forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.archaeopteryx.tools;
  27
  28 import java.io.BufferedWriter;
  29 import java.io.FileWriter;
  30 import java.io.IOException;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33 import java.util.regex.Matcher;
  34
  35 import javax.swing.JOptionPane;
  36
  37 import org.forester.archaeopteryx.AptxUtil;
  38 import org.forester.archaeopteryx.MainFrameApplication;
  39 import org.forester.evoinference.distance.NeighborJoining;
  40 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
  41 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  42 import org.forester.evoinference.tools.BootstrapResampler;
  43 import org.forester.io.parsers.FastaParser;
  44 import org.forester.msa.BasicMsa;
  45 import org.forester.msa.ClustalOmega;
  46 import org.forester.msa.Mafft;
  47 import org.forester.msa.Msa;
  48 import org.forester.msa.Msa.MSA_FORMAT;
  49 import org.forester.msa.MsaInferrer;
  50 import org.forester.msa.MsaMethods;
  51 import org.forester.msa.ResampleableMsa;
  52 import org.forester.phylogeny.Phylogeny;
  53 import org.forester.phylogeny.PhylogenyNode;
  54 import org.forester.phylogeny.data.Accession;
  55 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  56 import org.forester.sequence.Sequence;
  57 import org.forester.tools.ConfidenceAssessor;
  58 import org.forester.util.ForesterUtil;
  59
  60 public class PhylogeneticInferrer extends RunnableProcess {
  61
  62     private Msa                                _msa;
  63     private final MainFrameApplication         _mf;
  64     private final PhylogeneticInferenceOptions _options;
  65     private final List<Sequence>               _seqs;
  66     private final boolean                      DEBUG           = true;
  67     public final static String                 MSA_FILE_SUFFIX = ".aln";
  68     public final static String                 PWD_FILE_SUFFIX = ".pwd";
  69
  70     public PhylogeneticInferrer( final List<Sequence> seqs,
  71                                  final PhylogeneticInferenceOptions options,
  72                                  final MainFrameApplication mf ) {
  73         _msa = null;
  74         _seqs = seqs;
  75         _mf = mf;
  76         _options = options;
  77     }
  78
  79     public PhylogeneticInferrer( final Msa msa,
  80                                  final PhylogeneticInferenceOptions options,
  81                                  final MainFrameApplication mf ) {
  82         _msa = msa;
  83         _seqs = null;
  84         _mf = mf;
  85         _options = options;
  86     }
  87
  88     private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
  89         //        final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
  90         //        if ( DEBUG ) {
  91         //            System.out.println();
  92         //            System.out.println( "temp file: " + temp_seqs_file );
  93         //            System.out.println();
  94         //        }
  95         //        //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
  96         //        final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
  97         //        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
  98         //        writer.close();
  99         switch ( msa_prg ) {
 100             case MAFFT:
 101                 return runMAFFT( _seqs, processMafftOptions() );
 102             case CLUSTAL_O:
 103                 return runClustalOmega( _seqs, processMafftOptions() );
 104             default:
 105                 return null;
 106         }
 107     }
 108
 109     private List<String> processMafftOptions() {
 110         final String opts_str = _options.getMsaPrgParameters().trim().toLowerCase();
 111         final String[] opts_ary = opts_str.split( " " );
 112         final List<String> opts = new ArrayList<String>();
 113         boolean saw_quiet = false;
 114         for( final String opt : opts_ary ) {
 115             opts.add( opt );
 116             if ( opt.equals( "--quiet" ) ) {
 117                 saw_quiet = true;
 118             }
 119         }
 120         if ( !saw_quiet ) {
 121             opts.add( "--quiet" );
 122         }
 123         return opts;
 124     }
 125
 126     private Phylogeny inferPhylogeny( final Msa msa ) {
 127         BasicSymmetricalDistanceMatrix m = null;
 128         switch ( _options.getPwdDistanceMethod() ) {
 129             case KIMURA_DISTANCE:
 130                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
 131                 break;
 132             case POISSON_DISTANCE:
 133                 m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
 134                 break;
 135             case FRACTIONAL_DISSIMILARITY:
 136                 m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
 137                 break;
 138             default:
 139                 throw new RuntimeException( "invalid pwd method" );
 140         }
 141         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 142             BufferedWriter pwd_writer;
 143             try {
 144                 pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) );
 145                 m.write( pwd_writer );
 146                 pwd_writer.close();
 147             }
 148             catch ( final IOException e ) {
 149                 // TODO Auto-generated catch block
 150                 e.printStackTrace();
 151             }
 152         }
 153         final NeighborJoining nj = NeighborJoining.createInstance();
 154         final Phylogeny phy = nj.execute( m );
 155         PhylogeneticInferrer.extractFastaInformation( phy );
 156         return phy;
 157     }
 158
 159     private void infer() throws InterruptedException {
 160         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
 161         if ( ( _msa == null ) && ( _seqs == null ) ) {
 162             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
 163         }
 164         start( _mf, "phylogenetic inference" );
 165         if ( _msa == null ) {
 166             Msa msa = null;
 167             try {
 168                 msa = inferMsa( MSA_PRG.MAFFT );
 169             }
 170             catch ( final IOException e ) {
 171                 end( _mf );
 172                 JOptionPane.showMessageDialog( _mf,
 173                                                "Could not create multiple sequence alignment with \""
 174                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 175                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 176                                                        + e.getLocalizedMessage(),
 177                                                "Failed to Calculate MSA",
 178                                                JOptionPane.ERROR_MESSAGE );
 179                 if ( DEBUG ) {
 180                     e.printStackTrace();
 181                 }
 182                 return;
 183             }
 184             catch ( final Exception e ) {
 185                 end( _mf );
 186                 JOptionPane.showMessageDialog( _mf,
 187                                                "Could not create multiple sequence alignment with \""
 188                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 189                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 190                                                        + e.getLocalizedMessage(),
 191                                                "Unexpected Exception During MSA Calculation",
 192                                                JOptionPane.ERROR_MESSAGE );
 193                 if ( DEBUG ) {
 194                     e.printStackTrace();
 195                 }
 196                 return;
 197             }
 198             if ( msa == null ) {
 199                 end( _mf );
 200                 JOptionPane.showMessageDialog( _mf,
 201                                                "Could not create multiple sequence alignment with "
 202                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
 203                                                        + _options.getMsaPrgParameters() + "\"",
 204                                                "Failed to Calculate MSA",
 205                                                JOptionPane.ERROR_MESSAGE );
 206                 return;
 207             }
 208             if ( DEBUG ) {
 209                 System.out.println( msa.toString() );
 210                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 211             }
 212             final MsaMethods msa_tools = MsaMethods.createInstance();
 213             if ( _options.isExecuteMsaProcessing() ) {
 214                 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
 215                                                   _options.getMsaProcessingMinAllowedLength(),
 216                                                   msa );
 217                 if ( msa == null ) {
 218                     end( _mf );
 219                     JOptionPane.showMessageDialog( _mf,
 220                                                    "Less than two sequences longer than "
 221                                                            + _options.getMsaProcessingMinAllowedLength()
 222                                                            + " residues left after MSA processing",
 223                                                    "MSA Processing Settings Too Stringent",
 224                                                    JOptionPane.ERROR_MESSAGE );
 225                     return;
 226                 }
 227             }
 228             if ( DEBUG ) {
 229                 System.out.println( msa_tools.getIgnoredSequenceIds() );
 230                 System.out.println( msa.toString() );
 231                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 232             }
 233             _msa = msa;
 234         }
 235         final int n = _options.getBootstrapSamples();
 236         final long seed = _options.getRandomNumberGeneratorSeed();
 237         final Phylogeny master_phy = inferPhylogeny( _msa );
 238         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
 239             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
 240             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
 241                     .getLength(), n, seed );
 242             final Phylogeny[] eval_phys = new Phylogeny[ n ];
 243             for( int i = 0; i < n; ++i ) {
 244                 resampleable_msa.resample( resampled_column_positions[ i ] );
 245                 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
 246             }
 247             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
 248         }
 249         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
 250         //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 251         end( _mf );
 252         JOptionPane.showMessageDialog( _mf,
 253                                        "Inference successfully completed",
 254                                        "Inference Completed",
 255                                        JOptionPane.INFORMATION_MESSAGE );
 256     }
 257
 258     @Override
 259     public void run() {
 260         try {
 261             infer();
 262         }
 263         catch ( final InterruptedException e ) {
 264             // TODO need to handle this exception SOMEHOW!
 265             // TODO Auto-generated catch block
 266             e.printStackTrace();
 267         }
 268     }
 269
 270     private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
 271         Msa msa = null;
 272         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
 273                 .getCanonicalPath() );
 274         try {
 275             msa = mafft.infer( seqs, opts );
 276         }
 277         catch ( final IOException e ) {
 278             System.out.println( mafft.getErrorDescription() );
 279         }
 280         return msa;
 281     }
 282
 283     private Msa runClustalOmega( final List<Sequence> seqs, final List<String> opts ) throws IOException,
 284             InterruptedException {
 285         Msa msa = null;
 286         final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
 287                 .getCanonicalPath() );
 288         try {
 289             msa = clustalo.infer( seqs, opts );
 290         }
 291         catch ( final IOException e ) {
 292             System.out.println( clustalo.getErrorDescription() );
 293         }
 294         return msa;
 295     }
 296
 297     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
 298         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 299             try {
 300                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 301                         + MSA_FILE_SUFFIX ) );
 302                 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
 303                 msa_writer.close();
 304                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 305                         + PWD_FILE_SUFFIX ) );
 306                 m.write( pwd_writer );
 307                 pwd_writer.close();
 308             }
 309             catch ( final Exception e ) {
 310                 System.out.println( "Error: " + e.getMessage() );
 311             }
 312         }
 313     }
 314
 315     public static void extractFastaInformation( final Phylogeny phy ) {
 316         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 317             final PhylogenyNode node = iter.next();
 318             if ( !ForesterUtil.isEmpty( node.getName() ) ) {
 319                 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
 320                 if ( name_m.lookingAt() ) {
 321                     System.out.println();
 322                     // System.out.println( name_m.group( 1 ) );
 323                     // System.out.println( name_m.group( 2 ) );
 324                     // System.out.println( name_m.group( 3 ) );
 325                     // System.out.println( name_m.group( 4 ) );
 326                     final String acc_source = name_m.group( 1 );
 327                     final String acc = name_m.group( 2 );
 328                     final String seq_name = name_m.group( 3 );
 329                     final String tax_sn = name_m.group( 4 );
 330                     if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
 331                         AptxUtil.ensurePresenceOfSequence( node );
 332                         node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
 333                     }
 334                     if ( !ForesterUtil.isEmpty( seq_name ) ) {
 335                         AptxUtil.ensurePresenceOfSequence( node );
 336                         node.getNodeData().getSequence( 0 ).setName( seq_name );
 337                     }
 338                     if ( !ForesterUtil.isEmpty( tax_sn ) ) {
 339                         AptxUtil.ensurePresenceOfTaxonomy( node );
 340                         node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
 341                     }
 342                 }
 343             }
 344         }
 345     }
 346
 347     public enum MSA_PRG {
 348         MAFFT, CLUSTAL_O;
 349     }
 350 }