+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// Copyright (C) 2000-2001 Washington University School of Medicine
-// and Howard Hughes Medical Institute
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.Arrays;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sdi.SDIException;
-import org.forester.sdi.SDIR;
-import org.forester.sdi.SDIse;
-import org.forester.util.ForesterUtil;
-
-/*
- * Allows to infer duplications - speciations on all (rooted or unrooted) gene
- * trees in a directory by using method "infer" of class SDIunrooted. <p> The
- * output of this is a (re)rooted tree with speciation - duplication assigned
- * for each tree (in "gene tree directory" with suffix "suffix for gene trees"),
- * as well as a summary list ("outputfile name"). <p> The summary list contains
- * the following. The number in brackets indicates how many external nodes of
- * the gene tree had to be removed since the associated species was not found in
- * the species tree. "en" indicates the number of external nodes in the
- * resulting (analyzed and returned) gene tree. "d" are the number of
- * duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal
- * difference in tree heights (of the two subtrees at the root; this number is
- * 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene
- * tree(s). <p> The output file ending with "_Sdist" is a file which lists the
- * distribution of trees sizes, "_Ddist" lists the distribution of the sums of
- * duplications (up to a certain maximal size, set with final variables
- * MAX_EXT_NODE_DIST and MAX_DUP_DIST).
- *
- * @see SDIunrooted
- *
- * @author Christian M. Zmasek
- */
-public class sdi_dir {
-
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org";
- final static private String PRG_NAME = "sdi_dir";
- final static private String PRG_VERSION = "2.00";
- final static private String PRG_DATE = "2010.04.26";
-
- private static void errorInCommandLine() {
- System.out.println( "\nsdi_dir: Error in command line.\n" );
- System.out.print( "Usage: % sdi_dir [-options] <gene tree directory> <suffix for gene trees>" );
- System.out.println( " <species tree file name> <output directory> <outputfile name>" );
- System.out.println( "\nOptions:" );
- System.out.println( " -l to root by minimizing the mapping cost L (and also the sum of duplications)" );
- System.out.println( " -d to root by minimizing the sum of duplications" );
- System.out.println( " -h to root by minimizing tree height (can be used together with -l or -d)" );
- System.out.println( " -w to write assigned gene trees into output directory" );
- System.out.println( "\nGene tree directory" );
- System.out.println( " The directory from which to read phyloXML formatted gene trees which" );
- System.out.println( " contain taxonomic information in appropriate sub-elements of taxonomy" );
- System.out.println( " (see: www.phyloxml.org)." );
- System.out.println( " The gene trees can either be rooted, in which case no rooting with -l, -d, or -h " );
- System.out.println( " is necessary, or they can be unrooted, in which case rooting is mandatory." );
- System.out.println( "\nSuffix for gene trees" );
- System.out.println( " Suffix of the gene trees to analyze (e.g. \".phyloxml\")." );
- System.out.println( "\nSpecies tree file" );
- System.out.println( " In phyloXML format, taxonomic information in appropriate sub-elements of taxonomy." );
- System.out.println( " (see: www.phyloxml.org)." );
- System.out.println( "\nOutput directory" );
- System.out.println( " The directory into which the assigned gene trees will be written." );
- System.out.println( "\nOutputfile name" );
- System.out.println( " File name for summary output files." );
- System.out.println( "" );
- System.exit( -1 );
- }
-
- /**
- * Runs method "infer" of class SDIunrooted on all gene trees in directory
- * indir.
- * <p>
- * Trees are rooted by minimizing either the sum of duplications, the
- * mapping cost L, or the tree height (or combinations thereof). One
- * resulting tree for each (out of possibly many) is stored in outdir and a
- * summary outfile is created. The distributions of the tree sizes (name of
- * outfile + _Ddist) and the distributions of the sum of duplications per
- * tree (name of outfile + _Sdist) are written out as well.
- * <p>
- * If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are
- * rooted by minimizing by minimizing the mapping cost L.
- * <p>
- * If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are
- * false trees are assumed to be alreadty rooted.
- * <p>
- * (Last modified: 02/02/01)
- *
- * @see SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
- * @param indir
- * a directory containing gene trees in NHX format
- * @param species_tree_file
- * a species tree file in NHX format
- * @param outdir
- * a directory where to write trees
- * @param outfile
- * a file name for the summary file
- * @param suffix
- * a suffix for the trees to read (e.g. nhx), is case sensitive
- * @param write_trees
- * set to true to write out one tree with minmal duplications or
- * L each
- * @param minimize_mapping_cost
- * set to true to root by minimizing the mapping cost L
- * @param minimize_sum_of_dup
- * set to true to root by minimizing the sum of duplications
- * @param minimize_height
- * set to true to root by minimizing the tree height -- if
- * minimize_mapping_cost is set to true or minimize_sum_of_dup is
- * set to true, then out of the resulting trees with minimal
- * mapping cost or minimal number of duplications the tree with
- * the minimal height is chosen
- * @throws SDIException
- */
- public static void infer( final File indir,
- final File species_tree_file,
- final File outdir,
- final File outfile,
- String suffix,
- final boolean write_trees,
- final boolean minimize_mapping_cost,
- boolean minimize_sum_of_dup,
- final boolean minimize_height ) throws IOException, SDIException {
- final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
- // to be analyzed.
- final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]
- // to be analyzed.
- final int MAX_DUP_DIST = 50; // Max number of dups to output in dup
- // distribution ("_Ddist").
- final int MAX_EXT_NODE_DIST = 1000; // Max number of ext nodes to output
- // in size
- // distribution ("_Sdist").
- int successful = 0, number_of_too_small_trees = 0, number_of_too_large_trees = 0, dups = 0, c = 0, ext_nodes = 0, removed = 0;
- final int nodecount0 = 0;
- int j = 0;
- long total_number_of_d = 0, total_number_of_ext_nodes = 0, sum_costs = 0;
- double sum_tree_heights = 0.0, sum_subtree_diff = 0.0;
- Phylogeny species_tree = null;
- String filename = null;
- String[] filenames = null;
- Phylogeny[] trees = null;
- final int[] duplications = new int[ MAX_EXT_NODES - 1 ], // For dup
- // distribution.
- sizes = new int[ MAX_EXT_NODES - 1 ]; // For ext nodes dist.of
- // successfully assigned trees.
- File outtree = null;
- PrintWriter out = null, out_ddist = null, out_sdist = null;
- final File ddist_outfile = new File( outfile + "_Ddist" ), sdist_outfile = new File( outfile + "_Sdist" );
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.0#####" );
- df.setDecimalSeparatorAlwaysShown( true );
- if ( !indir.exists() || !indir.isDirectory() ) {
- throw new IllegalArgumentException( indir + " does not exist or is not a directory." );
- }
- if ( !outdir.exists() || !outdir.isDirectory() ) {
- throw new IllegalArgumentException( outdir + " does not exist or is not a directory." );
- }
- if ( outfile.exists() ) {
- throw new IllegalArgumentException( outfile + " does already exist." );
- }
- if ( ddist_outfile.exists() ) {
- throw new IllegalArgumentException( ddist_outfile + " does already exist." );
- }
- if ( sdist_outfile.exists() ) {
- throw new IllegalArgumentException( sdist_outfile + " does already exist." );
- }
- if ( !species_tree_file.exists() || !species_tree_file.isFile() ) {
- throw new IllegalArgumentException( species_tree_file + " does not exist or is not a file." );
- }
- if ( minimize_mapping_cost && minimize_sum_of_dup ) {
- minimize_sum_of_dup = false;
- }
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
- filenames = indir.list();
- Arrays.sort( filenames );
- suffix = suffix.trim();
- out = new PrintWriter( new FileWriter( outfile ), true );
- //nodecount0 = PhylogenyNode.getNodeCount();
- for( final String filename2 : filenames ) {
- filename = filename2;
- if ( ( suffix.length() < 1 ) || filename.endsWith( suffix ) ) {
- final File gene_tree_file = new File( indir.getPath(), filename );
- if ( gene_tree_file.exists() && gene_tree_file.isFile() ) {
- out.print( j + "\t" + filename );
- System.out.println( j + ": " + filename );
- j++;
- Phylogeny gene_tree = null;
- gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
- // Removes from gene_tree all species not found in
- // species_tree.
- removed = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
- if ( filename.length() < 8 ) {
- out.print( "\t\t\t[-" + removed + "]" );
- }
- else if ( filename.length() < 16 ) {
- out.print( "\t\t[-" + removed + "]" );
- }
- else {
- out.print( "\t[-" + removed + "]" );
- }
- if ( gene_tree.getNumberOfExternalNodes() < MIN_EXT_NODES ) {
- out.print( "\t<" + MIN_EXT_NODES + "en\n" );
- number_of_too_small_trees++;
- }
- else if ( gene_tree.getNumberOfExternalNodes() > MAX_EXT_NODES ) {
- out.print( "\t>" + MAX_EXT_NODES + "en\n" );
- number_of_too_large_trees++;
- }
- else {
- SDIR sdiunrooted = null;
- // PhylogenyNode.setNodeCount( nodecount0 );
- sdiunrooted = new SDIR();
- if ( minimize_mapping_cost || minimize_sum_of_dup || minimize_height ) {
- trees = sdiunrooted.infer( gene_tree,
- species_tree,
- minimize_mapping_cost,
- minimize_sum_of_dup,
- minimize_height,
- write_trees,
- 1 );
- dups = sdiunrooted.getMinimalDuplications();
- }
- else {
- final SDIse sdi = new SDIse( gene_tree, species_tree );
- trees = new Phylogeny[ 1 ];
- trees[ 0 ] = gene_tree;
- dups = sdi.getDuplicationsSum();
- c = sdi.computeMappingCostL();
- sum_costs += c;
- out.print( "\t L=" + c );
- }
- successful++;
- ext_nodes = gene_tree.getNumberOfExternalNodes();
- total_number_of_ext_nodes += ext_nodes;
- sizes[ ext_nodes ]++;
- out.print( "\t " + ext_nodes + "en" );
- total_number_of_d += dups;
- duplications[ dups ]++;
- out.print( "\t " + dups + "d" );
- if ( minimize_mapping_cost ) {
- c = sdiunrooted.getMinimalMappingCost();
- sum_costs += c;
- out.print( "\t L=" + c );
- }
- if ( minimize_height ) {
- out.print( "\t h=" + df.format( sdiunrooted.getMinimalTreeHeight() ) );
- out.print( "\t d=" + df.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
- sum_tree_heights += sdiunrooted.getMinimalTreeHeight();
- sum_subtree_diff += sdiunrooted.getMinimalDiffInSubTreeHeights();
- }
- out.println();
- if ( write_trees ) {
- outtree = new File( outdir, new File( filename2 ).getName() );
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( outtree, trees[ 0 ], 1 );
- }
- }
- }
- }
- }
- //PhylogenyNode.setNodeCount( nodecount0 );
- if ( minimize_mapping_cost ) {
- out.println( "\nRooted by minimizing mapping cost L." );
- System.out.println( "\nRooted by minimizing mapping cost L." );
- if ( minimize_height ) {
- out.println( "Selected tree(s) with minimal height out of resulting trees." );
- System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
- }
- }
- else if ( minimize_sum_of_dup ) {
- out.println( "\nRooted by minimizing sum of duplications." );
- System.out.println( "\nRooted by minimizing sum of duplications." );
- if ( minimize_height ) {
- out.println( "Selected tree(s) with minimal height out of resulting trees." );
- System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
- }
- }
- else if ( minimize_height ) {
- out.println( "\nRooted by minimizing tree height." );
- System.out.println( "\nRooted by minimizing tree height." );
- }
- else {
- out.println( "\nNo (re) rooting was performed." );
- System.out.println( "\nNo (re) rooting was performed." );
- }
- out.println( "\nTrees directory : " + indir );
- out.println( "Suffix for trees : " + suffix );
- out.println( "Species tree : " + species_tree_file );
- out.println( "Output directory : " + outdir );
- out.println( "Output file : " + outfile );
- out.println( "\nTotal number of attempts (tree files read) : " + j );
- out.println( "Total number of successfully assigned trees : " + successful );
- out.println( "Number of too small trees : " + number_of_too_small_trees );
- out.println( "Number of too large trees : " + number_of_too_large_trees );
- out.println( "\nSum of duplications : " + total_number_of_d );
- if ( minimize_mapping_cost ) {
- out.println( "Sum of mapping costs L : " + sum_costs );
- }
- if ( minimize_height ) {
- out.println( "Sum of tree heights : " + sum_tree_heights );
- out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
- }
- out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
- out.close();
- System.out.println( "\nTotal number of attempts (tree files read) : " + j );
- System.out.println( "Total number of successfully assigned trees : " + successful );
- System.out.println( "Number of too small trees : " + number_of_too_small_trees );
- System.out.println( "Number of too large trees : " + number_of_too_large_trees );
- System.out.println( "\nSum of duplications : " + total_number_of_d );
- if ( minimize_mapping_cost ) {
- System.out.println( "Sum of mapping costs L : " + sum_costs );
- }
- if ( minimize_height ) {
- System.out.println( "Sum of tree heights : " + sum_tree_heights );
- System.out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
- }
- System.out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
- out_ddist = new PrintWriter( new FileWriter( ddist_outfile ), true );
- for( int i = 0; ( i < duplications.length ) && ( i <= MAX_DUP_DIST ); ++i ) {
- out_ddist.println( i + " " + duplications[ i ] );
- }
- out_ddist.close();
- out_sdist = new PrintWriter( new FileWriter( sdist_outfile ), true );
- for( int i = 0; ( i < sizes.length ) && ( i <= MAX_EXT_NODE_DIST ); ++i ) {
- out_sdist.println( i + " " + sizes[ i ] );
- }
- out_sdist.close();
- } // infer
-
- /**
- * Main method for this class.
- * <p>
- * (Last modified: 04/26/10)
- *
- * @param [args[0]
- * -l to root by minimizing mapping cost L]
- * @param [args[0]
- * -d to root by minimizing sum of duplications]
- * @param [args[0]
- * -w to write out trees into outdir]
- * @param [args[0]
- * -h to root by minimizing tree height]
- * @param [args[0]
- * -n input trees are in New Hampshire format instead of NHX --
- * or gene tree is in NHX, but species information in gene tree
- * is only present in the form of SWISS-PROT sequence names]
- * @param args[0or1]
- * trees directory name
- * @param args[1or2]
- * suffix for gene trees
- * @param args[2or3]
- * speciestree file name
- * @param args[3or4]
- * output directory name
- * @param args[4or5]
- * output file name
- */
- public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
- // These are the default values.
- boolean minimize_mapping_cost = false;
- boolean minimize_sum_of_dup = false;
- boolean minimize_height = false;
- boolean write_trees = false;
- File indir = null;
- File speciestree_file = null;
- File outdir = null;
- File outfile = null;
- String suffix = null;
- if ( args.length == 5 ) {
- indir = new File( args[ 0 ] );
- suffix = args[ 1 ];
- speciestree_file = new File( args[ 2 ] );
- outdir = new File( args[ 3 ] );
- outfile = new File( args[ 4 ] );
- }
- else if ( args.length == 6 ) {
- if ( args[ 0 ].startsWith( "-" ) ) {
- minimize_mapping_cost = false;
- minimize_sum_of_dup = false;
- minimize_height = false;
- write_trees = false;
- if ( args[ 0 ].toLowerCase().indexOf( "w" ) != -1 ) {
- write_trees = true;
- }
- if ( args[ 0 ].toLowerCase().indexOf( "l" ) != -1 ) {
- minimize_mapping_cost = true;
- }
- if ( args[ 0 ].toLowerCase().indexOf( "d" ) != -1 ) {
- minimize_sum_of_dup = true;
- }
- if ( args[ 0 ].toLowerCase().indexOf( "h" ) != -1 ) {
- minimize_height = true;
- }
- }
- else {
- sdi_dir.errorInCommandLine();
- }
- indir = new File( args[ 1 ] );
- suffix = args[ 2 ];
- speciestree_file = new File( args[ 3 ] );
- outdir = new File( args[ 4 ] );
- outfile = new File( args[ 5 ] );
- }
- else {
- sdi_dir.errorInCommandLine();
- }
- if ( minimize_mapping_cost && minimize_sum_of_dup ) {
- minimize_sum_of_dup = false;
- }
- try {
- sdi_dir.infer( indir,
- speciestree_file,
- outdir,
- outfile,
- suffix,
- write_trees,
- minimize_mapping_cost,
- minimize_sum_of_dup,
- minimize_height );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, "error: " + e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( PRG_NAME, "OK." );
- }
-}
git://source.jalview.org / jalview.git / commitdiff