Java 11 integration;

[jalview.git] / src2 / fr / orsay / lri / varna / utils / TranslateFormatRNaseP.java

diff --git a/src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java b/src2/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
new file mode 100644 (file)
index 0000000..7c999e5
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+++ 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();
+       }
+}