X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FBatchBenchmarkPrepare.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Ftemplates%2FBatchBenchmarkPrepare.java;h=c3ab8ac55c27bffbea718f63665a54eefed7282d;hb=9f55415c9f8005e9dcd8243453883ff853fd5b76;hp=0000000000000000000000000000000000000000;hpb=d8e8c742b864e58406d13e21d124699a26b6492f;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java b/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
new file mode 100644
index 0000000..c3ab8ac
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
@@ -0,0 +1,98 @@
+/**
+ * File written by Raphael Champeimont
+ * UMR 7238 Genomique des Microorganismes
+ */
+package fr.orsay.lri.varna.models.templates;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import fr.orsay.lri.varna.factories.RNAFactory;
+
+public class BatchBenchmarkPrepare {
+
+	/**
+	 * 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");
+		if (!seqdir.exists()) {
+			seqdir.mkdir();
+		}
+		
+		File templateFile = new File(rootdir, "template.xml");
+		
+		ArrayList<String> seqnames = new ArrayList<String>();
+		ArrayList<String> sequences = new ArrayList<String>();
+		BatchBenchmark.readFASTA(new File(rootdir, "alignment.fasta"), seqnames, sequences);
+		
+		BufferedWriter outbufASS = new BufferedWriter(new FileWriter(new File(rootdir, "all_secondary_structures.fasta")));
+		
+		String consensusSecStr = sequences.get(0);
+		int[] consensusSecStrInt = RNAFactory.parseSecStr(consensusSecStr);
+		
+		List<File> templates = new ArrayList<File>();
+		for (int i=1; i<seqnames.size(); i++) {
+			String seqname = seqnames.get(i);
+			String sequence = sequences.get(i);
+			String sequenceUngapped = sequence.replaceAll("[\\.-]", "");
+			System.out.println(seqname);
+			String ss = "";
+			String nt = "";
+			for (int j=0; j<sequence.length(); j++) {
+				if (sequence.charAt(j) != '.' && sequence.charAt(j) != '-') {
+					if (consensusSecStr.charAt(j) == '-' || consensusSecStr.charAt(j) == '.') {
+						nt += sequence.charAt(j);
+						ss += '.';
+					} else {
+						int k = consensusSecStrInt[j];
+						// k is the matching base, is it aligned to a base in our sequence?
+						if (sequence.charAt(k) != '.' && sequence.charAt(k) != '-') {
+							nt += sequence.charAt(j);
+							ss += consensusSecStr.charAt(j);
+						} else {
+							nt += sequence.charAt(j);
+							ss += '.';
+						}
+					}
+				}
+			}
+			
+			if (!sequenceUngapped.equals(nt)) {
+				System.out.println(sequenceUngapped);
+				System.out.println(nt);
+				throw new Error("bug");
+			}
+			
+			// We now have the sequence with its secondary structure.
+			File outfile = new File(seqdir, seqname + ".dbn");
+			BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
+			outbuf.write(">" + seqname + "\n");
+			outbuf.write(nt + "\n");
+			outbuf.write(ss + "\n");
+			outbuf.close();
+			
+			outbufASS.write(">" + seqname + "\n");
+			outbufASS.write(ss + "\n");
+			
+			templates.add(templateFile);
+		}
+		
+		outbufASS.close();
+		
+	}
+	
+	public static void main(String[] args) throws Exception {
+		new BatchBenchmarkPrepare().benchmarkAllDir(new File(new File("templates"), "RNaseP_bact_a"));
+	}
+	
+}