X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FTranslateFormatRNaseP.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FTranslateFormatRNaseP.java;h=7c999e5b6d5de4d2fccf836b8504cd80ed2f8f5d;hb=9f55415c9f8005e9dcd8243453883ff853fd5b76;hp=0000000000000000000000000000000000000000;hpb=d8e8c742b864e58406d13e21d124699a26b6492f;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java b/src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
new file mode 100644
index 0000000..7c999e5
--- /dev/null
+++ b/src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
@@ -0,0 +1,53 @@
+/**
+ * File written by Raphael Champeimont
+ * UMR 7238 Genomique des Microorganismes
+ */
+package fr.orsay.lri.varna.utils;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class TranslateFormatRNaseP {
+	public static void main(String[] args) throws Exception {
+		File templatesDir = new File(new File(System.getProperty("user.dir")), "templates");
+		File infile = new File(new File(templatesDir, "RNaseP_bact_a"), "a_bacterial_rnas.gb");
+		File outfile = new File(new File(templatesDir, "RNaseP_bact_a"), "alignment.fasta");
+		
+		BufferedReader inbuf = new BufferedReader(new FileReader(infile));
+		String line = inbuf.readLine();
+		String seqname;
+		List<String> seqnames = new ArrayList<String>();
+		List<String> sequences = new ArrayList<String>();
+		while (line != null) {
+			if (line.length() != 0) {
+				if (line.startsWith("LOCUS")) {
+					String parts[] = line.split("\\s+");
+					seqname = parts[1];
+					seqnames.add(seqname);
+					sequences.add("");
+				}
+				if (line.startsWith(" ")) {
+					String parts[] = line.split("\\s+");
+					for (int i=2; i<parts.length; i++) {
+						sequences.set(sequences.size()-1, sequences.get(sequences.size()-1) + parts[i]);
+					}
+				}
+			}
+			line = inbuf.readLine();
+		}
+		inbuf.close();
+		
+		BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
+		for (int i=2; i<seqnames.size(); i++) {
+			outbuf.write(">" + seqnames.get(i) + "\n");
+			outbuf.write(sequences.get(i) + "\n");
+		}
+		outbuf.close();
+	}
+}