fasta to clustal format and write clustal input files.
--- /dev/null
+package compbio.data.sequence;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+
+import compbio.util.annotation.Immutable;
+
+/*
+ * RNA secondary structure
+ */
+
+@XmlAccessorType(XmlAccessType.FIELD)
+public final class RNAstruct {
+
+ private String sequence;
+ private String structure; // needs to be array to deal with all output
+ private Float minEnergy;
+ private Float energySum1; private Float energySum2;
+
+
+ public RNAstruct() {
+ // default JaxB Constructor
+ }
+
+ public RNAstruct(String sequence, String structure, Float minEnergy
+ , Float energySum1, Float energySum2) {
+ this.sequence = sequence;
+ this.structure = structure;
+ this.minEnergy = minEnergy;
+ this.energySum1 = energySum1;
+ this.energySum2 = energySum2;
+ }
+
+ public String getSequence() {
+ return sequence;
+ }
+
+ public String getStructure() {
+ return structure;
+ }
+
+ public Float getEnergy() {
+ return minEnergy;
+ }
+
+
+ @Override
+ public String toString() {
+ String newLine = System.getProperty("line.separator",".");
+ return sequence + newLine + structure + " (" + minEnergy.toString()
+ + " = " + energySum1.toString() + " + " + energySum2.toString()
+ + ")";
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj == null) {
+ return false;
+ }
+ if (!(obj instanceof RNAstruct)) {
+ return false;
+ }
+ RNAstruct st = (RNAstruct) obj;
+ if (!(this.getSequence() == st.getSequence() &&
+ this.getStructure() == st.getStructure() &&
+ this.getEnergy() == st.getEnergy())) {
+ return false;
+ }
+
+ return true;
+ }
+}
+
+
}\r
return annotations;\r
}\r
+ \r
+ /*\r
+ * Reads and parses the output of an RNAalifold job \r
+ * \r
+ * Currently only in the defualt no args format\r
+ */\r
+ public static RNAstruct readRNAalifoldResults(InputStream results) {\r
+ if (results == null) {\r
+ throw new NullPointerException(\r
+ "InputStream with results must be provided");\r
+ }\r
+ Scanner sc = new Scanner(results);\r
+ sc.useDelimiter("\\s+");\r
+ String sequence = sc.next();\r
+ String structure = sc.next();\r
+ // now get energy values out of the brackets\r
+ String regex = "-?[0-9]*\\.?[0-9]+";\r
+ Float minEnergy = Float.parseFloat(sc.findInLine(regex));\r
+ \r
+ RNAstruct rnastruct = new RNAstruct(sequence, structure, minEnergy,\r
+ Float.parseFloat(sc.findInLine(regex)), \r
+ Float.parseFloat(sc.findInLine(regex)));\r
+ \r
+ sc.close();\r
+ return rnastruct;\r
+ }\r
+ \r
+ \r
\r
/**\r
* Reads and parses Fasta or Clustal formatted file into a list of\r
return fastaSeqs;\r
}\r
\r
+ // This can't possibly be right for all cases!\r
+ // but it will do for now\r
+ \r
+ // As for the metadata. This function doesnt know what program\r
+ // generated it. How to handle the metadata!?\r
+ \r
+ public static void writeClustal(OutputStream outStream,\r
+ List<FastaSequence> sequences, char gapChar) \r
+ throws IOException {\r
+ \r
+ BufferedWriter writer = new BufferedWriter(\r
+ new OutputStreamWriter(outStream));\r
+ // will give AlignmentMetadata default type of CLUSTAL for now\r
+ AlignmentMetadata al = new AlignmentMetadata(Program.CLUSTAL, gapChar);\r
+ \r
+ ClustalAlignmentUtil.writeClustalAlignment(writer, \r
+ new Alignment(sequences, al));\r
+ \r
+ }\r
+\r
}\r
\r
enum DisemblResult {\r
package compbio.runner;\r
\r
import java.io.File;\r
+import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.ClustalAlignmentUtil;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAstruct;\r
import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
+ e.getLocalizedMessage(), e);\r
}\r
}\r
+ \r
+ public static void writeClustalInput(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {\r
+ \r
+ try {\r
+ File filein = new File(exec.getInput());\r
+ FileOutputStream fout = new FileOutputStream(filein);\r
+ log.debug("File path: " + filein.getAbsolutePath());\r
+ SequenceUtil.writeClustal(fout, sequences, gapChar);\r
+ fout.close();\r
+ } catch (IOException e) {\r
+ log.error("IOException while writing input file into the disk: "\r
+ + e.getLocalizedMessage(), e);\r
+ throw new JobSubmissionException(\r
+ "We are sorry but JABAWS server seems to have a problem! "\r
+ + e.getLocalizedMessage(), e);\r
+ }\r
+ }\r
+ \r
+ public static final RNAstruct readRNAStructFile(String workDirectory,\r
+ String structFile) throws IOException, FileNotFoundException {\r
+ assert !compbio.util.Util.isEmpty(workDirectory);\r
+ assert !compbio.util.Util.isEmpty(structFile);\r
+ File sfile = new File(compbio.engine.client.Util.getFullPath(\r
+ workDirectory, structFile));\r
+ log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());\r
+ if(!(sfile.exists() && sfile.length() > 0)) {\r
+ throw new FileNotFoundException("Result for the jobId "\r
+ + workDirectory + "with file name " + structFile\r
+ + " is not found!");\r
+ }\r
+ return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(\r
+ new FileInputStream(sfile));\r
+ }\r
+ \r
+ \r
\r
}\r
import java.io.BufferedReader;
import java.io.File;
+
+
import org.apache.log4j.Logger;
-import compbio.data.sequence.Alignment;
+import compbio.data.sequence.RNAstruct;
import compbio.data.sequence.UnknownFileFormatException;
import compbio.engine.client.PipedExecutable;
import compbio.engine.client.SkeletalExecutable;
@SuppressWarnings("unchecked")
@Override
// PlaceHolder method
- public String getResults(String workDirectory)
+ public RNAstruct getResults(String workDirectory)
throws ResultNotAvailableException {
try {
- // System.out.print(readRNAStruct(workDirectory, getOutput()));
- return readRNAStruct(workDirectory, getOutput());
+ // System.out.println("Specialread " + Util.readRNAStructFile(workDirectory, getOutput()).toString());
+ return Util.readRNAStructFile(workDirectory, getOutput());
+
} catch (FileNotFoundException e) {
log.error(e.getMessage(), e.getCause());
throw new ResultNotAvailableException(e);
}
}
+
+ // OLD :- the new methods for reading are found in
+ // - compbio.data.sequence.SequenceUtil and
+ // - compbio.runner.Util
// Simple and generic methods for reading a whole file
// Should surfice until a more detailed datamodel and parser are developed
- private static String readRNAStruct(String workDirectory,
- String structFile) throws IOException, FileNotFoundException {
- assert !compbio.util.Util.isEmpty(workDirectory);
- assert !compbio.util.Util.isEmpty(structFile);
- File sfile = new File(compbio.engine.client.Util.getFullPath(
- workDirectory, structFile));
- log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
- if(!(sfile.exists() && sfile.length() > 0)) {
- throw new FileNotFoundException("Result for the jobId "
- + workDirectory + "with file name " + structFile
- + " is not found!");
- }
- return readFile(sfile);
- }
-
- private static BufferedReader input;
- public static String readFile(File inputFile) throws
- FileNotFoundException, IOException {
-
- input = new BufferedReader(new FileReader(inputFile));
-
- String file = new String();
- String line = new String();
-
- while (true) {
- line = input.readLine();
-
- if (line != null) {
- file = file + line + "\r\n";
- } else break;
- }
- // Close file
- input.close();
- return file;
- }
+// private static String readRNAStruct(String workDirectory,
+// String structFile) throws IOException, FileNotFoundException {
+// assert !compbio.util.Util.isEmpty(workDirectory);
+// assert !compbio.util.Util.isEmpty(structFile);
+// File sfile = new File(compbio.engine.client.Util.getFullPath(
+// workDirectory, structFile));
+// log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
+// if(!(sfile.exists() && sfile.length() > 0)) {
+// throw new FileNotFoundException("Result for the jobId "
+// + workDirectory + "with file name " + structFile
+// + " is not found!");
+// }
+// return readFile(sfile);
+// }
+//
+// private static BufferedReader input;
+// public static String readFile(File inputFile) throws
+// FileNotFoundException, IOException {
+//
+// input = new BufferedReader(new FileReader(inputFile));
+//
+// String file = new String();
+// String line = new String();
+//
+// while (true) {
+// line = input.readLine();
+//
+// if (line != null) {
+// file = file + line + "\r\n";
+// } else break;
+// }
+// // Close file
+// input.close();
+// return file;
+// }
}
}\r
}\r
\r
+ // Potential Bug :- Sequence names are shortened to 2-3 letters\r
+ @Test\r
+ public void testReadFastaWriteClustal() {\r
+ \r
+ try {\r
+ FileInputStream fio = new FileInputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
+ assertNotNull(fio);\r
+ List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
+ assertNotNull(fseqs);\r
+ fio.close();\r
+ \r
+ char gapChar = '-';\r
+ FileOutputStream fou = new FileOutputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");\r
+ SequenceUtil.writeClustal(fou, fseqs, gapChar);\r
+ fou.close();\r
+ \r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ } \r
+ \r
+ \r
+\r
+ \r
+ \r
/**\r
* This test tests the loading of horizontally formatted Jronn output file\r
*/\r
}\r
}\r
}\r
+\r
@Test(groups = { AllTestSuit.test_group_runner })
public void testRunLocally() {
RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
+ rnaalifold.setInput(AllTestSuit.test_alignment_input).setOutput(test_outfile);
try{
ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
--- /dev/null
+package compbio.data.structure;
+
+import java.security.InvalidParameterException;
+import java.util.List;
+
+import javax.jws.WebMethod;
+import javax.jws.WebParam;
+import javax.jws.WebService;
+
+import compbio.data.msa.JABAService;
+import compbio.data.msa.JManagement;
+import compbio.data.msa.Metadata;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Option;
+import compbio.metadata.Preset;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+
+/*
+ * Interface for tools that results RNA secondary structure information
+ *
+ * Still Unsure whether a new interface is needed or whether secondary structre
+ * information could be exressed as a sequence annotation
+ */
+
+// effect of a different targetNamespace?
+@WebService(targetNamespace = JABAService.V2_SERVICE_NAMESPACE)
+public interface FoldWS<T>
+ extends
+ JABAService,
+ JManagement,
+ Metadata<T> {
+
+
+
+ @WebMethod
+ String fold(
+ @WebParam(name = )
+}
private static final LimitsManager<RNAalifold> limitMan = compbio.engine.client.Util
.getLimits(new RNAalifold().getType());
+ //public String fold()
+
+
ConfiguredExecutable<RNAalifold> init() throws JobSubmissionException {
RNAalifold rnaalifold = new RNAalifold();
rnaalifold.setInput(SkeletalExecutable.INPUT)
// PlaceHolder
public ChunkHolder pullExecStatistics(String jobId, long position) {
- WSUtil.validateJobId(jobId);
+// WSUtil.validateJobId(jobId);
// String file = Configurator.getWorkDirectory(jobId) + File.separator
// + RNAalifold.getStatFile();
// ChunkHolder cholder = WSUtil.pullFile(file, position);
// return cholder;
- return null;
+ return new ChunkHolder("", -1);
}
}
reportUsage(confExec, logger);\r
return jobId;\r
}\r
+ \r
+ // Hardcoded gapchar '-'\r
+ \r
+ public static <T> String fold(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<T> confExec, Logger logger,\r
+ String callingMethod, Limit<T> limit)\r
+ throws LimitExceededException, JobSubmissionException {\r
+ \r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\r
+ compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
+ AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+ String jobId = engine.submitJob(confExec);\r
+ reportUsage(confExec, logger);\r
+ return jobId;\r
+ }\r
\r
static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
if (GAUtils.IS_GA_ENABLED) {\r
git://source.jalview.org / jabaws.git / commitdiff