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.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() 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         final List<String> opts = processMafftOptions();
 100         return runMAFFT( _seqs, opts );
 101     }
 102
 103     private List<String> processMafftOptions() {
 104         final String opts_str = _options.getMsaPrgParameters().trim().toLowerCase();
 105         final String[] opts_ary = opts_str.split( " " );
 106         final List<String> opts = new ArrayList<String>();
 107         boolean saw_quiet = false;
 108         for( final String opt : opts_ary ) {
 109             opts.add( opt );
 110             if ( opt.equals( "--quiet" ) ) {
 111                 saw_quiet = true;
 112             }
 113         }
 114         if ( !saw_quiet ) {
 115             opts.add( "--quiet" );
 116         }
 117         return opts;
 118     }
 119
 120     private Phylogeny inferPhylogeny( final Msa msa ) {
 121         BasicSymmetricalDistanceMatrix m = null;
 122         switch ( _options.getPwdDistanceMethod() ) {
 123             case KIMURA_DISTANCE:
 124                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
 125                 break;
 126             case POISSON_DISTANCE:
 127                 m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
 128                 break;
 129             case FRACTIONAL_DISSIMILARITY:
 130                 m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
 131                 break;
 132             default:
 133                 throw new RuntimeException( "invalid pwd method" );
 134         }
 135         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 136             BufferedWriter pwd_writer;
 137             try {
 138                 pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) );
 139                 m.write( pwd_writer );
 140                 pwd_writer.close();
 141             }
 142             catch ( final IOException e ) {
 143                 // TODO Auto-generated catch block
 144                 e.printStackTrace();
 145             }
 146         }
 147         final NeighborJoining nj = NeighborJoining.createInstance();
 148         final Phylogeny phy = nj.execute( m );
 149         PhylogeneticInferrer.extractFastaInformation( phy );
 150         return phy;
 151     }
 152
 153     private void infer() throws InterruptedException {
 154         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
 155         if ( ( _msa == null ) && ( _seqs == null ) ) {
 156             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
 157         }
 158         start( _mf, "phylogenetic inference" );
 159         if ( _msa == null ) {
 160             Msa msa = null;
 161             try {
 162                 msa = inferMsa();
 163             }
 164             catch ( final IOException e ) {
 165                 end( _mf );
 166                 JOptionPane.showMessageDialog( _mf,
 167                                                "Could not create multiple sequence alignment with \""
 168                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 169                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 170                                                        + e.getLocalizedMessage(),
 171                                                "Failed to Calculate MSA",
 172                                                JOptionPane.ERROR_MESSAGE );
 173                 if ( DEBUG ) {
 174                     e.printStackTrace();
 175                 }
 176                 return;
 177             }
 178             catch ( final Exception e ) {
 179                 end( _mf );
 180                 JOptionPane.showMessageDialog( _mf,
 181                                                "Could not create multiple sequence alignment with \""
 182                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 183                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 184                                                        + e.getLocalizedMessage(),
 185                                                "Unexpected Exception During MSA Calculation",
 186                                                JOptionPane.ERROR_MESSAGE );
 187                 if ( DEBUG ) {
 188                     e.printStackTrace();
 189                 }
 190                 return;
 191             }
 192             if ( msa == null ) {
 193                 end( _mf );
 194                 JOptionPane.showMessageDialog( _mf,
 195                                                "Could not create multiple sequence alignment with "
 196                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
 197                                                        + _options.getMsaPrgParameters() + "\"",
 198                                                "Failed to Calculate MSA",
 199                                                JOptionPane.ERROR_MESSAGE );
 200                 return;
 201             }
 202             if ( DEBUG ) {
 203                 System.out.println( msa.toString() );
 204                 System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
 205             }
 206             final MsaMethods msa_tools = MsaMethods.createInstance();
 207             if ( _options.isExecuteMsaProcessing() ) {
 208                 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
 209                                                   _options.getMsaProcessingMinAllowedLength(),
 210                                                   msa );
 211                 if ( msa == null ) {
 212                     end( _mf );
 213                     JOptionPane.showMessageDialog( _mf,
 214                                                    "Less than two sequences longer than "
 215                                                            + _options.getMsaProcessingMinAllowedLength()
 216                                                            + " residues left after MSA processing",
 217                                                    "MSA Processing Settings Too Stringent",
 218                                                    JOptionPane.ERROR_MESSAGE );
 219                     return;
 220                 }
 221             }
 222             if ( DEBUG ) {
 223                 System.out.println( msa_tools.getIgnoredSequenceIds() );
 224                 System.out.println( msa.toString() );
 225                 System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() );
 226             }
 227             _msa = msa;
 228         }
 229         final int n = _options.getBootstrapSamples();
 230         final long seed = _options.getRandomNumberGeneratorSeed();
 231         final Phylogeny master_phy = inferPhylogeny( _msa );
 232         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
 233             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
 234             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
 235                     .getLength(), n, seed );
 236             final Phylogeny[] eval_phys = new Phylogeny[ n ];
 237             for( int i = 0; i < n; ++i ) {
 238                 resampleable_msa.resample( resampled_column_positions[ i ] );
 239                 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
 240             }
 241             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
 242         }
 243         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
 244         //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 245         end( _mf );
 246         JOptionPane.showMessageDialog( _mf,
 247                                        "Inference successfully completed",
 248                                        "Inference Completed",
 249                                        JOptionPane.INFORMATION_MESSAGE );
 250     }
 251
 252     @Override
 253     public void run() {
 254         try {
 255             infer();
 256         }
 257         catch ( final InterruptedException e ) {
 258             // TODO need to handle this exception SOMEHOW!
 259             // TODO Auto-generated catch block
 260             e.printStackTrace();
 261         }
 262     }
 263
 264     private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
 265         Msa msa = null;
 266         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
 267                 .getCanonicalPath() );
 268         try {
 269             msa = mafft.infer( seqs, opts );
 270         }
 271         catch ( final IOException e ) {
 272             System.out.println( mafft.getErrorDescription() );
 273         }
 274         return msa;
 275     }
 276
 277     private Msa runClustalOmega( final File input_seqs, final List<String> opts ) throws IOException,
 278             InterruptedException {
 279         Msa msa = null;
 280         final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
 281                 .getCanonicalPath() );
 282         try {
 283             msa = clustalo.infer( input_seqs, opts );
 284         }
 285         catch ( final IOException e ) {
 286             System.out.println( clustalo.getErrorDescription() );
 287         }
 288         return msa;
 289     }
 290
 291     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
 292         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 293             try {
 294                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 295                         + MSA_FILE_SUFFIX ) );
 296                 _msa.write( msa_writer );
 297                 msa_writer.close();
 298                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 299                         + PWD_FILE_SUFFIX ) );
 300                 m.write( pwd_writer );
 301                 pwd_writer.close();
 302             }
 303             catch ( final Exception e ) {
 304                 System.out.println( "Error: " + e.getMessage() );
 305             }
 306         }
 307     }
 308
 309     public static void extractFastaInformation( final Phylogeny phy ) {
 310         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 311             final PhylogenyNode node = iter.next();
 312             if ( !ForesterUtil.isEmpty( node.getName() ) ) {
 313                 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
 314                 if ( name_m.lookingAt() ) {
 315                     System.out.println();
 316                     // System.out.println( name_m.group( 1 ) );
 317                     // System.out.println( name_m.group( 2 ) );
 318                     // System.out.println( name_m.group( 3 ) );
 319                     // System.out.println( name_m.group( 4 ) );
 320                     final String acc_source = name_m.group( 1 );
 321                     final String acc = name_m.group( 2 );
 322                     final String seq_name = name_m.group( 3 );
 323                     final String tax_sn = name_m.group( 4 );
 324                     if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
 325                         AptxUtil.ensurePresenceOfSequence( node );
 326                         node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
 327                     }
 328                     if ( !ForesterUtil.isEmpty( seq_name ) ) {
 329                         AptxUtil.ensurePresenceOfSequence( node );
 330                         node.getNodeData().getSequence( 0 ).setName( seq_name );
 331                     }
 332                     if ( !ForesterUtil.isEmpty( tax_sn ) ) {
 333                         AptxUtil.ensurePresenceOfTaxonomy( node );
 334                         node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
 335                     }
 336                 }
 337             }
 338         }
 339     }
 340 }