X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=fd0127e432cd7cf73537285f65341a7933db438e;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=b4902b129bbd4ce8e253c4666e030ee1824512e5;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index b4902b1..fd0127e 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -7,7 +7,7 @@ // 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 @@ -17,485 +17,510 @@ // 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 +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; import java.io.File; -import java.io.FileWriter; import java.io.IOException; -import java.io.PrintWriter; +import java.math.RoundingMode; import java.util.ArrayList; -import java.util.HashMap; -import java.util.Vector; +import java.util.List; +import org.forester.datastructures.IntMatrix; +import org.forester.io.parsers.IteratingPhylogenyParser; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlParser; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.phylogeny.iterators.PreorderTreeIterator; -import org.forester.sdi.DistanceCalculator; -import org.forester.sdi.RIO; -import org.forester.sdi.SDIR; +import org.forester.rio.RIO; +import org.forester.rio.RIO.REROOTING; +import org.forester.rio.RIOException; +import org.forester.sdi.SDIException; +import org.forester.sdi.SDIutil.ALGORITHM; +import org.forester.util.BasicDescriptiveStatistics; +import org.forester.util.CommandLineArguments; +import org.forester.util.EasyWriter; import org.forester.util.ForesterUtil; public class rio { - final static private String PRG_NAME = "RIO"; - final static private String PRG_VERSION = "2.03 ALPHA"; - final static private String PRG_DATE = "2010.01.15"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/"; - final static private boolean TIME = true; - final static private boolean VERBOSE = true; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_COST = false; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_DUPS = true; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_HEIGHT = true; - final static private int WARN_NO_ORTHOS_DEFAULT = 2; - final static private int - // How many sd away from mean to root. - WARN_MORE_THAN_ONE_ORTHO_DEFAULT = 2; - // How many sd away from mean to LCA of orthos. - final static private double THRESHOLD_ULTRA_PARALOGS_DEFAULT = 50; - // How many sd away from mean to LCA of orthos. - final static private double WARN_ONE_ORTHO_DEFAULT = 2; + final static private String PRG_NAME = "rio"; + final static private String PRG_VERSION = "4.000 beta 10"; + final static private String PRG_DATE = "140211"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String GT_FIRST = "f"; + final static private String GT_LAST = "l"; + final static private String REROOTING_OPT = "r"; + final static private String OUTGROUP = "o"; + final static private String RETURN_SPECIES_TREE = "s"; + final static private String RETURN_BEST_GENE_TREE = "g"; + final static private String USE_SDIR = "b"; + final static private String TRANSFER_TAXONOMY_OPTION = "t"; - // Factor between the two distances to their LCA - // (larger/smaller). - // Factor between the two distances to their LCA - // (larger/smaller). - /** - * Calculates the mean and standard deviation of all nodes of Phylogeny t - * which have a bootstrap values zero or more. Returns null in case of - * failure (e.g t has no bootstrap values, or just one). - *

- * - * @param t - * reference to a tree with bootstrap values - * @return Array of doubles, [0] is the mean, [1] the standard deviation - */ - private static double[] calculateMeanBoostrapValue( final Phylogeny t ) { - double b = 0; - int n = 0; - long sum = 0; - double x = 0.0, mean = 0.0; - final double[] da = new double[ 2 ]; - final Vector bv = new Vector(); - PhylogenyNode node = null; - PreorderTreeIterator i = null; - i = new PreorderTreeIterator( t ); - // Calculates the mean. - while ( i.hasNext() ) { - node = i.next(); - if ( !( ( node.getParent() != null ) && node.getParent().isRoot() - && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode1() ) > 0 ) - && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode2() ) > 0 ) && ( node - .getParent().getChildNode2() == node ) ) ) { - b = PhylogenyMethods.getConfidenceValue( node ); - if ( b > 0 ) { - sum += b; - bv.addElement( new Double( b ) ); - n++; - } - } - // i.next(); + public static void main( final String[] args ) { + ForesterUtil.printProgramInformation( PRG_NAME, + "resampled inference of orthologs", + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + CommandLineArguments cla = null; + try { + cla = new CommandLineArguments( args ); } - if ( n < 2 ) { - return null; + catch ( final Exception e ) { + ForesterUtil.fatalError( e.getMessage() ); } - mean = ( double ) sum / n; - // Calculates the standard deviation. - sum = 0; - for( int j = 0; j < n; ++j ) { - b = ( bv.elementAt( j ) ).intValue(); - x = b - mean; - sum += ( x * x ); + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { + printHelp(); } - da[ 0 ] = mean; - da[ 1 ] = java.lang.Math.sqrt( sum / ( n - 1.0 ) ); - return da; - } - - private final static void errorInCommandLine() { - System.out.println( "\nrio: Error in command line.\n" ); - printHelp(); - System.exit( -1 ); - } - - // Uses DistanceCalculator to calculate distances. - private final static StringBuffer getDistances( final File tree_file_for_dist_val, - final File outfile, - final Phylogeny species_tree, - final String seq_name, - final ArrayList al_ortholog_names_for_dc, - final HashMap ortholog_hashmap, - final HashMap super_ortholog_hashmap, - final int warn_more_than_one_ortho, - final int warn_no_orthos, - final double warn_one_ortho, - final int bootstraps, - final double t_orthologs_dc ) throws IOException { - Phylogeny consensus_tree = null; - Phylogeny - // to be a consensus tree. - assigned_cons_tree = null; - final SDIR sdiunrooted = new SDIR(); - final ArrayList al_ortholog_nodes = new ArrayList(); - double m = 0.0; - double sd = 0.0; - double d = 0.0; - int n = 0; - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - consensus_tree = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ]; - PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, consensus_tree ); - assigned_cons_tree = sdiunrooted.infer( consensus_tree, - species_tree, - rio.MINIMIZE_COST, - rio.MINIMIZE_DUPS, - rio.MINIMIZE_HEIGHT, - true, - 1 )[ 0 ]; - final DistanceCalculator dc = new DistanceCalculator(); - final StringBuffer sb = new StringBuffer(); - sb.append( "Given the threshold for distance calculations (" + ForesterUtil.roundToInt( t_orthologs_dc ) - + "): " ); - // No orthologs. - if ( al_ortholog_names_for_dc.size() == 0 ) { - dc.setTree( assigned_cons_tree ); - // Remark. Calculation of mean and sd _does_ include the node - // with seq_name. - m = dc.getMean(); - sd = dc.getStandardDeviation(); - d = dc.getDistanceToRoot( seq_name ); - n = dc.getN(); - sb.append( "No sequence is considered orthologous to query." - + "\ndistance of query to root = " + ForesterUtil.FORMATTER_06.format( d ) - + "\nmean of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( m ) - + "\nsd of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( sd ) - + "\nn (sum of sequences in alignment plus query) = " + n ); - if ( !( ( ( m - ( warn_no_orthos * sd ) ) < d ) && ( ( m + ( warn_no_orthos * sd ) ) > d ) ) ) { - sb.append( "\nWARNING: distance of query to root is outside of mean+/-" + warn_no_orthos + "*sd!" ); - } - } - // One ortholog. - else if ( al_ortholog_names_for_dc.size() == 1 ) { - final String name_of_ortholog = al_ortholog_names_for_dc.get( 0 ); - al_ortholog_nodes.add( assigned_cons_tree.getNode( name_of_ortholog ) ); - al_ortholog_nodes.add( assigned_cons_tree.getNode( seq_name ) ); - dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes ); - // Remark. Calculation of mean _does_ include the node - // with seq_name. - d = dc.getDistanceToLCA( seq_name ); - final double d_o = dc.getDistanceToLCA( name_of_ortholog ); - sb.append( "One sequence is considered orthologous to query." + "\nLCA is LCA of query and its ortholog." - + "\ndistance of query to LCA = " + ForesterUtil.FORMATTER_06.format( d ) - + "\ndistance of ortholog to LCA = " + ForesterUtil.FORMATTER_06.format( d_o ) ); - if ( ( d_o > 0.0 ) - && ( d > 0.0 ) - && ( ( ( d_o >= d ) && ( ( d_o / d ) > warn_one_ortho ) ) || ( ( d_o < d ) && ( ( d / d_o ) > warn_one_ortho ) ) ) ) { - sb.append( "\nWARNING: Ratio of distances to LCA is greater than " + warn_one_ortho + "!" ); - } - else if ( ( ( d_o == 0.0 ) || ( d == 0.0 ) ) && ( ( d_o != 0.0 ) || ( d != 0.0 ) ) ) { - sb.append( "\nWARNING: Ratio could not be calculated, " + " one distance is 0.0!" ); - } - } - // More than one ortholog. - else { - for( int i = 0; i < al_ortholog_names_for_dc.size(); ++i ) { - al_ortholog_nodes.add( assigned_cons_tree.getNodeViaSequenceName( al_ortholog_names_for_dc.get( i ) ) ); - } - al_ortholog_nodes.add( assigned_cons_tree.getNodesViaSequenceName( seq_name ).get( 0 ) ); - dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes ); - // Remark. Calculation of mean and sd _does_ include the node - // with seq_name. - m = dc.getMean(); - sd = dc.getStandardDeviation(); - d = dc.getDistanceToLCA( seq_name ); - n = dc.getN(); - sb.append( "More than one sequence is considered orthologous to query." - + "\nLCA is LCA of query and its orthologs." - + "\ndistance of query to LCA = " - + ForesterUtil.FORMATTER_06.format( d ) - + "\nmean of distances (for query and its orthologs) to LCA = " - + ForesterUtil.FORMATTER_06.format( m ) - + "\nsd of distances (for query and its orthologs) to LCA = " - + ForesterUtil.FORMATTER_06.format( sd ) - + "\nn (sum of orthologs plus query) = " + n ); - if ( !( ( ( m - ( warn_more_than_one_ortho * sd ) ) < d ) && ( ( m + ( warn_more_than_one_ortho * sd ) ) > d ) ) ) { - sb.append( "\n!WARNING: distance of query to LCA is outside of mean+/-" + warn_more_than_one_ortho - + "*sd!" ); - } - } - return sb; - } - - public static void main( final String[] args ) { - ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW ); - File species_tree_file = null; - File multiple_trees_file = null; - File outfile = null; - File distance_matrix_file = null; - File tree_file_for_dist_val = null; - File tree_file_for_avg_bs = null; - String seq_name = ""; - String arg = ""; - boolean output_ultraparalogs = false; - ArrayList orthologs_al_for_dc = null; - double t_orthologs = 0.0; - double t_sn = 0.0; - double t_orthologs_dc = 0.0; - double[] bs_mean_sd = null; - int sort = 13; - Phylogeny species_tree = null; - RIO rio_instance = null; - PrintWriter out = null; - long time = 0; - int warn_no_orthos = WARN_NO_ORTHOS_DEFAULT; - int warn_more_than_one_ortho = WARN_MORE_THAN_ONE_ORTHO_DEFAULT; - double warn_one_ortho = WARN_ONE_ORTHO_DEFAULT; - double threshold_ultra_paralogs = THRESHOLD_ULTRA_PARALOGS_DEFAULT; - if ( args.length < 2 ) { + if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) { + System.out.println(); + System.out.println( "error: incorrect number of arguments" ); + System.out.println(); printHelp(); - System.exit( 0 ); } - else if ( ( args.length < 3 ) || ( args.length > 18 ) ) { - errorInCommandLine(); + final List allowed_options = new ArrayList(); + allowed_options.add( GT_FIRST ); + allowed_options.add( GT_LAST ); + allowed_options.add( REROOTING_OPT ); + allowed_options.add( OUTGROUP ); + allowed_options.add( USE_SDIR ); + allowed_options.add( RETURN_SPECIES_TREE ); + allowed_options.add( RETURN_BEST_GENE_TREE ); + allowed_options.add( TRANSFER_TAXONOMY_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options ); } - for( int i = 0; i < args.length; ++i ) { - if ( args[ i ].trim().charAt( 0 ) != 'p' ) { - if ( args[ i ].trim().length() < 3 ) { - errorInCommandLine(); - } - else { - arg = args[ i ].trim().substring( 2 ); - } + final File gene_trees_file = cla.getFile( 0 ); + final File species_tree_file = cla.getFile( 1 ); + final File orthology_outtable = cla.getFile( 2 ); + final File logfile; + if ( cla.getNumberOfNames() > 3 ) { + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); + } + } + else { + logfile = null; + } + boolean sdir = false; + if ( cla.isOptionSet( USE_SDIR ) ) { + if ( cla.isOptionHasAValue( USE_SDIR ) ) { + ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR ); + } + sdir = true; + if ( logfile != null ) { + ForesterUtil.fatalError( "no logfile output for SDIR algorithm" ); + } + } + String outgroup = null; + if ( cla.isOptionSet( OUTGROUP ) ) { + if ( !cla.isOptionHasAValue( OUTGROUP ) ) { + ForesterUtil.fatalError( "no value for -" + OUTGROUP ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" ); + } + outgroup = cla.getOptionValueAsCleanString( OUTGROUP ); + } + REROOTING rerooting = REROOTING.BY_ALGORITHM; + if ( cla.isOptionSet( REROOTING_OPT ) ) { + if ( !cla.isOptionHasAValue( REROOTING_OPT ) ) { + ForesterUtil.fatalError( "no value for -" + REROOTING_OPT ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" ); + } + final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase(); + if ( rerooting_str.equals( "none" ) ) { + rerooting = REROOTING.NONE; + } + else if ( rerooting_str.equals( "midpoint" ) ) { + rerooting = REROOTING.MIDPOINT; + } + else if ( rerooting_str.equals( "outgroup" ) ) { + rerooting = REROOTING.OUTGROUP; + } + else { + ForesterUtil + .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); + } + } + if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" ); + } + if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" ); + } + int gt_first = RIO.DEFAULT_RANGE; + int gt_last = RIO.DEFAULT_RANGE; + if ( cla.isOptionSet( GT_FIRST ) ) { + if ( !cla.isOptionHasAValue( GT_FIRST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_FIRST ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); } try { - switch ( args[ i ].trim().charAt( 0 ) ) { - case 'M': - multiple_trees_file = new File( arg ); - break; - case 'N': - seq_name = arg; - break; - case 'S': - species_tree_file = new File( arg ); - break; - case 'O': - outfile = new File( arg ); - break; - case 'D': - distance_matrix_file = new File( arg ); - break; - case 'T': - tree_file_for_dist_val = new File( arg ); - break; - case 't': - tree_file_for_avg_bs = new File( arg ); - break; - case 'p': - output_ultraparalogs = true; - break; - case 'P': - sort = Integer.parseInt( arg ); - if ( ( sort < 0 ) || ( sort > 17 ) ) { - errorInCommandLine(); - } - break; - case 'L': - t_orthologs = Double.parseDouble( arg ); - break; - case 'B': - t_sn = Double.parseDouble( arg ); - break; - case 'U': - t_orthologs_dc = Double.parseDouble( arg ); - break; - case 'v': - threshold_ultra_paralogs = Double.parseDouble( arg ); - break; - case 'X': - warn_more_than_one_ortho = Integer.parseInt( arg ); - break; - case 'Y': - warn_no_orthos = Integer.parseInt( arg ); - break; - case 'Z': - warn_one_ortho = Double.parseDouble( arg ); - break; - default: - errorInCommandLine(); - } + gt_first = cla.getOptionValueAsInt( GT_FIRST ); } - catch ( final Exception e ) { - errorInCommandLine(); + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" ); + } + if ( gt_first < 0 ) { + ForesterUtil.fatalError( "attempt to set index of first tree to analyze to: " + gt_first ); } } - if ( ( seq_name == "" ) || ( species_tree_file == null ) || ( multiple_trees_file == null ) - || ( outfile == null ) ) { - errorInCommandLine(); + if ( cla.isOptionSet( GT_LAST ) ) { + if ( !cla.isOptionHasAValue( GT_LAST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_LAST ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + try { + gt_last = cla.getOptionValueAsInt( GT_LAST ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" ); + } + if ( gt_last < 0 ) { + ForesterUtil.fatalError( "attempt to set index of last tree to analyze to: " + gt_last ); + } } - if ( ( sort < 0 ) || ( sort > 17 ) ) { - errorInCommandLine(); + if ( ( ( gt_last != RIO.DEFAULT_RANGE ) && ( gt_first != RIO.DEFAULT_RANGE ) ) && ( ( gt_last < gt_first ) ) ) { + ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to " + + gt_last ); } - if ( ( sort > 2 ) && ( distance_matrix_file == null ) ) { - errorInCommandLine(); + File return_species_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_SPECIES_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_SPECIES_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_SPECIES_TREE ); + } + final String s = cla.getOptionValueAsCleanString( RETURN_SPECIES_TREE ); + return_species_tree = new File( s ); + if ( return_species_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_species_tree + "\" already exists" ); + } } - if ( VERBOSE ) { - System.out.println( "\nMultiple trees file: " + multiple_trees_file ); - System.out.println( "Seq name: " + seq_name ); - System.out.println( "Species tree file: " + species_tree_file ); - System.out.println( "Outfile: " + outfile ); - if ( distance_matrix_file != null ) { - System.out.println( "Distance matrix file: " + distance_matrix_file ); + File return_gene_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_BEST_GENE_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_BEST_GENE_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_BEST_GENE_TREE ); } - if ( tree_file_for_dist_val != null ) { - if ( tree_file_for_avg_bs == null ) { - System.out.println( "Phy to read dists and calc mean support from: " + tree_file_for_dist_val ); - } - else { - System.out.println( "Phylogeny to read dist values from: " + tree_file_for_dist_val ); - } + final String s = cla.getOptionValueAsCleanString( RETURN_BEST_GENE_TREE ); + return_gene_tree = new File( s ); + if ( return_gene_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_gene_tree + "\" already exists" ); + } + } + boolean transfer_taxonomy = false; + if ( !sdir && cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) { + if ( return_gene_tree == null ) { + ForesterUtil.fatalError( "no point in transferring taxonomy data without returning best gene tree" ); + } + transfer_taxonomy = true; + } + ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file ); + ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); + if ( orthology_outtable.exists() ) { + ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); + } + long time = 0; + System.out.println( "Gene trees : " + gene_trees_file ); + System.out.println( "Species tree : " + species_tree_file ); + System.out.println( "All vs all orthology table: " + orthology_outtable ); + if ( logfile != null ) { + System.out.println( "Logfile : " + logfile ); + } + if ( gt_first != RIO.DEFAULT_RANGE ) { + System.out.println( "First gene tree to analyze: " + gt_first ); + } + if ( gt_last != RIO.DEFAULT_RANGE ) { + System.out.println( "Last gene tree to analyze : " + gt_last ); + } + String rerooting_str = ""; + switch ( rerooting ) { + case BY_ALGORITHM: { + rerooting_str = "by minimizing duplications"; + break; + } + case MIDPOINT: { + rerooting_str = "by midpoint method"; + break; } - if ( tree_file_for_avg_bs != null ) { - System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs ); + case OUTGROUP: { + rerooting_str = "by outgroup: " + outgroup; + break; } - System.out.println( "Sort: " + sort ); - System.out.println( "Threshold orthologs: " + t_orthologs ); - System.out.println( "Threshold subtree neighborings: " + t_sn ); - System.out.println( "Threshold orthologs for distance calc.: " + t_orthologs_dc ); - if ( output_ultraparalogs ) { - System.out.println( "Threshold ultra paralogs: " + threshold_ultra_paralogs ); + case NONE: { + rerooting_str = "none"; + break; } - System.out.println( "More than one ortholog sd diff: " + warn_more_than_one_ortho ); - System.out.println( "No orthologs sd diff: " + warn_no_orthos ); - System.out.println( "One ortholog factor : " + warn_one_ortho + "\n" ); } - if ( TIME && VERBOSE ) { - time = System.currentTimeMillis(); + System.out.println( "Re-rooting : " + rerooting_str ); + if ( !sdir ) { + System.out.println( "Non binary species tree : allowed" ); } - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; + else { + System.out.println( "Non binary species tree : disallowed" ); } - catch ( final Exception e ) { - e.printStackTrace(); - System.exit( -1 ); + if ( return_species_tree != null ) { + System.out.println( "Write used species tree to: " + return_species_tree ); } - if ( !species_tree.isRooted() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" ); - System.exit( -1 ); + if ( return_gene_tree != null ) { + System.out.println( "Write best gene tree to : " + return_gene_tree ); + System.out.println( "Transfer taxonomic data : " + transfer_taxonomy ); } - if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" ); - System.exit( -1 ); + time = System.currentTimeMillis(); + final ALGORITHM algorithm; + if ( sdir ) { + algorithm = ALGORITHM.SDIR; + } + else { + algorithm = ALGORITHM.GSDIR; } - rio_instance = new RIO(); - final StringBuffer output = new StringBuffer(); try { - if ( distance_matrix_file != null ) { - rio_instance.readDistanceMatrix( distance_matrix_file ); - } - rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name ); - output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs, t_sn ) ); - if ( tree_file_for_dist_val != null ) { - orthologs_al_for_dc = rio_instance.inferredOrthologsToArrayList( seq_name, t_orthologs_dc ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - if ( tree_file_for_avg_bs != null ) { - final Phylogeny p = factory.create( tree_file_for_avg_bs, new PhyloXmlParser() )[ 0 ]; - bs_mean_sd = calculateMeanBoostrapValue( p ); + final RIO rio; + boolean iterating = false; + final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true ); + if ( p instanceof PhyloXmlParser ) { + rio = RIO.executeAnalysis( gene_trees_file, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); + } + else { + iterating = true; + if ( p instanceof NHXParser ) { + final NHXParser nhx = ( NHXParser ) p; + nhx.setReplaceUnderscores( false ); + nhx.setIgnoreQuotes( true ); + nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); + } + else if ( p instanceof NexusPhylogeniesParser ) { + final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p; + nex.setReplaceUnderscores( false ); + nex.setIgnoreQuotes( true ); + nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else { - final Phylogeny p = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ]; - bs_mean_sd = calculateMeanBoostrapValue( p ); + throw new RuntimeException( "unknown parser type: " + p ); } - if ( ( bs_mean_sd != null ) && ( bs_mean_sd.length == 2 ) ) { - final double bs_mean = bs_mean_sd[ 0 ]; - final double bs_sd = bs_mean_sd[ 1 ]; - output.append( "\n\nMean bootstrap value of consensus tree (sd): " - + ForesterUtil.roundToInt( ( bs_mean * 100.0 ) / rio_instance.getBootstraps() ) + "% (+/-" - + ForesterUtil.roundToInt( ( bs_sd * 100.0 ) / rio_instance.getBootstraps() ) + "%)\n" ); + final IteratingPhylogenyParser ip = ( IteratingPhylogenyParser ) p; + ip.setSource( gene_trees_file ); + rio = RIO.executeAnalysis( ip, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); + } + if ( algorithm == ALGORITHM.GSDIR ) { + System.out.println( "Taxonomy linking based on : " + rio.getGSDIRtaxCompBase() ); + } + final IntMatrix m; + if ( iterating ) { + m = rio.getOrthologTable(); + } + else { + m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); + } + final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics(); + writeTable( orthology_outtable, stats.getN(), m ); + if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) { + writeLogFile( logfile, + rio, + species_tree_file, + gene_trees_file, + orthology_outtable, + PRG_NAME, + PRG_VERSION, + PRG_DATE, + ForesterUtil.getForesterLibraryInformation() ); + } + if ( return_species_tree != null ) { + writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" ); + } + if ( return_gene_tree != null ) { + String tt = ""; + if ( transfer_taxonomy ) { + tt = "(with transferred taxonomic data) "; } - output.append( "\n\nDistance values:\n" ); - output.append( getDistances( tree_file_for_dist_val, - outfile, - species_tree, - seq_name, - orthologs_al_for_dc, - rio_instance.getInferredOrthologs( seq_name ), - rio_instance.getInferredSuperOrthologs( seq_name ), - warn_more_than_one_ortho, - warn_no_orthos, - warn_one_ortho, - rio_instance.getBootstraps(), - t_orthologs_dc ) ); - } - if ( output_ultraparalogs ) { - output.append( "\n\nUltra paralogs:\n" ); - output.append( rio_instance - .inferredUltraParalogsToString( seq_name, sort > 2, threshold_ultra_paralogs ) ); - } - output.append( "\n\nSort priority: " + RIO.getOrder( sort ) ); - output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() ); - output.append( "\nSamples : " + rio_instance.getBootstraps() + "\n" ); - out = new PrintWriter( new FileWriter( outfile ), true ); + writeTree( rio.getMinDuplicationsGeneTree(), + return_gene_tree, + "Wrote (one) minimal duplication gene tree " + tt + "to" ); + } + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" ); + System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: " + + df.format( stats.sampleStandardDeviation() ) + ") (" + + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + if ( stats.getN() > 3 ) { + System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " (" + + df.format( ( 100.0 * stats.median() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + } + System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " (" + + df.format( ( 100.0 * stats.getMin() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " (" + + df.format( ( 100.0 * stats.getMax() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + System.out.println( "Gene tree internal nodes : " + rio.getIntNodesOfAnalyzedGeneTrees() ); + System.out.println( "Gene tree external nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() ); + } + catch ( final RIOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final SDIException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final OutOfMemoryError e ) { + ForesterUtil.outOfMemoryError( e ); } catch ( final Exception e ) { - ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() ); - e.printStackTrace(); - System.exit( -1 ); + ForesterUtil.unexpectedFatalError( e ); } - out.println( output ); - out.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); - if ( TIME && VERBOSE ) { - time = System.currentTimeMillis() - time; - ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); + catch ( final Error e ) { + ForesterUtil.unexpectedFatalError( e ); } - ForesterUtil.programMessage( PRG_NAME, "OK." ); + time = System.currentTimeMillis() - time; + System.out.println( "Time: " + time + "ms" ); + System.out.println( "OK" ); System.exit( 0 ); } private final static void printHelp() { - System.out.println( "M= (String) Multiple gene tree file (mandatory)" ); - System.out.println( "N= (String) Query sequence name (mandatory)" ); - System.out.println( "S= (String) Species tree file (mandatory)" ); - System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" ); - System.out.println( "D= (String) Distance matrix file for pairwise distances" ); - System.out.println( "T= (String) Phylogeny file for distances of query to LCA" ); - System.out.println( " of orthologs and for mean bootstrap value (if t= is not used)," ); - System.out.println( " must be binary )" ); - System.out.println( "t= (String) Phylogeny file for mean bootstrap value (if this option is used," ); - System.out.println( " the mean bootstrap value is not calculated from the tree read in" ); - System.out.println( " with T=), not necessary binary" ); - System.out.println( "p To output ultra paralogs" ); - System.out.println( "P= (int) Sort priority" ); - System.out.println( "L= (double) Threshold orthologs for output" ); - System.out.println( "U= (double) Threshold orthologs for distance calculation" ); - System.out.println( "X= (int) More than one ortholog: " ); - System.out.println( " numbers of sd the dist. to LCA has to differ from mean to generate a warning" ); - System.out.println( "Y= (int) No orthologs:" ); - System.out.println( " Numbers of sd the dist to root has to differ from mean to generate a warning" ); - System.out.println( "Z= (double) One ortholog:" ); - System.out.println( " threshold for factor between the two distances to their LCA (larger/smaller)" ); - System.out.println( " to generate a warning" ); + System.out.println( "Usage" ); System.out.println(); - System.out.println( " Sort priority (\"P=\"):" ); - System.out.println( RIO.getOrderHelp().toString() ); + System.out + .println( PRG_NAME + + " [options] [logfile]" ); System.out.println(); + System.out.println( " Options" ); + System.out.println( " -" + GT_FIRST + "= : first gene tree to analyze (0-based index)" ); + System.out.println( " -" + GT_LAST + "= : last gene tree to analyze (0-based index)" ); + System.out.println( " -" + REROOTING_OPT + + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); + System.out.println( " or 'outgroup' (default: by minizming duplications)" ); + System.out.println( " -" + OUTGROUP + + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); + System.out + .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); + System.out.println( " -" + RETURN_BEST_GENE_TREE + + "= : to write (one) minimal duplication gene tree to file" ); System.out - .println( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=out\"" ); + .println( " -" + + TRANSFER_TAXONOMY_OPTION + + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" + + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); + System.out.println( " -" + USE_SDIR + + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); + System.out.println( " disallowed, as are most options)" ); System.out.println(); + System.out.println( " Formats" ); + System.out + .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); + System.out + .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); + System.out + .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); + System.out.println( " in the species tree." ); + System.out.println(); + System.out.println( " Examples" ); + System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" ); + System.out.println(); + System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" ); + System.out.println(); + System.exit( -1 ); + } + + private static void writeLogFile( final File logfile, + final RIO rio, + final File species_tree_file, + final File gene_trees_file, + final File outtable, + final String prg_name, + final String prg_v, + final String prg_date, + final String f ) throws IOException { + final EasyWriter out = ForesterUtil.createEasyWriter( logfile ); + out.println( prg_name ); + out.println( "version : " + prg_v ); + out.println( "date : " + prg_date ); + out.println( "based on: " + f ); + out.println( "----------------------------------" ); + out.println( "Gene trees : " + gene_trees_file ); + out.println( "Species tree : " + species_tree_file ); + out.println( "All vs all orthology table : " + outtable ); + out.flush(); + out.println( rio.getLog().toString() ); + out.close(); + System.out.println( "Wrote log to \"" + logfile + "\"" ); + } + + private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m ) + throws IOException { + final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile ); + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" ); + df.setDecimalSeparatorAlwaysShown( false ); + df.setRoundingMode( RoundingMode.HALF_UP ); + for( int i = 0; i < m.size(); ++i ) { + w.print( "\t" ); + w.print( m.getLabel( i ) ); + } + w.println(); + for( int x = 0; x < m.size(); ++x ) { + w.print( m.getLabel( x ) ); + for( int y = 0; y < m.size(); ++y ) { + w.print( "\t" ); + if ( x == y ) { + if ( m.get( x, y ) != gene_trees_analyzed ) { + ForesterUtil.unexpectedFatalError( "diagonal value is off" ); + } + w.print( "-" ); + } + else { + w.print( df.format( ( ( double ) m.get( x, y ) ) / gene_trees_analyzed ) ); + } + } + w.println(); + } + w.close(); + System.out.println( "Wrote table to \"" + table_outfile + "\"" ); + } + + private static void writeTree( final Phylogeny p, final File f, final String comment ) throws IOException { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( f, p, 0 ); + System.out.println( comment + " \"" + f + "\"" ); } }