X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=d915234a62abde03932eb2dce07008b20e1c7217;hb=c73326f29a91a733a71bfe36192dbd30e4f49af8;hp=88e344432ab6b55e9032d2395d6d41c17053d51f;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 88e3444..d915234 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -2,10 +2,7 @@ // 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 +// Copyright (C) 2017 Christian M. Zmasek // All rights reserved // // This library is free software; you can redistribute it and/or @@ -22,480 +19,733 @@ // 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.FilenameFilter; import java.io.IOException; -import java.io.PrintWriter; import java.util.ArrayList; -import java.util.HashMap; -import java.util.Vector; +import java.util.Arrays; +import java.util.List; -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -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.RIOUtil; +import org.forester.sdi.SDIutil.ALGORITHM; +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; + public final static String PRG_NAME = "rio"; + public final static String PRG_VERSION = "5.900"; + public final static String PRG_DATE = "170420"; + 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 USE_SDIR = "s"; + final static private String GENE_TREES_SUFFIX_OPTION = "g"; + final static private String MAPPINGS_DIR_OPTION = "m"; + final static private String MAPPINGS_SUFFIX_OPTION = "ms"; + final static private String CONSENSUS_TREES_DIR_OPTION = "co"; + final static private String CONSENSUS_TREES_SUFFIX_OPTION = "cos"; + final static private String MAPPINGS_SUFFIX_DEFAULT = ".nim"; + final static private String CONSENSUS_TREE_SUFFIX_DEFAULT = ".xml"; + final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION = "c"; + final static private String GENE_TREES_SUFFIX_DEFAULT = ".mlt"; + final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5; - // 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++; - } + 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 ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( e.getMessage() ); + } + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { + printHelp(); + } + 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(); + } + 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( GENE_TREES_SUFFIX_OPTION ); + allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION ); + allowed_options.add( MAPPINGS_DIR_OPTION ); + allowed_options.add( MAPPINGS_SUFFIX_OPTION ); + allowed_options.add( CONSENSUS_TREES_DIR_OPTION ); + allowed_options.add( CONSENSUS_TREES_SUFFIX_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options ); + } + final File gene_trees_file = cla.getFile( 0 ); + final boolean use_dir; + File indir = null; + File outdir = null; + if ( gene_trees_file.isDirectory() ) { + if ( !gene_trees_file.exists() ) { + ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" does not exist" ); + } + if ( gene_trees_file.listFiles().length < 1 ) { + ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" is empty" ); } - // i.next(); + use_dir = true; + indir = gene_trees_file; } - if ( n < 2 ) { - return null; + else { + use_dir = false; } - 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 ); + final File species_tree_file = cla.getFile( 1 ); + File orthology_outtable = null; + if ( use_dir ) { + outdir = cla.getFile( 2 ); } - 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 ) { - printHelp(); - System.exit( 0 ); + orthology_outtable = cla.getFile( 2 ); } - else if ( ( args.length < 3 ) || ( args.length > 18 ) ) { - errorInCommandLine(); + File logfile; + if ( use_dir ) { + if ( ( cla.getNumberOfNames() < 4 ) ) { + System.out.println(); + System.out.println( "error: incorrect number of arguments" ); + System.out.println(); + printHelp(); + } + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); + } } - for( int i = 0; i < args.length; ++i ) { - if ( args[ i ].trim().charAt( 0 ) != 'p' ) { - if ( args[ i ].trim().length() < 3 ) { - errorInCommandLine(); + else { + if ( cla.getNumberOfNames() > 3 ) { + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); } - else { - arg = args[ i ].trim().substring( 2 ); + } + 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 ( !use_dir && logfile != null ) { + ForesterUtil.fatalError( "no logfile output for SDIR algorithm" ); + } + } + String outgroup = null; + if ( cla.isOptionSet( OUTGROUP ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" ); + } + if ( use_dir ) { + ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" ); + } + if ( !cla.isOptionHasAValue( OUTGROUP ) ) { + ForesterUtil.fatalError( "no value for -" + OUTGROUP ); + } + 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" ) ) { + if ( use_dir ) { + ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" ); } + 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 ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( GT_FIRST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_FIRST ); } 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 IOException e ) { + ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" ); } - catch ( final Exception e ) { - errorInCommandLine(); + 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 ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( GT_LAST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_LAST ); + } + 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(); + double ortholog_group_cutoff = ORTHOLOG_GROUPS_CUTOFF_DEFAULT; + if ( cla.isOptionSet( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "ortholog groups cutoff for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION ); + } + try { + ortholog_group_cutoff = cla.getOptionValueAsDouble( ORTHOLOG_GROUPS_CUTOFF_OPTION ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse double for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + " option" ); + } + if ( ortholog_group_cutoff < 0 ) { + ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff ); + } + if ( ortholog_group_cutoff > 1 ) { + ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff ); + } } - 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 ); + if ( !use_dir ) { + ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file ); + } + final String gene_trees_suffix; + if ( cla.isOptionSet( GENE_TREES_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil.fatalError( "no gene tree suffix option when operating on indivual gene trees" ); } - 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 ); - } + if ( !cla.isOptionHasAValue( GENE_TREES_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + GENE_TREES_SUFFIX_OPTION ); } - if ( tree_file_for_avg_bs != null ) { - System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs ); + gene_trees_suffix = cla.getOptionValueAsCleanString( GENE_TREES_SUFFIX_OPTION ); + } + else { + gene_trees_suffix = GENE_TREES_SUFFIX_DEFAULT; + } + final boolean perform_id_mapping; + final File id_mapping_dir; + if ( cla.isOptionSet( MAPPINGS_DIR_OPTION ) ) { + id_mapping_dir = new File( cla.getOptionValue( MAPPINGS_DIR_OPTION ) ); + perform_id_mapping = true; + if ( !use_dir ) { + ForesterUtil.fatalError( "no id mapping when operating on indivual gene trees" ); } - 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 ); + if ( !id_mapping_dir.exists() ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" does not exist" ); + } + if ( !id_mapping_dir.isDirectory() ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is not a directory" ); + } + if ( id_mapping_dir.listFiles().length < 1 ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is empty" ); } - 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(); + else { + id_mapping_dir = null; + perform_id_mapping = false; } - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; + final String id_mapping_suffix; + if ( cla.isOptionSet( MAPPINGS_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil.fatalError( "no id mapping file suffix option when operating on indivual gene trees" ); + } + if ( !perform_id_mapping ) { + ForesterUtil.fatalError( "no id mapping directory given" ); + } + if ( !cla.isOptionHasAValue( MAPPINGS_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + MAPPINGS_SUFFIX_OPTION ); + } + id_mapping_suffix = cla.getOptionValueAsCleanString( MAPPINGS_SUFFIX_OPTION ); } - catch ( final Exception e ) { - e.printStackTrace(); - System.exit( -1 ); + else { + id_mapping_suffix = MAPPINGS_SUFFIX_DEFAULT; } - if ( !species_tree.isRooted() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" ); - System.exit( -1 ); + boolean perform_gsdir_on_best_tree; + final File best_trees_indir; + if ( cla.isOptionSet( CONSENSUS_TREES_DIR_OPTION ) ) { + best_trees_indir = new File( cla.getOptionValue( CONSENSUS_TREES_DIR_OPTION ) ); + perform_gsdir_on_best_tree = true; + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree GSDIR analysis when operating on individual gene trees" ); + } + if ( !best_trees_indir.exists() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" does not exist" ); + } + if ( !best_trees_indir.isDirectory() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" is not a directory" ); + } + if ( best_trees_indir.listFiles().length < 1 ) { + ForesterUtil + .fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + "\" is empty" ); + } + } + else { + best_trees_indir = null; + perform_gsdir_on_best_tree = false; + } + final String best_trees_suffix; + if ( cla.isOptionSet( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree suffix option when operating on individual gene trees" ); + } + if ( !perform_gsdir_on_best_tree ) { + ForesterUtil.fatalError( "no consensus (\"best\") gene tree directory given" ); + } + if ( !cla.isOptionHasAValue( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + CONSENSUS_TREES_SUFFIX_OPTION ); + } + best_trees_suffix = cla.getOptionValueAsCleanString( CONSENSUS_TREES_SUFFIX_OPTION ); } - if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" ); - System.exit( -1 ); + else { + best_trees_suffix = CONSENSUS_TREE_SUFFIX_DEFAULT; + } + //////////////////////////////// + ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); + if ( !use_dir && orthology_outtable.exists() ) { + ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); } - rio_instance = new RIO(); - final StringBuffer output = new StringBuffer(); + long time = 0; 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 ); + if ( use_dir ) { + System.out.println( "Gene trees in-dir :\t" + indir.getCanonicalPath() ); + System.out.println( "Gene trees suffix :\t" + gene_trees_suffix ); + } + else { + System.out.println( "Gene trees :\t" + gene_trees_file.getCanonicalPath() ); + } + System.out.println( "Species tree :\t" + species_tree_file.getCanonicalPath() ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + if ( perform_id_mapping ) { + try { + System.out.println( "Id mappings in-dir :\t" + id_mapping_dir.getCanonicalPath() ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + System.out.println( "Id mappings suffix :\t" + id_mapping_suffix ); + } + if ( perform_gsdir_on_best_tree ) { + try { + System.out.println( "Consensus (\"best\") gene tree dir :\t" + best_trees_indir.getCanonicalPath() ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + System.out.println( "Consensus (\"best\") gene tree suffix :\t" + best_trees_suffix ); + } + if ( use_dir ) { + System.out.println( "Out-dir :\t" + outdir ); + } + else { + System.out.println( "All vs all orthology results table :\t" + orthology_outtable ); + } + if ( logfile != null ) { + System.out.println( "Logfile :\t" + logfile ); + } + System.out.println( "Ortholog groups cutoff :\t" + ortholog_group_cutoff ); + if ( gt_first != RIO.DEFAULT_RANGE ) { + System.out.println( "First gene tree to analyze :\t" + gt_first ); + } + if ( gt_last != RIO.DEFAULT_RANGE ) { + System.out.println( "Last gene tree to analyze :\t" + gt_last ); + } + String rerooting_str = ""; + switch ( rerooting ) { + case BY_ALGORITHM: { + rerooting_str = "by minimizing duplications"; + break; + } + case MIDPOINT: { + rerooting_str = "by midpoint method"; + break; + } + case OUTGROUP: { + rerooting_str = "by outgroup: " + outgroup; + break; + } + case NONE: { + rerooting_str = "none"; + break; + } + } + System.out.println( "Re-rooting : \t" + rerooting_str ); + if ( !sdir ) { + System.out.println( "Non binary species tree :\tallowed" ); + } + else { + System.out.println( "Non binary species tree :\tdisallowed" ); + } + time = System.currentTimeMillis(); + final ALGORITHM algorithm; + if ( sdir ) { + algorithm = ALGORITHM.SDIR; + } + else { + algorithm = ALGORITHM.GSDIR; + } + EasyWriter log = null; + if ( use_dir ) { + if ( outdir.exists() ) { + if ( !outdir.isDirectory() ) { + ForesterUtil.fatalError( PRG_NAME, + "out-directory [" + outdir + "] already exists but is not a directory" ); + } + } + else { + final boolean success = outdir.mkdirs(); + if ( !success ) { + ForesterUtil.fatalError( PRG_NAME, "could not create out-directory [" + outdir + "]" ); + } + } + final String species_tree_file_name = species_tree_file.getName(); + final File gene_trees_files[] = indir.listFiles( new FilenameFilter() { + + @Override + public boolean accept( final File dir, final String name ) { + return ( ( name.endsWith( gene_trees_suffix ) ) && !( name.equals( species_tree_file_name ) ) ); + } + } ); + if ( gene_trees_files.length < 1 ) { + ForesterUtil.fatalError( PRG_NAME, + "in-directory [" + indir + + "] does not contain any gene tree files with suffix " + + gene_trees_suffix ); + } + try { + log = ForesterUtil.createEasyWriter( logfile ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( PRG_NAME, "could not create [" + logfile + "]" ); + } + Arrays.sort( gene_trees_files ); + try { + log.print( "# program" ); + log.print( "\t" ); + log.print( PRG_NAME ); + log.println(); + log.print( "# version" ); + log.print( "\t" ); + log.print( PRG_VERSION ); + log.println(); + log.print( "# date" ); + log.print( "\t" ); + log.print( PRG_DATE ); + log.println(); + log.print( "# Algorithm " ); + log.print( "\t" ); + log.print( algorithm.toString() ); + log.println(); + log.print( "# Gene trees in-dir" ); + log.print( "\t" ); + log.print( indir.getCanonicalPath() ); + log.println(); + log.print( "# Gene trees suffix" ); + log.print( "\t" ); + log.print( gene_trees_suffix ); + log.println(); + log.print( "# Species tree" ); + log.print( "\t" ); + log.print( species_tree_file.getCanonicalPath() ); + log.println(); + log.print( "# Out-dir" ); + log.print( "\t" ); + log.print( outdir.getCanonicalPath() ); + log.println(); + log.print( "# Logfile" ); + log.print( "\t" ); + log.print( logfile.getCanonicalPath() ); + log.println(); + log.print( "# Ortholog groups cutoff" ); + log.print( "\t" ); + log.print( Double.toString( ortholog_group_cutoff ) ); + log.println(); + if ( gt_first != RIO.DEFAULT_RANGE ) { + log.print( "# First gene tree to analyze" ); + log.print( "\t" ); + log.print( Integer.toString( gt_first ) ); + log.println(); + } + if ( gt_last != RIO.DEFAULT_RANGE ) { + log.print( "# Last gene tree to analyze" ); + log.print( "\t" ); + log.print( Integer.toString( gt_last ) ); + log.println(); + } + log.print( "# Re-rooting" ); + log.print( "\t" ); + log.print( rerooting_str ); + log.println(); + log.print( "# Non binary species tree" ); + log.print( "\t" ); + if ( !sdir ) { + log.print( "allowed" ); } else { - final Phylogeny p = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ]; - bs_mean_sd = calculateMeanBoostrapValue( p ); + log.print( "disallowed" ); + } + log.println(); + log.println(); + log.print( "NAME" ); + log.print( "\t" ); + log.print( "EXT NODES" ); + log.print( "\t" ); + log.print( ortholog_group_cutoff + " O GROUPS" ); + log.print( "\t" ); + log.print( "0.05 O GROUPS" ); + log.print( "\t" ); + log.print( "0.25 O GROUPS" ); + log.print( "\t" ); + log.print( "0.5 O GROUPS" ); + log.print( "\t" ); + log.print( "0.75 O GROUPS" ); + log.print( "\t" ); + log.print( "0.95 O GROUPS" ); + log.print( "\t" ); + if ( perform_gsdir_on_best_tree ) { + log.print( "BEST TREE DUP" ); + log.print( "\t" ); + log.print( "MEDIAN DUP - BEST TREE DUP" ); + log.print( "\t" ); + } + log.print( "MEDIAN DUP" ); + log.print( "\t" ); + log.print( "MEAN DUP" ); + log.print( "\t" ); + log.print( "MEAN DUP SD" ); + log.print( "\t" ); + log.print( "MIN DUP" ); + log.print( "\t" ); + log.print( "MAX DUP" ); + log.print( "\t" ); + log.print( "REMOVED EXT NODES" ); + log.print( "\t" ); + log.print( "N" ); + log.println(); + } + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + int counter = 1; + for( final File gf : gene_trees_files ) { + String outname = gf.getName(); + System.out + .print( "\r " ); + System.out.print( "\r" + counter + "/" + gene_trees_files.length + ": " + outname ); + counter++; + if ( outname.indexOf( "." ) > 0 ) { + outname = outname.substring( 0, outname.lastIndexOf( "." ) ); } - 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" ); + try { + RIOUtil.executeAnalysis( gf, + species_tree_file, + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHO_OUTTABLE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.LOGFILE_SUFFIX ), + outgroup, + rerooting, + gt_first, + gt_last, + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), + true, + algorithm, + true, + log, + ortholog_group_cutoff, + perform_id_mapping, + id_mapping_dir, + id_mapping_suffix, + perform_gsdir_on_best_tree, + outdir, + best_trees_indir, + best_trees_suffix ); } - 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 ); + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + } + System.out + .print( "\r " ); + System.out.println(); } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() ); - e.printStackTrace(); - System.exit( -1 ); - } - out.println( output ); - out.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); - if ( TIME && VERBOSE ) { + else { + String outname = ForesterUtil.removeFileExtension( orthology_outtable.toString() ); + RIOUtil.executeAnalysis( gene_trees_file, + species_tree_file, + orthology_outtable, + null, + new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), + logfile, + outgroup, + rerooting, + gt_first, + gt_last, + new File( outname + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), + algorithm == ALGORITHM.GSDIR, + algorithm, + false, + null, + ortholog_group_cutoff, + false, + null, + null, + false, + null, + null, + null ); + } + if ( !use_dir ) { time = System.currentTimeMillis() - time; - ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); + System.out.println( "Time :\t" + time + "ms" ); + } + else { + try { + log.close(); + } + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + time = System.currentTimeMillis() - time; + System.out.println( "Time :\t" + time + "ms" ); } - ForesterUtil.programMessage( PRG_NAME, "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( PRG_NAME + + " [options] [logfile]" ); + System.out.println(); + System.out.println( PRG_NAME + " [options] " ); System.out.println(); - System.out.println( " Sort priority (\"P=\"):" ); - System.out.println( RIO.getOrderHelp().toString() ); 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( " -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + + "= : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" ); + 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( " -" + 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( " -" + GENE_TREES_SUFFIX_OPTION + + "= : suffix for gene trees when operating on gene tree directories (default: " + + GENE_TREES_SUFFIX_DEFAULT + ")" ); + System.out.println( " -" + MAPPINGS_DIR_OPTION + "=

: directory for id mapping files" ); + System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "= : suffix for id mapping files (default: " + + MAPPINGS_SUFFIX_DEFAULT + ")" ); + System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION + + "= : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" ); + System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION + + "= : suffix for consenus (\"best\") gene trees (default: " + CONSENSUS_TREE_SUFFIX_DEFAULT + + ")" ); + /// + 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( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=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 -s gene_trees.nh species.xml outtable.tsv" ); + System.out.println( " rio gene_trees.nh species.xml outtable.tsv log.txt" ); + System.out.println( " rio -c=0.9 -f=10 -l=100 -r=none gene_trees.xml species.xml outtable.tsv log.txt" ); + System.out.println( " rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" ); + System.out.println( " rio -g=.mlt -m=id_maps_dir -ms=.nim -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); + System.out.println( " rio -m=id_maps_dir -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); + System.out + .println( " rio -m=id_maps_dir -co=consensus_dir -cos=.xml -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); System.out.println(); + System.exit( -1 ); } }