forester/java/src/org/forester/application/rio.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2017 Christian M. Zmasek
   6 // All rights reserved
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  23
  24 package org.forester.application;
  25
  26 import java.io.File;
  27 import java.io.FilenameFilter;
  28 import java.io.IOException;
  29 import java.util.ArrayList;
  30 import java.util.Arrays;
  31 import java.util.List;
  32
  33 import org.forester.rio.RIO;
  34 import org.forester.rio.RIO.REROOTING;
  35 import org.forester.rio.RIOUtil;
  36 import org.forester.sdi.SDIutil.ALGORITHM;
  37 import org.forester.util.CommandLineArguments;
  38 import org.forester.util.EasyWriter;
  39 import org.forester.util.ForesterUtil;
  40
  41 public class rio {
  42
  43     public final static String  PRG_NAME                       = "rio";
  44     public final static String  PRG_VERSION                    = "5.000";
  45     public final static String  PRG_DATE                       = "170411";
  46     final static private String E_MAIL                         = "phyloxml@gmail.com";
  47     final static private String WWW                            = "https://sites.google.com/site/cmzmasek/home/software/forester";
  48     final static private String HELP_OPTION_1                  = "help";
  49     final static private String LOGFILE_SUFFIX                 = "_RIO_log.tsv";
  50     final static private String STRIPPED_SPECIES_TREE_SUFFIX   = "_RIO_sst.xml";
  51     final static private String ORTHO_OUTTABLE_SUFFIX          = "_RIO_orthologies.tsv";
  52     final static private String ORTHO_OUTTABLE_WITH_MAP_SUFFIX = "_RIO_orthologies_ext_map.tsv";
  53     final static private String OUT_MIN_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_min_dup_";
  54     final static private String OUT_MED_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_med_dup_";
  55     final static private String ORTHOLOG_GROUPS_SUFFIX         = "_RIO_ortholog_groups.tsv";
  56     final static private String HELP_OPTION_2                  = "h";
  57     final static private String GT_FIRST                       = "f";
  58     final static private String GT_LAST                        = "l";
  59     final static private String REROOTING_OPT                  = "r";
  60     final static private String OUTGROUP                       = "o";
  61     final static private String USE_SDIR                       = "s";
  62     final static private String GENE_TREES_SUFFIX_OPTION       = "g";
  63     final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION  = "c";
  64     final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5;
  65
  66     public static void main( final String[] args ) {
  67         ForesterUtil.printProgramInformation( PRG_NAME,
  68                                               "resampled inference of orthologs",
  69                                               PRG_VERSION,
  70                                               PRG_DATE,
  71                                               E_MAIL,
  72                                               WWW,
  73                                               ForesterUtil.getForesterLibraryInformation() );
  74         CommandLineArguments cla = null;
  75         try {
  76             cla = new CommandLineArguments( args );
  77         }
  78         catch ( final Exception e ) {
  79             ForesterUtil.fatalError( e.getMessage() );
  80         }
  81         if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
  82             printHelp();
  83         }
  84         if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
  85             System.out.println();
  86             System.out.println( "error: incorrect number of arguments" );
  87             System.out.println();
  88             printHelp();
  89         }
  90         final List<String> allowed_options = new ArrayList<String>();
  91         allowed_options.add( GT_FIRST );
  92         allowed_options.add( GT_LAST );
  93         allowed_options.add( REROOTING_OPT );
  94         allowed_options.add( OUTGROUP );
  95         allowed_options.add( USE_SDIR );
  96         allowed_options.add( GENE_TREES_SUFFIX_OPTION );
  97         allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION );
  98         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  99         if ( dissallowed_options.length() > 0 ) {
 100             ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options );
 101         }
 102         final File gene_trees_file = cla.getFile( 0 );
 103         final boolean use_dir;
 104         File indir = null;
 105         File outdir = null;
 106         if ( gene_trees_file.isDirectory() ) {
 107             if ( !gene_trees_file.exists() ) {
 108                 ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" does not exist" );
 109             }
 110             use_dir = true;
 111             indir = gene_trees_file;
 112         }
 113         else {
 114             use_dir = false;
 115         }
 116         final File species_tree_file = cla.getFile( 1 );
 117         File orthology_outtable = null;
 118         if ( use_dir ) {
 119             outdir = cla.getFile( 2 );
 120         }
 121         else {
 122             orthology_outtable = cla.getFile( 2 );
 123         }
 124         File logfile;
 125         if ( use_dir ) {
 126             if ( ( cla.getNumberOfNames() < 4 ) ) {
 127                 System.out.println();
 128                 System.out.println( "error: incorrect number of arguments" );
 129                 System.out.println();
 130                 printHelp();
 131             }
 132             logfile = cla.getFile( 3 );
 133             if ( logfile.exists() ) {
 134                 ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
 135             }
 136         }
 137         else {
 138             if ( cla.getNumberOfNames() > 3 ) {
 139                 logfile = cla.getFile( 3 );
 140                 if ( logfile.exists() ) {
 141                     ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
 142                 }
 143             }
 144             else {
 145                 logfile = null;
 146             }
 147         }
 148         boolean sdir = false;
 149         if ( cla.isOptionSet( USE_SDIR ) ) {
 150             if ( cla.isOptionHasAValue( USE_SDIR ) ) {
 151                 ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR );
 152             }
 153             sdir = true;
 154             if ( !use_dir && logfile != null ) {
 155                 ForesterUtil.fatalError( "no logfile output for SDIR algorithm" );
 156             }
 157         }
 158         String outgroup = null;
 159         if ( cla.isOptionSet( OUTGROUP ) ) {
 160             if ( sdir ) {
 161                 ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" );
 162             }
 163             if ( use_dir ) {
 164                 ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" );
 165             }
 166             if ( !cla.isOptionHasAValue( OUTGROUP ) ) {
 167                 ForesterUtil.fatalError( "no value for -" + OUTGROUP );
 168             }
 169             outgroup = cla.getOptionValueAsCleanString( OUTGROUP );
 170         }
 171         REROOTING rerooting = REROOTING.BY_ALGORITHM;
 172         if ( cla.isOptionSet( REROOTING_OPT ) ) {
 173             if ( !cla.isOptionHasAValue( REROOTING_OPT ) ) {
 174                 ForesterUtil.fatalError( "no value for -" + REROOTING_OPT );
 175             }
 176             if ( sdir ) {
 177                 ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" );
 178             }
 179             final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase();
 180             if ( rerooting_str.equals( "none" ) ) {
 181                 rerooting = REROOTING.NONE;
 182             }
 183             else if ( rerooting_str.equals( "midpoint" ) ) {
 184                 rerooting = REROOTING.MIDPOINT;
 185             }
 186             else if ( rerooting_str.equals( "outgroup" ) ) {
 187                 if ( use_dir ) {
 188                     ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" );
 189                 }
 190                 rerooting = REROOTING.OUTGROUP;
 191             }
 192             else {
 193                 ForesterUtil
 194                         .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
 195             }
 196         }
 197         if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) {
 198             ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" );
 199         }
 200         if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) {
 201             ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" );
 202         }
 203         int gt_first = RIO.DEFAULT_RANGE;
 204         int gt_last = RIO.DEFAULT_RANGE;
 205         if ( cla.isOptionSet( GT_FIRST ) ) {
 206             if ( sdir ) {
 207                 ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
 208             }
 209             if ( !cla.isOptionHasAValue( GT_FIRST ) ) {
 210                 ForesterUtil.fatalError( "no value for -" + GT_FIRST );
 211             }
 212             try {
 213                 gt_first = cla.getOptionValueAsInt( GT_FIRST );
 214             }
 215             catch ( final IOException e ) {
 216                 ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" );
 217             }
 218             if ( gt_first < 0 ) {
 219                 ForesterUtil.fatalError( "attempt to set index of first tree to analyze to: " + gt_first );
 220             }
 221         }
 222         if ( cla.isOptionSet( GT_LAST ) ) {
 223             if ( sdir ) {
 224                 ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
 225             }
 226             if ( !cla.isOptionHasAValue( GT_LAST ) ) {
 227                 ForesterUtil.fatalError( "no value for -" + GT_LAST );
 228             }
 229             try {
 230                 gt_last = cla.getOptionValueAsInt( GT_LAST );
 231             }
 232             catch ( final IOException e ) {
 233                 ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" );
 234             }
 235             if ( gt_last < 0 ) {
 236                 ForesterUtil.fatalError( "attempt to set index of last tree to analyze to: " + gt_last );
 237             }
 238         }
 239         if ( ( ( gt_last != RIO.DEFAULT_RANGE ) && ( gt_first != RIO.DEFAULT_RANGE ) ) && ( ( gt_last < gt_first ) ) ) {
 240             ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to "
 241                     + gt_last );
 242         }
 243         double ortholog_group_cutoff = ORTHOLOG_GROUPS_CUTOFF_DEFAULT;
 244         if ( cla.isOptionSet( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) {
 245             if ( sdir ) {
 246                 ForesterUtil.fatalError( "ortholog groups cutoff for SDIR algorithm" );
 247             }
 248             if ( !cla.isOptionHasAValue( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) {
 249                 ForesterUtil.fatalError( "no value for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION );
 250             }
 251             try {
 252                 ortholog_group_cutoff = cla.getOptionValueAsDouble( ORTHOLOG_GROUPS_CUTOFF_OPTION );
 253             }
 254             catch ( final IOException e ) {
 255                 ForesterUtil.fatalError( "could not parse double for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + " option" );
 256             }
 257             if ( ortholog_group_cutoff < 0 ) {
 258                 ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff );
 259             }
 260             if ( ortholog_group_cutoff > 1 ) {
 261                 ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff );
 262             }
 263         }
 264         if ( !use_dir ) {
 265             ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file );
 266         }
 267         final String gene_trees_suffix;
 268         if ( cla.isOptionSet( GENE_TREES_SUFFIX_OPTION ) ) {
 269             if ( !use_dir ) {
 270                 ForesterUtil.fatalError( "no gene tree suffix option when operating on indivual gene trees" );
 271             }
 272             if ( !cla.isOptionHasAValue( GENE_TREES_SUFFIX_OPTION ) ) {
 273                 ForesterUtil.fatalError( "no value for -" + GENE_TREES_SUFFIX_OPTION );
 274             }
 275             gene_trees_suffix = cla.getOptionValueAsCleanString( GENE_TREES_SUFFIX_OPTION );
 276         }
 277         else {
 278             gene_trees_suffix = ".mlt";
 279         }
 280         ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
 281         if ( !use_dir && orthology_outtable.exists() ) {
 282             ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
 283         }
 284         long time = 0;
 285         try {
 286             if ( use_dir ) {
 287                 System.out.println( "Gene trees in-dir                   :\t" + indir.getCanonicalPath() );
 288                 System.out.println( "Gene trees suffix                   :\t" + gene_trees_suffix );
 289             }
 290             else {
 291                 System.out.println( "Gene trees                          :\t" + gene_trees_file.getCanonicalPath() );
 292             }
 293             System.out.println( "Species tree                        :\t" + species_tree_file.getCanonicalPath() );
 294         }
 295         catch ( final IOException e ) {
 296             ForesterUtil.fatalError( e.getLocalizedMessage() );
 297         }
 298         if ( use_dir ) {
 299             System.out.println( "Out-dir                             :\t" + outdir );
 300         }
 301         else {
 302             System.out.println( "All vs all orthology results table  :\t" + orthology_outtable );
 303         }
 304         if ( logfile != null ) {
 305             System.out.println( "Logfile                             :\t" + logfile );
 306         }
 307         System.out.println( "Ortholog groups cutoff              :\t" + ortholog_group_cutoff );
 308         if ( gt_first != RIO.DEFAULT_RANGE ) {
 309             System.out.println( "First gene tree to analyze          :\t" + gt_first );
 310         }
 311         if ( gt_last != RIO.DEFAULT_RANGE ) {
 312             System.out.println( "Last gene tree to analyze           :\t" + gt_last );
 313         }
 314         String rerooting_str = "";
 315         switch ( rerooting ) {
 316             case BY_ALGORITHM: {
 317                 rerooting_str = "by minimizing duplications";
 318                 break;
 319             }
 320             case MIDPOINT: {
 321                 rerooting_str = "by midpoint method";
 322                 break;
 323             }
 324             case OUTGROUP: {
 325                 rerooting_str = "by outgroup: " + outgroup;
 326                 break;
 327             }
 328             case NONE: {
 329                 rerooting_str = "none";
 330                 break;
 331             }
 332         }
 333         System.out.println( "Re-rooting                          : \t" + rerooting_str );
 334         if ( !sdir ) {
 335             System.out.println( "Non binary species tree             :\tallowed" );
 336         }
 337         else {
 338             System.out.println( "Non binary species tree             :\tdisallowed" );
 339         }
 340         time = System.currentTimeMillis();
 341         final ALGORITHM algorithm;
 342         if ( sdir ) {
 343             algorithm = ALGORITHM.SDIR;
 344         }
 345         else {
 346             algorithm = ALGORITHM.GSDIR;
 347         }
 348         EasyWriter log = null;
 349         if ( use_dir ) {
 350             if ( outdir.exists() ) {
 351                 if ( !outdir.isDirectory() ) {
 352                     ForesterUtil.fatalError( PRG_NAME,
 353                                              "out-directory [" + outdir + "] already exists but is not a directory" );
 354                 }
 355             }
 356             else {
 357                 final boolean success = outdir.mkdirs();
 358                 if ( !success ) {
 359                     ForesterUtil.fatalError( PRG_NAME, "could not create out-directory [" + outdir + "]" );
 360                 }
 361             }
 362             final String species_tree_file_name = species_tree_file.getName();
 363             final File gene_trees_files[] = indir.listFiles( new FilenameFilter() {
 364
 365                 @Override
 366                 public boolean accept( final File dir, final String name ) {
 367                     return ( ( name.endsWith( gene_trees_suffix ) ) && !( name.equals( species_tree_file_name ) ) );
 368                 }
 369             } );
 370             if ( gene_trees_files.length < 1 ) {
 371                 ForesterUtil.fatalError( PRG_NAME,
 372                                          "in-directory [" + indir
 373                                                  + "] does not contain any gene tree files with suffix "
 374                                                  + gene_trees_suffix );
 375             }
 376             try {
 377                 log = ForesterUtil.createEasyWriter( logfile );
 378             }
 379             catch ( final IOException e ) {
 380                 ForesterUtil.fatalError( PRG_NAME, "could not create [" + logfile + "]" );
 381             }
 382             Arrays.sort( gene_trees_files );
 383             try {
 384                 log.print( "# program" );
 385                 log.print( "\t" );
 386                 log.print( PRG_NAME );
 387                 log.println();
 388                 log.print( "# version" );
 389                 log.print( "\t" );
 390                 log.print( PRG_VERSION );
 391                 log.println();
 392                 log.print( "# date" );
 393                 log.print( "\t" );
 394                 log.print( PRG_DATE );
 395                 log.println();
 396                 log.print( "# Algorithm " );
 397                 log.print( "\t" );
 398                 log.print( algorithm.toString() );
 399                 log.println();
 400                 log.print( "# Gene trees in-dir" );
 401                 log.print( "\t" );
 402                 log.print( indir.getCanonicalPath() );
 403                 log.println();
 404                 log.print( "# Gene trees suffix" );
 405                 log.print( "\t" );
 406                 log.print( gene_trees_suffix );
 407                 log.println();
 408                 log.print( "# Species tree" );
 409                 log.print( "\t" );
 410                 log.print( species_tree_file.getCanonicalPath() );
 411                 log.println();
 412                 log.print( "# Out-dir" );
 413                 log.print( "\t" );
 414                 log.print( outdir.getCanonicalPath() );
 415                 log.println();
 416                 log.print( "# Logfile" );
 417                 log.print( "\t" );
 418                 log.print( logfile.getCanonicalPath() );
 419                 log.println();
 420                 log.print( "# Ortholog groups cutoff" );
 421                 log.print( "\t" );
 422                 log.print( Double.toString( ortholog_group_cutoff ) );
 423                 log.println();
 424                 if ( gt_first != RIO.DEFAULT_RANGE ) {
 425                     log.print( "# First gene tree to analyze" );
 426                     log.print( "\t" );
 427                     log.print( Integer.toString( gt_first ) );
 428                     log.println();
 429                 }
 430                 if ( gt_last != RIO.DEFAULT_RANGE ) {
 431                     log.print( "# Last gene tree to analyze" );
 432                     log.print( "\t" );
 433                     log.print( Integer.toString( gt_last ) );
 434                     log.println();
 435                 }
 436                 log.print( "# Re-rooting" );
 437                 log.print( "\t" );
 438                 log.print( rerooting_str );
 439                 log.println();
 440                 log.print( "# Non binary species tree" );
 441                 log.print( "\t" );
 442                 if ( !sdir ) {
 443                     log.print( "allowed" );
 444                 }
 445                 else {
 446                     log.print( "disallowed" );
 447                 }
 448                 log.println();
 449                 log.println();
 450                 log.print( "NAME" );
 451                 log.print( "\t" );
 452                 log.print( "EXT NODES" );
 453                 log.print( "\t" );
 454                 log.print( ortholog_group_cutoff + " O GROUPS" );
 455                 log.print( "\t" );
 456                 log.print( "0.05 O GROUPS" );
 457                 log.print( "\t" );
 458                 log.print( "0.25 O GROUPS" );
 459                 log.print( "\t" );
 460                 log.print( "0.5 O GROUPS" );
 461                 log.print( "\t" );
 462                 log.print( "0.75 O GROUPS" );
 463                 log.print( "\t" );
 464                 log.print( "0.95 O GROUPS" );
 465                 log.print( "\t" );
 466                 log.print( "MEDIAN DUP" );
 467                 log.print( "\t" );
 468                 log.print( "MEAN DUP" );
 469                 log.print( "\t" );
 470                 log.print( "MEAN DUP SD" );
 471                 log.print( "\t" );
 472                 log.print( "MIN DUP" );
 473                 log.print( "\t" );
 474                 log.print( "MAX DUP" );
 475                 log.print( "\t" );
 476                 log.print( "REMOVED EXT NODES" );
 477                 log.print( "\t" );
 478                 log.print( "N" );
 479                 log.println();
 480             }
 481             catch ( IOException e ) {
 482                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 483             }
 484             int counter = 1;
 485             for( final File gf : gene_trees_files ) {
 486                 String outname = gf.getName();
 487                 System.out
 488                         .print( "\r                                                                                            " );
 489                 System.out.print( "\r" + counter + "/" + gene_trees_files.length + ": " + outname );
 490                 counter++;
 491                 if ( outname.indexOf( "." ) > 0 ) {
 492                     outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 493                 }
 494                 try {
 495                     boolean perform_id_mapping = true;
 496                     File id_mapping_dir = new File( "mappings" );
 497                     String id_mapping_suffix = ".nim";
 498                     RIOUtil.executeAnalysis( gf,
 499                                              species_tree_file,
 500                                              new File( outdir.getCanonicalFile() + "/" + outname
 501                                                      + ORTHO_OUTTABLE_SUFFIX ),
 502                                              new File( outdir.getCanonicalFile() + "/" + outname
 503                                                      + ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
 504                                              new File( outdir.getCanonicalFile() + "/" + outname
 505                                                      + ORTHOLOG_GROUPS_SUFFIX ),
 506                                              new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ),
 507                                              outgroup,
 508                                              rerooting,
 509                                              gt_first,
 510                                              gt_last,
 511                                              new File( outdir.getCanonicalFile() + "/" + outname
 512                                                      + STRIPPED_SPECIES_TREE_SUFFIX ),
 513                                              new File( outdir.getCanonicalFile() + "/" + outname
 514                                                      + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
 515                                              new File( outdir.getCanonicalFile() + "/" + outname
 516                                                      + OUT_MED_DUP_GENE_TREE_SUFFIX ),
 517                                              true,
 518                                              algorithm,
 519                                              true,
 520                                              log,
 521                                              ortholog_group_cutoff,
 522                                              perform_id_mapping,
 523                                              id_mapping_dir,
 524                                              id_mapping_suffix );
 525                 }
 526                 catch ( IOException e ) {
 527                     ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 528                 }
 529             }
 530             System.out
 531                     .print( "\r                                                                                        " );
 532             System.out.println();
 533         }
 534         else {
 535             String outname = orthology_outtable.toString();
 536             if ( outname.indexOf( "." ) > 0 ) {
 537                 outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 538             }
 539             RIOUtil.executeAnalysis( gene_trees_file,
 540                                      species_tree_file,
 541                                      orthology_outtable,
 542                                      null,
 543                                      new File( outname + ORTHOLOG_GROUPS_SUFFIX ),
 544                                      logfile,
 545                                      outgroup,
 546                                      rerooting,
 547                                      gt_first,
 548                                      gt_last,
 549                                      new File( outname + STRIPPED_SPECIES_TREE_SUFFIX ),
 550                                      new File( outname + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
 551                                      new File( outname + OUT_MED_DUP_GENE_TREE_SUFFIX ),
 552                                      algorithm == ALGORITHM.GSDIR,
 553                                      algorithm,
 554                                      false,
 555                                      null,
 556                                      ortholog_group_cutoff,
 557                                      false,
 558                                      null,
 559                                      null );
 560         }
 561         if ( !use_dir ) {
 562             time = System.currentTimeMillis() - time;
 563             System.out.println( "Time                                :\t" + time + "ms" );
 564         }
 565         else {
 566             try {
 567                 log.close();
 568             }
 569             catch ( IOException e ) {
 570                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 571             }
 572             time = System.currentTimeMillis() - time;
 573             System.out.println( "Time                                :\t" + time + "ms" );
 574         }
 575         System.exit( 0 );
 576     }
 577
 578     private final static void printHelp() {
 579         System.out.println( "Usage" );
 580         System.out.println();
 581         System.out.println( PRG_NAME
 582                 + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
 583         System.out.println();
 584         System.out.println( PRG_NAME + " [options] <gene trees indir> <species tree infile> <outdir> <logfile>" );
 585         System.out.println();
 586         System.out.println();
 587         System.out.println( " Options" );
 588         System.out.println( "  -" + GT_FIRST + "=<first>     : first gene tree to analyze (0-based index)" );
 589         System.out.println( "  -" + GT_LAST + "=<last>      : last gene tree to analyze (0-based index)" );
 590         System.out.println( "  -" + ORTHOLOG_GROUPS_CUTOFF_OPTION
 591                 + "=<cutoff>    : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" );
 592         System.out.println( "  -" + REROOTING_OPT
 593                 + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
 594         System.out.println( "                   or 'outgroup' (default: by minizming duplications)" );
 595         System.out.println( "  -" + OUTGROUP
 596                 + "=<outgroup>  : for rooting by outgroup, name of outgroup (external gene tree node)" );
 597         System.out.println( "  -" + USE_SDIR
 598                 + "             : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
 599         System.out.println( "                   disallowed, as are most options)" );
 600         System.out.println( "  -" + GENE_TREES_SUFFIX_OPTION
 601                 + "=<suffix>    : suffix for gene trees when operating on gene tree directories (default: .mlt)" );
 602         System.out.println();
 603         System.out.println( " Formats" );
 604         System.out
 605                 .println( "  The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," );
 606         System.out
 607                 .println( "  but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" );
 608         System.out
 609                 .println( "  extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" );
 610         System.out.println( "  in the species tree." );
 611         System.out.println();
 612         System.out.println( " Examples" );
 613         System.out.println( "  rio -s gene_trees.nh species.xml outtable.tsv" );
 614         System.out.println( "  rio gene_trees.nh species.xml outtable.tsv log.txt" );
 615         System.out.println( "  rio -c=0.9 -f=10 -l=100 -r=none gene_trees.xml species.xml outtable.tsv log.txt" );
 616         System.out.println( "  rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" );
 617         System.out.println();
 618         System.exit( -1 );
 619     }
 620 }