forester/java/src/org/forester/application/sdi_dir.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 // Copyright (C) 2000-2001 Washington University School of Medicine
   8 // and Howard Hughes Medical Institute
   9 // All rights reserved
  10 //
  11 // This library is free software; you can redistribute it and/or
  12 // modify it under the terms of the GNU Lesser General Public
  13 // License as published by the Free Software Foundation; either
  14 // version 2.1 of the License, or (at your option) any later version.
  15 //
  16 // This library is distributed in the hope that it will be useful,
  17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  19 // Lesser General Public License for more details.
  20 //
  21 // You should have received a copy of the GNU Lesser General Public
  22 // License along with this library; if not, write to the Free Software
  23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: www.phylosoft.org/forester
  27
  28 package org.forester.application;
  29
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.PrintWriter;
  34 import java.util.Arrays;
  35
  36 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  37 import org.forester.io.writers.PhylogenyWriter;
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.phylogeny.PhylogenyMethods;
  40 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  41 import org.forester.phylogeny.factories.PhylogenyFactory;
  42 import org.forester.sdi.SDIR;
  43 import org.forester.sdi.SDIse;
  44 import org.forester.util.ForesterUtil;
  45
  46 /*
  47  * Allows to infer duplications - speciations on all (rooted or unrooted) gene
  48  * trees in a directory by using method "infer" of class SDIunrooted. <p> The
  49  * output of this is a (re)rooted tree with speciation - duplication assigned
  50  * for each tree (in "gene tree directory" with suffix "suffix for gene trees"),
  51  * as well as a summary list ("outputfile name"). <p> The summary list contains
  52  * the following. The number in brackets indicates how many external nodes of
  53  * the gene tree had to be removed since the associated species was not found in
  54  * the species tree. "en" indicates the number of external nodes in the
  55  * resulting (analyzed and returned) gene tree. "d" are the number of
  56  * duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal
  57  * difference in tree heights (of the two subtrees at the root; this number is
  58  * 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene
  59  * tree(s). <p> The output file ending with "_Sdist" is a file which lists the
  60  * distribution of trees sizes, "_Ddist" lists the distribution of the sums of
  61  * duplications (up to a certain maximal size, set with final variables
  62  * MAX_EXT_NODE_DIST and MAX_DUP_DIST).
  63  *
  64  * @see SDIunrooted
  65  *
  66  * @author Christian M. Zmasek
  67  */
  68 public class sdi_dir {
  69
  70     final static private String E_MAIL      = "czmasek@burnham.org";
  71     final static private String WWW         = "www.phylosoft.org";
  72     final static private String PRG_NAME    = "sdi_dir";
  73     final static private String PRG_VERSION = "2.00";
  74     final static private String PRG_DATE    = "2010.04.26";
  75
  76     private static void errorInCommandLine() {
  77         System.out.println( "\nsdi_dir: Error in command line.\n" );
  78         System.out.print( "Usage: % sdi_dir [-options] <gene tree directory> <suffix for gene trees>" );
  79         System.out.println( " <species tree file name> <output directory> <outputfile name>" );
  80         System.out.println( "\nOptions:" );
  81         System.out.println( " -l to root by minimizing the mapping cost L (and also the sum of duplications)" );
  82         System.out.println( " -d to root by minimizing the sum of duplications" );
  83         System.out.println( " -h to root by minimizing tree height (can be used together with -l or -d)" );
  84         System.out.println( " -w to write assigned gene trees into output directory" );
  85         System.out.println( "\nGene tree directory" );
  86         System.out.println( " The directory from which to read phyloXML formatted gene trees which" );
  87         System.out.println( " contain taxonomic information in appropriate sub-elements of taxonomy" );
  88         System.out.println( " (see: www.phyloxml.org)." );
  89         System.out.println( " The gene trees can either be rooted, in which case no rooting with -l, -d, or -h " );
  90         System.out.println( " is necessary, or they can be unrooted, in which case rooting is mandatory." );
  91         System.out.println( "\nSuffix for gene trees" );
  92         System.out.println( " Suffix of the gene trees to analyze (e.g. \".phyloxml\")." );
  93         System.out.println( "\nSpecies tree file" );
  94         System.out.println( " In phyloXML format, taxonomic information in appropriate sub-elements of taxonomy." );
  95         System.out.println( " (see: www.phyloxml.org)." );
  96         System.out.println( "\nOutput directory" );
  97         System.out.println( " The directory into which the assigned gene trees will be written." );
  98         System.out.println( "\nOutputfile name" );
  99         System.out.println( " File name for summary output files." );
 100         System.out.println( "" );
 101         System.exit( -1 );
 102     }
 103
 104     /**
 105      * Runs method "infer" of class SDIunrooted on all gene trees in directory
 106      * indir.
 107      * <p>
 108      * Trees are rooted by minimizing either the sum of duplications, the
 109      * mapping cost L, or the tree height (or combinations thereof). One
 110      * resulting tree for each (out of possibly many) is stored in outdir and a
 111      * summary outfile is created. The distributions of the tree sizes (name of
 112      * outfile + _Ddist) and the distributions of the sum of duplications per
 113      * tree (name of outfile + _Sdist) are written out as well.
 114      * <p>
 115      * If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are
 116      * rooted by minimizing by minimizing the mapping cost L.
 117      * <p>
 118      * If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are
 119      * false trees are assumed to be alreadty rooted.
 120      * <p>
 121      * (Last modified: 02/02/01)
 122      *
 123      * @see SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
 124      * @param indir
 125      *            a directory containing gene trees in NHX format
 126      * @param species_tree_file
 127      *            a species tree file in NHX format
 128      * @param outdir
 129      *            a directory where to write trees
 130      * @param outfile
 131      *            a file name for the summary file
 132      * @param suffix
 133      *            a suffix for the trees to read (e.g. nhx), is case sensitive
 134      * @param write_trees
 135      *            set to true to write out one tree with minmal duplications or
 136      *            L each
 137      * @param minimize_mapping_cost
 138      *            set to true to root by minimizing the mapping cost L
 139      * @param minimize_sum_of_dup
 140      *            set to true to root by minimizing the sum of duplications
 141      * @param minimize_height
 142      *            set to true to root by minimizing the tree height -- if
 143      *            minimize_mapping_cost is set to true or minimize_sum_of_dup is
 144      *            set to true, then out of the resulting trees with minimal
 145      *            mapping cost or minimal number of duplications the tree with
 146      *            the minimal height is chosen
 147      */
 148     public static void infer( final File indir,
 149                               final File species_tree_file,
 150                               final File outdir,
 151                               final File outfile,
 152                               String suffix,
 153                               final boolean write_trees,
 154                               final boolean minimize_mapping_cost,
 155                               boolean minimize_sum_of_dup,
 156                               final boolean minimize_height ) throws IOException {
 157         final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
 158         // to be analyzed.
 159         final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]
 160         // to be analyzed.
 161         final int MAX_DUP_DIST = 50; // Max number of dups to output in dup
 162         // distribution ("_Ddist").
 163         final int MAX_EXT_NODE_DIST = 1000; // Max number of ext nodes to output
 164         // in size
 165         // distribution ("_Sdist").
 166         int successful = 0, number_of_too_small_trees = 0, number_of_too_large_trees = 0, dups = 0, c = 0, ext_nodes = 0, removed = 0;
 167         final int nodecount0 = 0;
 168         int j = 0;
 169         long total_number_of_d = 0, total_number_of_ext_nodes = 0, sum_costs = 0;
 170         double sum_tree_heights = 0.0, sum_subtree_diff = 0.0;
 171         Phylogeny species_tree = null;
 172         String filename = null;
 173         String[] filenames = null;
 174         Phylogeny[] trees = null;
 175         final int[] duplications = new int[ MAX_EXT_NODES - 1 ], // For dup
 176         // distribution.
 177         sizes = new int[ MAX_EXT_NODES - 1 ]; // For ext nodes dist.of
 178         // successfully assigned trees.
 179         File outtree = null;
 180         PrintWriter out = null, out_ddist = null, out_sdist = null;
 181         final File ddist_outfile = new File( outfile + "_Ddist" ), sdist_outfile = new File( outfile + "_Sdist" );
 182         final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.0#####" );
 183         df.setDecimalSeparatorAlwaysShown( true );
 184         if ( !indir.exists() || !indir.isDirectory() ) {
 185             throw new IllegalArgumentException( indir + " does not exist or is not a directory." );
 186         }
 187         if ( !outdir.exists() || !outdir.isDirectory() ) {
 188             throw new IllegalArgumentException( outdir + " does not exist or is not a directory." );
 189         }
 190         if ( outfile.exists() ) {
 191             throw new IllegalArgumentException( outfile + " does already exist." );
 192         }
 193         if ( ddist_outfile.exists() ) {
 194             throw new IllegalArgumentException( ddist_outfile + " does already exist." );
 195         }
 196         if ( sdist_outfile.exists() ) {
 197             throw new IllegalArgumentException( sdist_outfile + " does already exist." );
 198         }
 199         if ( !species_tree_file.exists() || !species_tree_file.isFile() ) {
 200             throw new IllegalArgumentException( species_tree_file + " does not exist or is not a file." );
 201         }
 202         if ( minimize_mapping_cost && minimize_sum_of_dup ) {
 203             minimize_sum_of_dup = false;
 204         }
 205         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 206         species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
 207         filenames = indir.list();
 208         Arrays.sort( filenames );
 209         suffix = suffix.trim();
 210         out = new PrintWriter( new FileWriter( outfile ), true );
 211         //nodecount0 = PhylogenyNode.getNodeCount();
 212         for( int i = 0; i < filenames.length; ++i ) {
 213             filename = filenames[ i ];
 214             if ( ( suffix.length() < 1 ) || filename.endsWith( suffix ) ) {
 215                 final File gene_tree_file = new File( indir.getPath(), filename );
 216                 if ( gene_tree_file.exists() && gene_tree_file.isFile() ) {
 217                     out.print( j + "\t" + filename );
 218                     System.out.println( j + ": " + filename );
 219                     j++;
 220                     Phylogeny gene_tree = null;
 221                     gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 222                     // Removes from gene_tree all species not found in
 223                     // species_tree.
 224                     removed = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
 225                     if ( filename.length() < 8 ) {
 226                         out.print( "\t\t\t[-" + removed + "]" );
 227                     }
 228                     else if ( filename.length() < 16 ) {
 229                         out.print( "\t\t[-" + removed + "]" );
 230                     }
 231                     else {
 232                         out.print( "\t[-" + removed + "]" );
 233                     }
 234                     if ( gene_tree.getNumberOfExternalNodes() < MIN_EXT_NODES ) {
 235                         out.print( "\t<" + MIN_EXT_NODES + "en\n" );
 236                         number_of_too_small_trees++;
 237                     }
 238                     else if ( gene_tree.getNumberOfExternalNodes() > MAX_EXT_NODES ) {
 239                         out.print( "\t>" + MAX_EXT_NODES + "en\n" );
 240                         number_of_too_large_trees++;
 241                     }
 242                     else {
 243                         SDIR sdiunrooted = null;
 244                         // PhylogenyNode.setNodeCount( nodecount0 );
 245                         sdiunrooted = new SDIR();
 246                         if ( minimize_mapping_cost || minimize_sum_of_dup || minimize_height ) {
 247                             trees = sdiunrooted.infer( gene_tree,
 248                                                        species_tree,
 249                                                        minimize_mapping_cost,
 250                                                        minimize_sum_of_dup,
 251                                                        minimize_height,
 252                                                        write_trees,
 253                                                        1 );
 254                             dups = sdiunrooted.getMinimalDuplications();
 255                         }
 256                         else {
 257                             final SDIse sdi = new SDIse( gene_tree, species_tree );
 258                             trees = new Phylogeny[ 1 ];
 259                             trees[ 0 ] = gene_tree;
 260                             dups = sdi.getDuplicationsSum();
 261                             c = sdi.computeMappingCostL();
 262                             sum_costs += c;
 263                             out.print( "\t L=" + c );
 264                         }
 265                         successful++;
 266                         ext_nodes = gene_tree.getNumberOfExternalNodes();
 267                         total_number_of_ext_nodes += ext_nodes;
 268                         sizes[ ext_nodes ]++;
 269                         out.print( "\t " + ext_nodes + "en" );
 270                         total_number_of_d += dups;
 271                         duplications[ dups ]++;
 272                         out.print( "\t " + dups + "d" );
 273                         if ( minimize_mapping_cost ) {
 274                             c = sdiunrooted.getMinimalMappingCost();
 275                             sum_costs += c;
 276                             out.print( "\t L=" + c );
 277                         }
 278                         if ( minimize_height ) {
 279                             out.print( "\t h=" + df.format( sdiunrooted.getMinimalTreeHeight() ) );
 280                             out.print( "\t d=" + df.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
 281                             sum_tree_heights += sdiunrooted.getMinimalTreeHeight();
 282                             sum_subtree_diff += sdiunrooted.getMinimalDiffInSubTreeHeights();
 283                         }
 284                         out.println();
 285                         if ( write_trees ) {
 286                             outtree = new File( outdir, new File( filenames[ i ] ).getName() );
 287                             final PhylogenyWriter writer = new PhylogenyWriter();
 288                             writer.toPhyloXML( outtree, trees[ 0 ], 1 );
 289                         }
 290                     }
 291                 }
 292             }
 293         }
 294         //PhylogenyNode.setNodeCount( nodecount0 );
 295         if ( minimize_mapping_cost ) {
 296             out.println( "\nRooted by minimizing mapping cost L." );
 297             System.out.println( "\nRooted by minimizing mapping cost L." );
 298             if ( minimize_height ) {
 299                 out.println( "Selected tree(s) with minimal height out of resulting trees." );
 300                 System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
 301             }
 302         }
 303         else if ( minimize_sum_of_dup ) {
 304             out.println( "\nRooted by minimizing sum of duplications." );
 305             System.out.println( "\nRooted by minimizing sum of duplications." );
 306             if ( minimize_height ) {
 307                 out.println( "Selected tree(s) with minimal height out of resulting trees." );
 308                 System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
 309             }
 310         }
 311         else if ( minimize_height ) {
 312             out.println( "\nRooted by minimizing tree height." );
 313             System.out.println( "\nRooted by minimizing tree height." );
 314         }
 315         else {
 316             out.println( "\nNo (re) rooting was performed." );
 317             System.out.println( "\nNo (re) rooting was performed." );
 318         }
 319         out.println( "\nTrees directory  : " + indir );
 320         out.println( "Suffix for trees : " + suffix );
 321         out.println( "Species tree     : " + species_tree_file );
 322         out.println( "Output directory : " + outdir );
 323         out.println( "Output file      : " + outfile );
 324         out.println( "\nTotal number of attempts (tree files read)       : " + j );
 325         out.println( "Total number of successfully assigned trees      : " + successful );
 326         out.println( "Number of too small trees                        : " + number_of_too_small_trees );
 327         out.println( "Number of too large trees                        : " + number_of_too_large_trees );
 328         out.println( "\nSum of duplications                                   : " + total_number_of_d );
 329         if ( minimize_mapping_cost ) {
 330             out.println( "Sum of mapping costs L                                : " + sum_costs );
 331         }
 332         if ( minimize_height ) {
 333             out.println( "Sum of tree heights                                   : " + sum_tree_heights );
 334             out.println( "Sum of differences in subtree heights                 : " + sum_subtree_diff );
 335         }
 336         out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
 337         out.close();
 338         System.out.println( "\nTotal number of attempts (tree files read)       : " + j );
 339         System.out.println( "Total number of successfully assigned trees      : " + successful );
 340         System.out.println( "Number of too small trees                        : " + number_of_too_small_trees );
 341         System.out.println( "Number of too large trees                        : " + number_of_too_large_trees );
 342         System.out.println( "\nSum of duplications                                   : " + total_number_of_d );
 343         if ( minimize_mapping_cost ) {
 344             System.out.println( "Sum of mapping costs L                                : " + sum_costs );
 345         }
 346         if ( minimize_height ) {
 347             System.out.println( "Sum of tree heights                                   : " + sum_tree_heights );
 348             System.out.println( "Sum of differences in subtree heights                 : " + sum_subtree_diff );
 349         }
 350         System.out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
 351         out_ddist = new PrintWriter( new FileWriter( ddist_outfile ), true );
 352         for( int i = 0; ( i < duplications.length ) && ( i <= MAX_DUP_DIST ); ++i ) {
 353             out_ddist.println( i + " " + duplications[ i ] );
 354         }
 355         out_ddist.close();
 356         out_sdist = new PrintWriter( new FileWriter( sdist_outfile ), true );
 357         for( int i = 0; ( i < sizes.length ) && ( i <= MAX_EXT_NODE_DIST ); ++i ) {
 358             out_sdist.println( i + " " + sizes[ i ] );
 359         }
 360         out_sdist.close();
 361     } // infer
 362
 363     /**
 364      * Main method for this class.
 365      * <p>
 366      * (Last modified: 04/26/10)
 367      *
 368      * @param [args[0]
 369      *            -l to root by minimizing mapping cost L]
 370      * @param [args[0]
 371      *            -d to root by minimizing sum of duplications]
 372      * @param [args[0]
 373      *            -w to write out trees into outdir]
 374      * @param [args[0]
 375      *            -h to root by minimizing tree height]
 376      * @param [args[0]
 377      *            -n input trees are in New Hampshire format instead of NHX --
 378      *            or gene tree is in NHX, but species information in gene tree
 379      *            is only present in the form of SWISS-PROT sequence names]
 380      * @param args[0or1]
 381      *            trees directory name
 382      * @param args[1or2]
 383      *            suffix for gene trees
 384      * @param args[2or3]
 385      *            speciestree file name
 386      * @param args[3or4]
 387      *            output directory name
 388      * @param args[4or5]
 389      *            output file name
 390      */
 391     public static void main( final String args[] ) {
 392         ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
 393         // These are the default values.
 394         boolean minimize_mapping_cost = false;
 395         boolean minimize_sum_of_dup = false;
 396         boolean minimize_height = false;
 397         boolean write_trees = false;
 398         File indir = null;
 399         File speciestree_file = null;
 400         File outdir = null;
 401         File outfile = null;
 402         String suffix = null;
 403         if ( args.length == 5 ) {
 404             indir = new File( args[ 0 ] );
 405             suffix = args[ 1 ];
 406             speciestree_file = new File( args[ 2 ] );
 407             outdir = new File( args[ 3 ] );
 408             outfile = new File( args[ 4 ] );
 409         }
 410         else if ( args.length == 6 ) {
 411             if ( args[ 0 ].startsWith( "-" ) ) {
 412                 minimize_mapping_cost = false;
 413                 minimize_sum_of_dup = false;
 414                 minimize_height = false;
 415                 write_trees = false;
 416                 if ( args[ 0 ].toLowerCase().indexOf( "w" ) != -1 ) {
 417                     write_trees = true;
 418                 }
 419                 if ( args[ 0 ].toLowerCase().indexOf( "l" ) != -1 ) {
 420                     minimize_mapping_cost = true;
 421                 }
 422                 if ( args[ 0 ].toLowerCase().indexOf( "d" ) != -1 ) {
 423                     minimize_sum_of_dup = true;
 424                 }
 425                 if ( args[ 0 ].toLowerCase().indexOf( "h" ) != -1 ) {
 426                     minimize_height = true;
 427                 }
 428             }
 429             else {
 430                 sdi_dir.errorInCommandLine();
 431             }
 432             indir = new File( args[ 1 ] );
 433             suffix = args[ 2 ];
 434             speciestree_file = new File( args[ 3 ] );
 435             outdir = new File( args[ 4 ] );
 436             outfile = new File( args[ 5 ] );
 437         }
 438         else {
 439             sdi_dir.errorInCommandLine();
 440         }
 441         if ( minimize_mapping_cost && minimize_sum_of_dup ) {
 442             minimize_sum_of_dup = false;
 443         }
 444         try {
 445             sdi_dir.infer( indir,
 446                            speciestree_file,
 447                            outdir,
 448                            outfile,
 449                            suffix,
 450                            write_trees,
 451                            minimize_mapping_cost,
 452                            minimize_sum_of_dup,
 453                            minimize_height );
 454         }
 455         catch ( final Exception e ) {
 456             ForesterUtil.fatalError( PRG_NAME, "error: " + e.getLocalizedMessage() );
 457         }
 458         ForesterUtil.programMessage( PRG_NAME, "OK." );
 459     }
 460 }