// 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).
- * <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++;
- }
- }
- // 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<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 {
- 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 ) {
+ 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<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( 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 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 ( !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" );
}
- if ( tree_file_for_avg_bs != null ) {
- System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs );
+ }
+ 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" );
}
- 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 );
+ 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;
+ }
+ case OUTGROUP: {
+ rerooting_str = "by outgroup: " + outgroup;
+ break;
+ }
+ 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] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
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( " -" + 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( " -" + RETURN_SPECIES_TREE + "=<outfile> : to write the (stripped) species tree to file" );
+ System.out.println( " -" + RETURN_BEST_GENE_TREE
+ + "=<outfile> : 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 + "\"" );
}
}
git://source.jalview.org / jalview.git / blobdiff