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.File;
  30 import java.io.FileWriter;
  31 import java.io.IOException;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34 import java.util.regex.Matcher;
  35
  36 import javax.swing.JOptionPane;
  37
  38 import org.forester.archaeopteryx.AptxUtil;
  39 import org.forester.archaeopteryx.MainFrameApplication;
  40 import org.forester.evoinference.distance.NeighborJoining;
  41 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
  42 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  43 import org.forester.evoinference.tools.BootstrapResampler;
  44 import org.forester.io.parsers.FastaParser;
  45 import org.forester.msa.BasicMsa;
  46 import org.forester.msa.ClustalOmega;
  47 import org.forester.msa.Mafft;
  48 import org.forester.msa.Msa;
  49 import org.forester.msa.Msa.MSA_FORMAT;
  50 import org.forester.msa.MsaInferrer;
  51 import org.forester.msa.MsaMethods;
  52 import org.forester.msa.ResampleableMsa;
  53 import org.forester.phylogeny.Phylogeny;
  54 import org.forester.phylogeny.PhylogenyNode;
  55 import org.forester.phylogeny.data.Accession;
  56 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  57 import org.forester.sequence.Sequence;
  58 import org.forester.tools.ConfidenceAssessor;
  59 import org.forester.util.ForesterUtil;
  60
  61 public class PhylogeneticInferrer extends RunnableProcess {
  62
  63     private Msa                                _msa;
  64     private final MainFrameApplication         _mf;
  65     private final PhylogeneticInferenceOptions _options;
  66     private final List<Sequence>               _seqs;
  67     private final boolean                      DEBUG           = true;
  68     public final static String                 MSA_FILE_SUFFIX = ".aln";
  69     public final static String                 PWD_FILE_SUFFIX = ".pwd";
  70
  71     public PhylogeneticInferrer( final List<Sequence> seqs,
  72                                  final PhylogeneticInferenceOptions options,
  73                                  final MainFrameApplication mf ) {
  74         _msa = null;
  75         _seqs = seqs;
  76         _mf = mf;
  77         _options = options;
  78     }
  79
  80     public PhylogeneticInferrer( final Msa msa,
  81                                  final PhylogeneticInferenceOptions options,
  82                                  final MainFrameApplication mf ) {
  83         _msa = msa;
  84         _seqs = null;
  85         _mf = mf;
  86         _options = options;
  87     }
  88
  89     private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
  90         //        final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
  91         //        if ( DEBUG ) {
  92         //            System.out.println();
  93         //            System.out.println( "temp file: " + temp_seqs_file );
  94         //            System.out.println();
  95         //        }
  96         //        //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
  97         //        final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
  98         //        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
  99         //        writer.close();
 100         switch ( msa_prg ) {
 101             case MAFFT:
 102                 return runMAFFT( _seqs, processMafftOptions() );
 103
 104             case CLUSTAL_O:
 105                 return runClustalOmega( _seqs, processMafftOptions() );
 106             default:
 107                 return null;
 108         }
 109
 110
 111     }
 112
 113     private List<String> processMafftOptions() {
 114         final String opts_str = _options.getMsaPrgParameters().trim().toLowerCase();
 115         final String[] opts_ary = opts_str.split( " " );
 116         final List<String> opts = new ArrayList<String>();
 117         boolean saw_quiet = false;
 118         for( final String opt : opts_ary ) {
 119             opts.add( opt );
 120             if ( opt.equals( "--quiet" ) ) {
 121                 saw_quiet = true;
 122             }
 123         }
 124         if ( !saw_quiet ) {
 125             opts.add( "--quiet" );
 126         }
 127         return opts;
 128     }
 129
 130     private Phylogeny inferPhylogeny( final Msa msa ) {
 131         BasicSymmetricalDistanceMatrix m = null;
 132         switch ( _options.getPwdDistanceMethod() ) {
 133             case KIMURA_DISTANCE:
 134                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
 135                 break;
 136             case POISSON_DISTANCE:
 137                 m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
 138                 break;
 139             case FRACTIONAL_DISSIMILARITY:
 140                 m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
 141                 break;
 142             default:
 143                 throw new RuntimeException( "invalid pwd method" );
 144         }
 145         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 146             BufferedWriter pwd_writer;
 147             try {
 148                 pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) );
 149                 m.write( pwd_writer );
 150                 pwd_writer.close();
 151             }
 152             catch ( final IOException e ) {
 153                 // TODO Auto-generated catch block
 154                 e.printStackTrace();
 155             }
 156         }
 157         final NeighborJoining nj = NeighborJoining.createInstance();
 158         final Phylogeny phy = nj.execute( m );
 159         PhylogeneticInferrer.extractFastaInformation( phy );
 160         return phy;
 161     }
 162
 163     private void infer() throws InterruptedException {
 164         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
 165         if ( ( _msa == null ) && ( _seqs == null ) ) {
 166             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
 167         }
 168         start( _mf, "phylogenetic inference" );
 169         if ( _msa == null ) {
 170             Msa msa = null;
 171             try {
 172                 msa = inferMsa( MSA_PRG.MAFFT );
 173             }
 174             catch ( final IOException e ) {
 175                 end( _mf );
 176                 JOptionPane.showMessageDialog( _mf,
 177                                                "Could not create multiple sequence alignment with \""
 178                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 179                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 180                                                        + e.getLocalizedMessage(),
 181                                                "Failed to Calculate MSA",
 182                                                JOptionPane.ERROR_MESSAGE );
 183                 if ( DEBUG ) {
 184                     e.printStackTrace();
 185                 }
 186                 return;
 187             }
 188             catch ( final Exception e ) {
 189                 end( _mf );
 190                 JOptionPane.showMessageDialog( _mf,
 191                                                "Could not create multiple sequence alignment with \""
 192                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 193                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 194                                                        + e.getLocalizedMessage(),
 195                                                "Unexpected Exception During MSA Calculation",
 196                                                JOptionPane.ERROR_MESSAGE );
 197                 if ( DEBUG ) {
 198                     e.printStackTrace();
 199                 }
 200                 return;
 201             }
 202             if ( msa == null ) {
 203                 end( _mf );
 204                 JOptionPane.showMessageDialog( _mf,
 205                                                "Could not create multiple sequence alignment with "
 206                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
 207                                                        + _options.getMsaPrgParameters() + "\"",
 208                                                "Failed to Calculate MSA",
 209                                                JOptionPane.ERROR_MESSAGE );
 210                 return;
 211             }
 212             if ( DEBUG ) {
 213                 System.out.println( msa.toString() );
 214                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 215             }
 216             final MsaMethods msa_tools = MsaMethods.createInstance();
 217             if ( _options.isExecuteMsaProcessing() ) {
 218                 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
 219                                                   _options.getMsaProcessingMinAllowedLength(),
 220                                                   msa );
 221                 if ( msa == null ) {
 222                     end( _mf );
 223                     JOptionPane.showMessageDialog( _mf,
 224                                                    "Less than two sequences longer than "
 225                                                            + _options.getMsaProcessingMinAllowedLength()
 226                                                            + " residues left after MSA processing",
 227                                                    "MSA Processing Settings Too Stringent",
 228                                                    JOptionPane.ERROR_MESSAGE );
 229                     return;
 230                 }
 231             }
 232             if ( DEBUG ) {
 233                 System.out.println( msa_tools.getIgnoredSequenceIds() );
 234                 System.out.println( msa.toString() );
 235                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 236             }
 237             _msa = msa;
 238         }
 239         final int n = _options.getBootstrapSamples();
 240         final long seed = _options.getRandomNumberGeneratorSeed();
 241         final Phylogeny master_phy = inferPhylogeny( _msa );
 242         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
 243             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
 244             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
 245                     .getLength(), n, seed );
 246             final Phylogeny[] eval_phys = new Phylogeny[ n ];
 247             for( int i = 0; i < n; ++i ) {
 248                 resampleable_msa.resample( resampled_column_positions[ i ] );
 249                 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
 250             }
 251             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
 252         }
 253         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
 254         //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 255         end( _mf );
 256         JOptionPane.showMessageDialog( _mf,
 257                                        "Inference successfully completed",
 258                                        "Inference Completed",
 259                                        JOptionPane.INFORMATION_MESSAGE );
 260     }
 261
 262     @Override
 263     public void run() {
 264         try {
 265             infer();
 266         }
 267         catch ( final InterruptedException e ) {
 268             // TODO need to handle this exception SOMEHOW!
 269             // TODO Auto-generated catch block
 270             e.printStackTrace();
 271         }
 272     }
 273
 274     private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
 275         Msa msa = null;
 276         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
 277                 .getCanonicalPath() );
 278         try {
 279             msa = mafft.infer( seqs, opts );
 280         }
 281         catch ( final IOException e ) {
 282             System.out.println( mafft.getErrorDescription() );
 283         }
 284         return msa;
 285     }
 286
 287     private Msa runClustalOmega( final List<Sequence> seqs, final List<String> opts ) throws IOException,
 288             InterruptedException {
 289         Msa msa = null;
 290         final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
 291                 .getCanonicalPath() );
 292         try {
 293             msa = clustalo.infer( seqs, opts );
 294         }
 295         catch ( final IOException e ) {
 296             System.out.println( clustalo.getErrorDescription() );
 297         }
 298         return msa;
 299     }
 300
 301     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
 302         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 303             try {
 304                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 305                         + MSA_FILE_SUFFIX ) );
 306                 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
 307                 msa_writer.close();
 308                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 309                         + PWD_FILE_SUFFIX ) );
 310                 m.write( pwd_writer );
 311                 pwd_writer.close();
 312             }
 313             catch ( final Exception e ) {
 314                 System.out.println( "Error: " + e.getMessage() );
 315             }
 316         }
 317     }
 318
 319     public static void extractFastaInformation( final Phylogeny phy ) {
 320         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 321             final PhylogenyNode node = iter.next();
 322             if ( !ForesterUtil.isEmpty( node.getName() ) ) {
 323                 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
 324                 if ( name_m.lookingAt() ) {
 325                     System.out.println();
 326                     // System.out.println( name_m.group( 1 ) );
 327                     // System.out.println( name_m.group( 2 ) );
 328                     // System.out.println( name_m.group( 3 ) );
 329                     // System.out.println( name_m.group( 4 ) );
 330                     final String acc_source = name_m.group( 1 );
 331                     final String acc = name_m.group( 2 );
 332                     final String seq_name = name_m.group( 3 );
 333                     final String tax_sn = name_m.group( 4 );
 334                     if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
 335                         AptxUtil.ensurePresenceOfSequence( node );
 336                         node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
 337                     }
 338                     if ( !ForesterUtil.isEmpty( seq_name ) ) {
 339                         AptxUtil.ensurePresenceOfSequence( node );
 340                         node.getNodeData().getSequence( 0 ).setName( seq_name );
 341                     }
 342                     if ( !ForesterUtil.isEmpty( tax_sn ) ) {
 343                         AptxUtil.ensurePresenceOfTaxonomy( node );
 344                         node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
 345                     }
 346                 }
 347             }
 348         }
 349     }
 350
 351     public enum MSA_PRG {
 352         MAFFT, CLUSTAL_O;
 353     }
 354 }