JAL-2805 made needed color set methods public

[jalview.git] / forester / java / src / org / forester / application / fasta_split.java

diff --git a/forester/java/src/org/forester/application/fasta_split.java b/forester/java/src/org/forester/application/fasta_split.java
index 5b10110..5dc963c 100644 (file)
--- a/forester/java/src/org/forester/application/fasta_split.java
+++ b/forester/java/src/org/forester/application/fasta_split.java
@@ -20,8 +20,10 @@
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+//
+// "java -Xmx1024m -cp path\to\forester.jar org.forester.application.fasta_split
+//
+//
 
 package org.forester.application;
 
@@ -45,8 +47,8 @@ import org.forester.util.ForesterUtil;
 public final class fasta_split {
 
     final static private String PRG_NAME    = "fasta_split";
-    final static private String PRG_VERSION = "1.00";
-    final static private String PRG_DATE    = "150320";
+    final static private String PRG_VERSION = "1.01";
+    final static private String PRG_DATE    = "170718";
 
     public static void main( final String args[] ) {
         ForesterUtil.printProgramInformation( fasta_split.PRG_NAME, fasta_split.PRG_VERSION, fasta_split.PRG_DATE );
@@ -75,6 +77,9 @@ public final class fasta_split {
         if ( !ForesterUtil.isEmpty( error ) ) {
             ForesterUtil.fatalError( PRG_NAME, error );
         }
+        if ( !outdir.exists() ) {
+            new File( outdir.toString() ).mkdir();
+        }
         if ( !outdir.isDirectory() ) {
             ForesterUtil.fatalError( PRG_NAME, outdir + " is not a directory" );
         }
@@ -88,6 +93,7 @@ public final class fasta_split {
         if ( ( seqs == null ) || seqs.isEmpty() ) {
             ForesterUtil.fatalError( PRG_NAME, infile + " appears empty" );
         }
+        System.out.println( "Read " + seqs.size() + " sequences" );
         final Map<String, List<MolecularSequence>> output = new HashMap<String, List<MolecularSequence>>();
         for( final MolecularSequence seq : seqs ) {
             final Matcher m = pa.matcher( seq.getIdentifier() );
@@ -99,28 +105,47 @@ public final class fasta_split {
                 output.get( key ).add( seq );
             }
             else {
-                ForesterUtil.fatalError( PRG_NAME, pattern_str + " not found in sequence " + seq.getIdentifier() );
+                System.out.println( "warning: " + pattern_str + " not found in sequence \"" + seq.getIdentifier()
+                        + "\"" );
+                final String key = "unknown";
+                if ( !output.containsKey( key ) ) {
+                    output.put( key, new ArrayList<MolecularSequence>() );
+                }
+                output.get( key ).add( seq );
             }
         }
         int c = 0;
+        int seqs_written = 0;
         for( final Map.Entry<String, List<MolecularSequence>> entry : output.entrySet() ) {
-            final File of = new File( outdir.getAbsolutePath().toString() + "/" + entry.getKey() + ".fasta" );
+            String s = entry.getKey().trim();
+            s = s.replaceAll( "[\\./\\*\\s]+", "_" );
+            s = s.replaceAll( "\\(", "~" );
+            s = s.replaceAll( "\\)", "~" );
+            final File of = new File( outdir.getAbsolutePath().toString() + "/" + s + ".fasta" );
             if ( of.exists() ) {
                 ForesterUtil.fatalError( PRG_NAME, of + " already exists" );
             }
-            System.out.println( ++c + ": writing " + of );
+            System.out.println( ++c + ": writing " + of + " [" + entry.getValue().size() + " seqs]" );
+            
             try {
                 SequenceWriter.writeSeqs( entry.getValue(), of, SEQ_FORMAT.FASTA, 60 );
             }
             catch ( final IOException e ) {
                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
             }
+            seqs_written += entry.getValue().size();
         }
+        System.out.println( "Wrote " + seqs_written + " sequences" );
     }
 
     private static void argumentsError() {
         System.out.println( PRG_NAME + " <pattern> <infile> <outdir>" );
         System.out.println();
+        System.out.println( "Examples: " );
+        System.out.println( "  " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" );
+        System.out.println( "  " + PRG_NAME + " \"(\\S+?)\\|\" seqs.fasta outdir" );
+        System.out.println( "  " + PRG_NAME + " \"OS=(.+?)[A-Z]{2}=\" seqs.fasta outdir" );
+        System.out.println();
         System.exit( -1 );
     }
 }