// 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
// 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.SDIException;
-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).
- * <p>
- *
- * @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<Double> bv = new Vector<Double>();
- 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<String> allowed_options = new ArrayList<String>();
+ 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<String> al_ortholog_names_for_dc,
- final HashMap<String, Integer> ortholog_hashmap,
- final HashMap<String, Integer> 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, SDIException {
- Phylogeny consensus_tree = null;
- Phylogeny
- // to be a consensus tree.
- assigned_cons_tree = null;
- final SDIR sdiunrooted = new SDIR();
- final ArrayList<PhylogenyNode> al_ortholog_nodes = new ArrayList<PhylogenyNode>();
- 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<String> 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 ) );
- }
- rio_instance.inferredOrthologTableToFile( new File( "table" ) );
- 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] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
+ System.out.println();
+ System.out.println( PRG_NAME + " [options] <gene trees indir> <species tree infile> <outdir> <logfile>" );
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> : first gene tree to analyze (0-based index)" );
+ System.out.println( " -" + GT_LAST + "=<last> : last gene tree to analyze (0-based index)" );
+ System.out.println( " -" + ORTHOLOG_GROUPS_CUTOFF_OPTION
+ + "=<cutoff> : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" );
+ System.out.println( " -" + REROOTING_OPT
+ + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
+ System.out.println( " or 'outgroup' (default: by minizming duplications)" );
+ System.out.println( " -" + OUTGROUP
+ + "=<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> : suffix for gene trees when operating on gene tree directories (default: "
+ + GENE_TREES_SUFFIX_DEFAULT + ")" );
+ System.out.println( " -" + MAPPINGS_DIR_OPTION + "=<dir> : directory for id mapping files" );
+ System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "=<suffix> : suffix for id mapping files (default: "
+ + MAPPINGS_SUFFIX_DEFAULT + ")" );
+ System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION
+ + "=<dir> : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" );
+ System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION
+ + "=<suffix> : 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 );
}
}
git://source.jalview.org / jalview.git / blobdiff