true); entryParser.setEndOfRecord("//"); ChangeTable changeT = new ChangeTable(); changeT.setSplitter( "EXPRESS", new RegexSplitter(Pattern.compile("([^;]+)"), 1) ); changeT.setChanger("ALN", ChangeTable.STRING_TO_INT); changeT.setChanger("SCOUNT", ChangeTable.STRING_TO_INT); ValueChanger changer = new ValueChanger(listener, changeT); SplitAndProp splitAndProp = new SplitAndProp( listener, Pattern.compile("(\\S+?)=([^;\\s]*)") ); TagDelegator entryListener = new TagDelegator(changer); entryListener.setListener("STS", splitAndProp); entryListener.setListener("PROTSIM", splitAndProp); entryListener.setListener("SEQUENCE", splitAndProp); entryListener.setListener("TXMAP", new HandleMapInterval(listener)); return new ParserListener(entryParser, entryListener); } catch (CloneNotSupportedException cnse) { throw new BioError(cnse); } } /** * Generate a tag-value parser for the library info unigene files. * * @param listener the TagValueListener to pass events onto * @return a ParserListener that is ready to consume unigene lib.info files */ public static ParserListener buildLibInfoParser(TagValueListener listener) throws IOException, ParserException{ RegexParser parser = new RegexParser(); parser.setContinueOnEmptyTag(false); parser.setEndOfRecord(TagValueParser.EMPTY_LINE_EOR); parser.setMergeSameTag(false); parser.setPattern(Pattern.compile("([^=]+)=(.*)")); parser.setTagGroup(1); parser.setValueGroup(2); return new ParserListener(parser, listener); } private static class SplitAndProp extends SimpleTagValueWrapper { private Pattern splitPattern; public SplitAndProp(TagValueListener delegate, Pattern splitPattern) { super(delegate); this.splitPattern = splitPattern; } public void value(TagValueContext tvc, Object value) throws ParserException { TagValueListener delegate = super.getDelegate(); delegate.startRecord(); String sv = (String) value; Matcher m = splitPattern.matcher(sv); while(m.find()) { String k = m.group(1); String v = m.group(2); delegate.startTag(k); delegate.value(tvc, v); delegate.endTag(); } delegate.endRecord(); } } private static class HandleMapInterval extends SimpleTagValueWrapper { private Pattern pattern; public HandleMapInterval(TagValueListener tvl) { super(tvl); pattern = Pattern.compile("([^-]+-[^;]+);\\s+\\w+=([^;]+);\\s+\\w+=(\\S+)"); } public void value(TagValueContext tvc, Object value) throws ParserException { TagValueListener delegate = super.getDelegate(); delegate.startRecord(); String sv = (String) value; Matcher m = pattern.matcher(sv); if(!m.find()) { throw new ParserException("Could not parse line: " + sv); } delegate.startTag("INTERVAL"); delegate.value(tvc, m.group(1)); delegate.endTag(); delegate.startTag("MARKER"); delegate.value(tvc, m.group(2)); delegate.endTag(); delegate.startTag("RHPANEL"); delegate.value(tvc, m.group(3)); delegate.endTag(); delegate.endRecord(); } } /** *Register a UnigeneFactory.
* *This method is for developers who have written their own UnigeneFactory * implementations. By default, jdbc and file URLs are handled by built-in * factories.
* *When you register a factory, it will be used for all URLs that is can * accept. If a factory is registered afterwards that can accept the same URL, * the first factory registered will be used.
* * @param factory the UnigeneFactory to register */ public static void registerFactory(UnigeneFactory factory) { factories.add(factory); } /** *Register a UnigeneFactory.
* *This method is for developers who wish to unregister a factory.
* * @param factory the UnigeneFactory to unregister */ public static void unregisterFactory(UnigeneFactory factory) { factories.remove(factory); } /** * Load a UnigeneDB instance referred to by a URL. * * @param dbURL the URL location the database * @return a UnigeneDB instance * @throws BioException if there was no UnigeneFactory able to process that * URL or if there was some error connecting */ public static UnigeneDB loadUnigene(URL dbURL) throws BioException { return findFactory(dbURL).loadUnigene(dbURL); } /** * Create a new UnigeneDB instance referred to by a URL. * * @param dbURL the URL location the database * @return a UnigeneDB instance * @throws BioException if there was no UnigeneFactory able to process that * URL or if there was some error creating it */ public static UnigeneDB createUnigene(URL dbURL) throws BioException { return findFactory(dbURL).createUnigene(dbURL); } /** * Find the UnigeneFactory that can accept a URL. * *This method is for developers only. The normal way to interact * with factories is to call UnigeneTools.loadUnigene() and * UnigeneTools.createUnigene()
* * @param dbURL the URL to find a factory for * @return the UnigeneFactory that accepts that URL * @throws BioException if there is no factory for that type of URL */ public static UnigeneFactory findFactory(URL dbURL) throws BioException { for(Iterator i = factories.iterator(); i.hasNext(); ) { UnigeneFactory factory = (UnigeneFactory) i.next(); if(factory.canAccept(dbURL)) { return factory; } } throw new BioException("No factory for unigene url: " + dbURL); } }