Create FASTA writer for QuatSymm multiple alignment

README.md

@@ -1,6 +1,6 @@
 [![Build Status](https://travis-ci.org/rcsb/symmetry.png)](https://travis-ci.org/rcsb/symmetry)
 
-# Symmetry in Biomolecular Structures
+# Symmetry in Protein Structures
 
 This project collects tools to detect, analyze, and visualize **protein symmetry**. This includes the CE-Symm tool for **internal symmetry**, a tool for **quaternary symmetry**, and other experiments relating to symmetry. 
 
@@ -14,34 +14,43 @@ User interfaces are available within the [symmetry-tools](https://github.com/rcs
 
 <img src="docu/img/1u6d_symmetry.png" align="left" width="150" alt="C6 internal symmetry in PDB:1U6D" title="PDB:1U6D" />
 
-CE-Symm is a tool for detecting internal symmetry in protein structures. CE-Symm version 2 is able to detect both open and closed symmetry and provide a multiple alignment of all repeats. 
+CE-Symm is a tool for detecting internal symmetry in protein structures.
+CE-Symm version 2 is able to detect both open and closed symmetry and provide a multiple alignment of all repeats. 
 
-See [CE-Symm documentation](symmetry-tools/docs/CeSymm.md) for more details.
+See [CE-Symm documentation](symmetry-tools/docs/CeSymm.md) for more details on how to use the tool.
 
-When using CE-Symm, please cite:
+If you find CE-Symm useful for your research, please consider citing:
 
-CE-Symm version 2:
+#### CE-Symm version 2:
 
 **Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm**<br/>
 *Spencer E Bliven, Aleix Lafita, Peter W Rose, Guido Capitani, Andreas Prlić, & Philip E Bourne* <br/>
 [PLOS Computational Biology (2019) 15 (4):e1006842.](https://journals.plos.org/ploscompbiol/article/citation?id=10.1371/journal.pcbi.1006842) <br/>
 [![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006842-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006842) [![pubmed](https://img.shields.io/badge/pubmed-31009453-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/31009453)
 
-CE-Symm version 1:
+#### CE-Symm version 1:
 
 **Systematic detection of internal symmetry in proteins using CE-Symm**<br/>
 *Douglas Myers-Turnbull, Spencer E Bliven, Peter W Rose, Zaid K Aziz, Philippe Youkharibache, Philip E Bourne, & Andreas Prlić* <br/>
 [J Mol Biol (2013) 426 (11): 2255–2268.](https://doi.org/10.1016/j.jmb.2014.03.010) <br/>
 [![doi](https://img.shields.io/badge/doi-10.1016%2Fj.jmb.2014.03.010-blue.svg?style=flat)](https://doi.org/10.1016/j.jmb.2014.03.010) [![pubmed](https://img.shields.io/badge/pubmed-24681267-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/24681267)
 
-### Quaternary Symmetry
+### QuatSymm
 
 <img src="docu/img/1G63.jpg" alt="Tetrahedral symmetry of PDB:1G63" title="PDB:1G63" style="float: left; width:150px" align="left" width="150"/>
 
-The QuatSymm tool is used for identifying quaternary symmetry in protein complexes. It is also able to tolerate mutations and detect pseudosymmetry in complexes with structurally homologous subunits.
+The QuatSymm tool is used for identifying quaternary symmetry in protein complexes.
+It is also able to detect pseudosymmetry in complexes with structurally homologous subunits.
+The QuatSymm tool is used by the RCSB Protein Data Bank's [quaternary symmetry analysis](http://www.rcsb.org/pdb/browse/stoichiometry.do) and it has also been utilized to assess protein assembly predictions at [CASP challenges](https://predictioncenter.org/).
+
 See [QuatSymm documentation](symmetry-tools/docs/QuatSymm.md) for more details.
 
-The QuatSymm algorithms are used by the RCSB Protein Data Bank's [quaternary symmetry analysis](http://www.rcsb.org/pdb/browse/stoichiometry.do). The tool was also utilized for biological assembly assessment during the 1[2th Critical Assessment of Structure Prediction in 2016](https://doi.org/10.1002/prot.25408).
+If you find the QuatSymm tool useful for your research, please consider citing the following publications where it has been described:
+
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte* <br/>
+[PLOS Computational Biology 15(2): e1006791](http://dx.plos.org/10.1371/journal.pcbi.1006791) <br/>
+[![doi](http://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791)
 
 
 ## Dependencies

symmetry-tools/src/main/java/main/QuatSymmMain.java

@@ -37,6 +37,7 @@
 import org.slf4j.LoggerFactory;
 
 import workers.QuatSymmWorker;
+import writers.QuatSymmFastaWriter;
 import writers.QuatSymmStatsWriter;
 import writers.QuatSymmWriter;
 
@@ -162,6 +163,18 @@ public static void main(String[] args) throws InterruptedException {
 				logger.error(e.getMessage());
 			}
 		}
+
+		if (cli.hasOption("fasta")) {
+			String filename = cli.getOptionValue("fasta");
+			if(filename == null || filename.isEmpty())
+				filename = "-"; // standard out
+			try {
+				writers.add(new QuatSymmFastaWriter(filename));
+			} catch (IOException e) {
+				logger.error("Error: Ignoring file " + filename + ".");
+				logger.error(e.getMessage());
+			}
+		}
 
 		// Default Writer
 		if (writers.isEmpty() && !cli.hasOption("noverbose")) {
@@ -379,6 +392,14 @@ private static Options getOptions() {
 				.argName("file")
 				.desc("Output a tsv file with detailed symmetry information (default)")
 				.build());
+		options.addOption(Option
+				.builder("f")
+				.longOpt("fasta")
+				.hasArg()
+				.optionalArg(true)
+				.argName("file")
+				.desc("Output alignment as FASTA alignment output")
+				.build());
 
 		// jmol
 		grp = new OptionGroup();

symmetry-tools/src/main/java/writers/QuatSymmFastaWriter.java

@@ -0,0 +1,55 @@
+package writers;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIdentifier;
+import org.biojava.nbio.structure.align.client.StructureName;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+
+/**
+ * Writes the QuatSymm multiple alignment in FASTA format in a single
+ * file. Different entries are split by the characters '//'.
+ * 
+ * @author Aleix Lafita
+ *
+ */
+public class QuatSymmFastaWriter extends QuatSymmWriter {
+	public QuatSymmFastaWriter(String filename) throws IOException {
+		super(filename);
+	}
+
+	@Override
+	public synchronized void writeResult(String identifier,
+			QuatSymmetryResults result) throws StructureException {
+		if (result != null ) {
+			for (SubunitCluster cluster:result.getSubunitClusters()){
+				// There is bug because Structure Identifiers are null - quick fix here
+				List<StructureIdentifier> structident = cluster.getSubunits().stream()
+						.map(n -> new StructureName(identifier + "_" + n.getName()))
+						.collect(Collectors.toList());
+
+				MultipleAlignment alignment = cluster.getMultipleAlignment();
+				alignment.getEnsemble().setStructureIdentifiers(structident);
+				if(alignment != null) {
+					writer.write(MultipleAlignmentWriter.toFASTA(alignment));
+				}
+				writer.println("//");
+				writer.flush();
+			}
+		}
+	}
+
+	@Override
+	public synchronized void writeHeader() throws IOException {
+		// No header for Fasta files
+	}
+
+
+
+}

symmetry-tools/src/main/java/writers/QuatSymmWriter.java

@@ -26,6 +26,6 @@ public QuatSymmWriter(String filename) throws IOException {
 	 * @throws IOException
 	 */
 	abstract public void writeResult(String identifier,
-			QuatSymmetryResults result) throws IOException;
+			QuatSymmetryResults result) throws Exception;
 
 }