forester/java/src/org/forester/application/gsdi.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   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.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.io.Writer;
  31 import java.text.SimpleDateFormat;
  32 import java.util.ArrayList;
  33 import java.util.Date;
  34 import java.util.List;
  35
  36 import org.forester.io.parsers.PhylogenyParser;
  37 import org.forester.io.parsers.nhx.NHXParser;
  38 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  39 import org.forester.io.parsers.util.ParserUtils;
  40 import org.forester.io.writers.PhylogenyWriter;
  41 import org.forester.phylogeny.Phylogeny;
  42 import org.forester.phylogeny.PhylogenyMethods;
  43 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  44 import org.forester.phylogeny.factories.PhylogenyFactory;
  45 import org.forester.sdi.GSDI;
  46 import org.forester.sdi.SDI;
  47 import org.forester.sdi.SDI.TaxonomyComparisonBase;
  48 import org.forester.sdi.SDIse;
  49 import org.forester.util.CommandLineArguments;
  50 import org.forester.util.ForesterUtil;
  51
  52 public final class gsdi {
  53
  54     private enum BASE_ALGORITHM {
  55         GSDI, SDI
  56     }
  57     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE     = true;
  58     final static private String STRIP_OPTION                               = "s";
  59     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION        = "g";
  60     final static private String SDI_OPTION                                 = "b";
  61     final static private String MOST_PARSIMONIOUS_OPTION                   = "m";
  62     final static private String GUESS_FORMAT_OF_SPECIES_TREE               = "q";
  63     final static private String HELP_OPTION_1                              = "help";
  64     final static private String HELP_OPTION_2                              = "h";
  65     final static private String DEFAULT_OUTFILE_SUFFIX                     = "_gsdi_out.phylo.xml";
  66     final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
  67     final static private String LOGFILE_SUFFIX                             = "_gsdi_log.txt";
  68     final static private String PRG_NAME                                   = "gsdi";
  69     final static private String PRG_VERSION                                = "0.901";
  70     final static private String PRG_DATE                                   = "120608";
  71     final static private String PRG_DESC                                   = "general speciation duplication inference";
  72     final static private String E_MAIL                                     = "phylosoft@gmail.com";
  73     final static private String WWW                                        = "www.phylosoft.org/forester";
  74
  75     public static void main( final String args[] ) {
  76         try {
  77             ForesterUtil.printProgramInformation( PRG_NAME,
  78                                                   PRG_DESC,
  79                                                   PRG_VERSION,
  80                                                   PRG_DATE,
  81                                                   E_MAIL,
  82                                                   WWW,
  83                                                   ForesterUtil.getForesterLibraryInformation() );
  84             CommandLineArguments cla = null;
  85             try {
  86                 cla = new CommandLineArguments( args );
  87             }
  88             catch ( final Exception e ) {
  89                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  90             }
  91             if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
  92                 System.out.println();
  93                 gsdi.print_help();
  94                 System.exit( 0 );
  95             }
  96             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
  97                 System.out.println();
  98                 System.out.println( "Wrong number of arguments." );
  99                 System.out.println();
 100                 gsdi.print_help();
 101                 System.exit( -1 );
 102             }
 103             final List<String> allowed_options = new ArrayList<String>();
 104             allowed_options.add( gsdi.STRIP_OPTION );
 105             allowed_options.add( gsdi.SDI_OPTION );
 106             allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
 107             allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
 108             allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 109             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 110             if ( dissallowed_options.length() > 0 ) {
 111                 ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
 112             }
 113             execute( cla );
 114         }
 115         catch ( final IOException e ) {
 116             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 117         }
 118     }
 119
 120     private static void execute( final CommandLineArguments cla ) throws IOException {
 121         BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
 122         boolean strip = false;
 123         boolean most_parsimonous_duplication_model = false;
 124         boolean species_tree_in_phyloxml = true;
 125         boolean allow_stripping_of_gene_tree = false;
 126         if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
 127             strip = true;
 128         }
 129         if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
 130             base_algorithm = BASE_ALGORITHM.SDI;
 131         }
 132         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
 133             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 134                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
 135             }
 136             most_parsimonous_duplication_model = true;
 137         }
 138         if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
 139             species_tree_in_phyloxml = false;
 140         }
 141         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 142             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 143                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
 144             }
 145             allow_stripping_of_gene_tree = true;
 146         }
 147         Phylogeny species_tree = null;
 148         Phylogeny gene_tree = null;
 149         File gene_tree_file = null;
 150         File species_tree_file = null;
 151         File out_file = null;
 152         File log_file = null;
 153         Writer log_writer = null;
 154         try {
 155             gene_tree_file = cla.getFile( 0 );
 156             species_tree_file = cla.getFile( 1 );
 157             if ( cla.getNumberOfNames() == 3 ) {
 158                 out_file = cla.getFile( 2 );
 159             }
 160             else {
 161                 out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
 162             }
 163             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 164         }
 165         catch ( final IllegalArgumentException e ) {
 166             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 167         }
 168         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 169             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 170         }
 171         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 172             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 173         }
 174         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 175             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 176         }
 177         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 178             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 179         }
 180         try {
 181             log_writer = ForesterUtil.createBufferedWriter( log_file );
 182         }
 183         catch ( final IOException e ) {
 184             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 185         }
 186         try {
 187             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 188             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 189         }
 190         catch ( final IOException e ) {
 191             ForesterUtil.fatalError( gsdi.PRG_NAME,
 192                                      "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
 193         }
 194         try {
 195             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 196             if ( species_tree_in_phyloxml ) {
 197                 species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
 198             }
 199             else {
 200                 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 201                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 202                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 203                 }
 204                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 205                 final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
 206                 switch ( comp_base ) {
 207                     case SCIENTIFIC_NAME:
 208                         PhylogenyMethods
 209                                 .transferNodeNameToField( species_tree,
 210                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1 );
 211                         break;
 212                     case CODE:
 213                         PhylogenyMethods.transferNodeNameToField( species_tree,
 214                                                                   PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE );
 215                         break;
 216                     case ID:
 217                         PhylogenyMethods.transferNodeNameToField( species_tree,
 218                                                                   PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID );
 219                         break;
 220                     default:
 221                         ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
 222                 }
 223             }
 224         }
 225         catch ( final IOException e ) {
 226             ForesterUtil.fatalError( gsdi.PRG_NAME,
 227                                      "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
 228         }
 229         gene_tree.setRooted( true );
 230         species_tree.setRooted( true );
 231         if ( !gene_tree.isCompletelyBinary() ) {
 232             ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary" );
 233         }
 234         if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 235             if ( !species_tree.isCompletelyBinary() ) {
 236                 ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
 237                         + "\") is not completely binary, use GSDI instead" );
 238             }
 239         }
 240         // For timing.
 241         // gene_tree = Helper.createBalancedTree( 10 );
 242         // species_tree = Helper.createBalancedTree( 13 );
 243         // species_tree = Helper.createUnbalancedTree( 1024 );
 244         // gene_tree = Helper.createUnbalancedTree( 8192 );
 245         // species_tree = gene_tree.copyTree();
 246         // gene_tree = species_tree.copyTree();
 247         // Helper.numberSpeciesInOrder( species_tree );
 248         // Helper.numberSpeciesInOrder( gene_tree );
 249         // Helper.randomizeSpecies( 1, 8192, gene_tree );
 250         // Helper.intervalNumberSpecies( gene_tree, 4096 );
 251         // Helper.numberSpeciesInDescOrder( gene_tree );
 252         log_writer.write( PRG_NAME + " " + PRG_VERSION + " " + PRG_DATE );
 253         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 254         log_writer.write( PRG_DESC );
 255         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 256         log_writer.write( PRG_DESC );
 257         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 258         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 259         log_writer.write( new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 260         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 261         System.out.println();
 262         System.out.println( "Strip species tree: " + strip );
 263         log_writer.write( "Strip species tree: " + strip );
 264         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 265         SDI sdi = null;
 266         final long start_time = new Date().getTime();
 267         try {
 268             if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
 269                 System.out.println();
 270                 System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
 271                 System.out.println( "Allow stripping of gene tree nodes    : " + allow_stripping_of_gene_tree );
 272                 log_writer.write( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
 273                 log_writer.write( ForesterUtil.LINE_SEPARATOR );
 274                 log_writer.write( "Allow stripping of gene tree nodes    : " + allow_stripping_of_gene_tree );
 275                 log_writer.write( ForesterUtil.LINE_SEPARATOR );
 276                 sdi = new GSDI( gene_tree,
 277                                 species_tree,
 278                                 most_parsimonous_duplication_model,
 279                                 allow_stripping_of_gene_tree );
 280             }
 281             else {
 282                 System.out.println();
 283                 System.out.println( "Using SDIse algorithm" );
 284                 log_writer.write( "Using SDIse algorithm" );
 285                 log_writer.write( ForesterUtil.LINE_SEPARATOR );
 286                 sdi = new SDIse( gene_tree, species_tree );
 287             }
 288         }
 289         catch ( final Exception e ) {
 290             ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 291         }
 292         System.out.println();
 293         System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
 294         log_writer.write( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
 295         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 296         try {
 297             final PhylogenyWriter writer = new PhylogenyWriter();
 298             writer.toPhyloXML( out_file, gene_tree, 0 );
 299         }
 300         catch ( final IOException e ) {
 301             ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
 302         }
 303         System.out.println();
 304         System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
 305         System.out.println();
 306         log_writer.write( "Wrote resulting gene tree to: " + out_file );
 307         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 308         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
 309             sdi.computeMappingCostL();
 310             System.out.println( "Mapping cost                    : " + sdi.computeMappingCostL() );
 311             log_writer.write( "Mapping cost                    : " + sdi.computeMappingCostL() );
 312             log_writer.write( ForesterUtil.LINE_SEPARATOR );
 313         }
 314         System.out.println( "Number of duplications          : " + sdi.getDuplicationsSum() );
 315         log_writer.write( "Number of duplications          : " + sdi.getDuplicationsSum() );
 316         log_writer.write( ForesterUtil.LINE_SEPARATOR );
 317         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) && !most_parsimonous_duplication_model ) {
 318             final int duplications = ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum();
 319             System.out.println( "Number of potential duplications: " + duplications );
 320             log_writer.write( "Number of potential duplications: " + duplications );
 321             log_writer.write( ForesterUtil.LINE_SEPARATOR );
 322         }
 323         if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
 324             final int spec = ( ( GSDI ) sdi ).getSpeciationsSum();
 325             System.out.println( "Number of speciations            : " + spec );
 326             log_writer.write( "Number of speciations            : " + spec );
 327             log_writer.write( ForesterUtil.LINE_SEPARATOR );
 328         }
 329         System.out.println();
 330         //  some stat on gene tree:
 331         //      filename, name
 332         //      number of external nodes, strppided nodes
 333         //  some stats on sepcies tree, external nodes,
 334         //  filename, name
 335         //  internal nodes
 336         //  how many of which are polytomies
 337         //wrote log file to
 338         //  if ( allow_stripping_of_gene_tree ) {
 339         //      stripped x nodes, y external nodes remain
 340         //  }
 341     }
 342
 343     private static void print_help() {
 344         System.out.println( "Usage: " + gsdi.PRG_NAME
 345                 + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [outfile]" );
 346         System.out.println();
 347         System.out.println( "Options:" );
 348         //    System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + );
 349         System.out.println( " -" + gsdi.STRIP_OPTION
 350                 + ": to strip the species tree of unneeded species prior to duplication inference" );
 351         System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
 352         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
 353                 + ": use most parimonious duplication model for GSDI: " );
 354         System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
 355         System.out.println( "     as unknown because of polytomies in the species tree" );
 356         System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 357                 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 358         System.out.println();
 359         System.out.println( "Species tree:" );
 360         System.out
 361                 .println( " In phyloXML format (unless option -"
 362                         + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 363                         + " is used, in which case the species matching between gene tree and species tree must be via scientific name), with taxonomy data in appropriate fields" );
 364         System.out.println();
 365         System.out.println( "Gene tree:" );
 366         System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" );
 367         System.out.println();
 368         System.out.println( "Example:" );
 369         //  System.out.println( "gsdi
 370         //    System.out.println();
 371         System.out.println( "Note -- GSDI algorithm is under development" );
 372         System.out.println();
 373     }
 374 }