phylotastic hackathon at NESCENT 120607

diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java
new file mode 100644 (file)
index 0000000..46e5bee
--- /dev/null
+++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java
@@ -0,0 +1,140 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2012 Christian M. Zmasek
+// Copyright (C) 2008-2012 Burnham Institute for Medical Research
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// 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: www.phylosoft.org/forester
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.SortedSet;
+
+import org.forester.archaeopteryx.tools.SequenceDataRetriver;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class gene_tree_preprocess {
+
+    final static private String HELP_OPTION_1 = "help";
+    final static private String HELP_OPTION_2 = "h";
+    final static private String FROM_OPTION   = "f";
+    final static private String TO_OPTION     = "t";
+    final static private String STEP_OPTION   = "s";
+    final static private String WINDOW_OPTION = "w";
+    final static private String PRG_NAME      = "gene_tree_preprocess";
+    final static private String PRG_DESC      = "gene tree preprocessing for SDI analysis";
+    final static private String PRG_VERSION   = "1.00";
+    final static private String PRG_DATE      = "2012.06.07";
+    final static private String E_MAIL        = "phylosoft@gmail.com";
+    final static private String WWW           = "www.phylosoft.org/forester/";
+
+    public static void main( final String[] args ) {
+        try {
+            final CommandLineArguments cla = new CommandLineArguments( args );
+            if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length != 1 ) ) {
+                printHelp();
+                System.exit( 0 );
+            }
+            final File in = cla.getFile( 0 );
+            Phylogeny phy = null;
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            try {
+                phy = factory.create( in, ParserUtils.createParserDependingOnFileType( in, true ) )[ 0 ];
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME,
+                                         "failed to read target phylogenies from [" + in + "]: "
+                                                 + e.getLocalizedMessage() );
+            }
+            final File outtree = new File( ForesterUtil.removeSuffix( in.toString() )
+                    + "_preprocessed_gene_tree.phylo.xml" );
+            final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" );
+            checkForOutputFileWriteability( outtree );
+            checkForOutputFileWriteability( removed_nodes );
+            if ( phy.getNumberOfExternalNodes() < 2 ) {
+                ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
+                        + " external node(s), aborting" );
+            }
+            final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy );
+            for( final String remove_me : not_found ) {
+                System.out.println( " not found: " + not_found );
+                PhylogenyMethods.removeNode( phy.getNode( remove_me ), phy );
+            }
+            if ( phy.getNumberOfExternalNodes() < 2 ) {
+                ForesterUtil.fatalError( PRG_NAME,
+                                         "after removal of unresolvable external nodes, phylogeny has "
+                                                 + phy.getNumberOfExternalNodes() + " external node(s), aborting" );
+            }
+            try {
+                final PhylogenyWriter writer = new PhylogenyWriter();
+                writer.toPhyloXML( phy, 0, outtree );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME, "failed to write to [" + outtree + "]: " + e.getLocalizedMessage() );
+            }
+            //  ForesterUtil.programMessage( PRG_NAME, "wrote output to: [" + outfile + "]" );
+            ForesterUtil.programMessage( PRG_NAME, "OK" );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+        }
+    }
+
+    public static void checkForOutputFileWriteability( final File outfile ) {
+        final String error = ForesterUtil.isWritableFile( outfile );
+        if ( !ForesterUtil.isEmpty( error ) ) {
+            ForesterUtil.fatalError( PRG_NAME, error );
+        }
+    }
+
+    private static void printHelp() {
+        ForesterUtil.printProgramInformation( PRG_NAME,
+                                              PRG_DESC,
+                                              PRG_VERSION,
+                                              PRG_DATE,
+                                              E_MAIL,
+                                              WWW,
+                                              ForesterUtil.getForesterLibraryInformation() );
+        System.out.println( "Usage:" );
+        System.out.println();
+        System.out.println( PRG_NAME + " <options> <msa input file>" );
+        System.out.println();
+        System.out.println( " options: " );
+        System.out.println();
+        System.out.println( "   -" + FROM_OPTION + "=<integer>: from (msa column)" );
+        System.out.println( "   -" + TO_OPTION + "=<integer>: to (msa column)" );
+        System.out.println( "    or" );
+        System.out.println( "   -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );
+        System.out.println( "   -" + STEP_OPTION + "=<integer>: step size (msa columns)" );
+        System.out.println();
+        System.out.println();
+        System.out.println();
+    }
+}

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
index 508d60f..b5a8968 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
@@ -47,6 +47,8 @@ import org.forester.ws.seqdb.SequenceDatabaseEntry;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 
 public final class SequenceDataRetriver extends RunnableProcess {
+    
+    public final static int DEFAULT_LINES_TO_RETURN = 50;
 
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
@@ -189,23 +191,23 @@ public final class SequenceDataRetriver extends RunnableProcess {
                     if ( DEBUG ) {
                         System.out.println( "uniprot: " + query );
                     }
-                    db_entry = SequenceDbWsTools.obtainUniProtEntry( query, 200 );
+                    db_entry = SequenceDbWsTools.obtainUniProtEntry( query, DEFAULT_LINES_TO_RETURN );
                 }
                 if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) {
                     if ( DEBUG ) {
                         System.out.println( "embl: " + query );
                     }
-                    db_entry = SequenceDbWsTools.obtainEmblEntry(  new Identifier( query ), 200 );
+                    db_entry = SequenceDbWsTools.obtainEmblEntry(  new Identifier( query ), DEFAULT_LINES_TO_RETURN );
                     if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) {
                         db = Db.EMBL;
                     }
                 }
             }
             else if ( ( db == Db.REFSEQ ) && ( id != null ) ) {
-                db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, 200 );
+                db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, DEFAULT_LINES_TO_RETURN );
             }
             else if ( ( db == Db.NCBI ) && ( id != null ) ) {
-                db_entry = SequenceDbWsTools.obtainEmblEntry( id, 200 );
+                db_entry = SequenceDbWsTools.obtainEmblEntry( id, DEFAULT_LINES_TO_RETURN );
             }
             if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
                 if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {

diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index 36dfda4..8ee4522 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -481,6 +481,15 @@ public final class PhylogenyWriter {
         writer.flush();
         writer.close();
     }
+    
+    public void toPhyloXML( final Phylogeny phy,
+                            final int phyloxml_level,
+                            final File out_file ) throws IOException {
+        final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
+        toPhyloXML( writer, phy, phyloxml_level );
+        writer.flush();
+        writer.close();
+    }
 
     public void toPhyloXML( final Writer writer,
                             final List<Phylogeny> trees,