// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import java.io.File;
import java.io.FileWriter;
-import java.io.IOException;
import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Vector;
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.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;
-
- // 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();
- }
- if ( n < 2 ) {
- return null;
- }
- 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 );
- }
- da[ 0 ] = mean;
- da[ 1 ] = java.lang.Math.sqrt( sum / ( n - 1.0 ) );
- return da;
- }
+ 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;
private final static void errorInCommandLine() {
System.out.println( "\nrio: Error in command line.\n" );
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;
+ double threshold_ultra_paralogs = 0.0;
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 );
else if ( ( args.length < 3 ) || ( args.length > 18 ) ) {
errorInCommandLine();
}
- for( int i = 0; i < args.length; ++i ) {
- if ( args[ i ].trim().charAt( 0 ) != 'p' ) {
- if ( args[ i ].trim().length() < 3 ) {
+ for( final String arg2 : args ) {
+ if ( arg2.trim().charAt( 0 ) != 'p' ) {
+ if ( arg2.trim().length() < 3 ) {
errorInCommandLine();
}
else {
- arg = args[ i ].trim().substring( 2 );
+ arg = arg2.trim().substring( 2 );
}
}
try {
- switch ( args[ i ].trim().charAt( 0 ) ) {
+ switch ( arg2.trim().charAt( 0 ) ) {
case 'M':
multiple_trees_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 '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();
}
|| ( outfile == null ) ) {
errorInCommandLine();
}
- if ( ( sort < 0 ) || ( sort > 17 ) ) {
- errorInCommandLine();
- }
- if ( ( sort > 2 ) && ( distance_matrix_file == null ) ) {
+ if ( ( sort < 0 ) || ( sort > 2 ) ) {
errorInCommandLine();
}
if ( VERBOSE ) {
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 ( 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 ( tree_file_for_avg_bs != null ) {
- System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs );
- }
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 );
}
- 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();
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 );
- }
- else {
- final Phylogeny p = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ];
- bs_mean_sd = calculateMeanBoostrapValue( 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" );
- }
- 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 ) );
- }
+ output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs ) );
if ( output_ultraparalogs ) {
output.append( "\n\nUltra paralogs:\n" );
- output.append( rio_instance
- .inferredUltraParalogsToString( seq_name, sort > 2, threshold_ultra_paralogs ) );
+ output.append( rio_instance.inferredUltraParalogsToString( seq_name, 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" );
+ output.append( "\nSamples : " + rio_instance.getNumberOfSamples() + "\n" );
out = new PrintWriter( new FileWriter( outfile ), true );
}
catch ( final Exception e ) {
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();
System.out.println( " Sort priority (\"P=\"):" );
System.out.println( RIO.getOrderHelp().toString() );
System.out.println();
git://source.jalview.org / jalview.git / blobdiff