import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
-import java.math.RoundingMode;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Iterator;
import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-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.rio.RIO;
import org.forester.rio.RIO.REROOTING;
-import org.forester.rio.RIOException;
-import org.forester.sdi.SDIException;
+import org.forester.rio.RIOUtil;
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 = "5.000";
- final static private String PRG_DATE = "170411";
+ public final static String PRG_NAME = "rio";
+ public final static String PRG_VERSION = "5.000";
+ public final static String PRG_DATE = "170411";
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";
outname = outname.substring( 0, outname.lastIndexOf( "." ) );
}
try {
- executeAnalysis( gf,
+ RIOUtil.executeAnalysis( gf,
species_tree_file,
new File( outdir.getCanonicalFile() + "/" + outname + ORTHO_OUTTABLE_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname + ORTHOLOG_GROUPS_SUFFIX ),
if ( outname.indexOf( "." ) > 0 ) {
outname = outname.substring( 0, outname.lastIndexOf( "." ) );
}
- executeAnalysis( gene_trees_file,
+ RIOUtil.executeAnalysis( gene_trees_file,
species_tree_file,
orthology_outtable,
new File( outname + ORTHOLOG_GROUPS_SUFFIX ),
System.exit( 0 );
}
- private static final void executeAnalysis( final File gene_trees_file,
- final File species_tree_file,
- final File orthology_outtable,
- final File orthology_groups_outfile,
- final File logfile,
- final String outgroup,
- final REROOTING rerooting,
- final int gt_first,
- final int gt_last,
- final File return_species_tree,
- final File return_min_dup_gene_tree,
- final File return_median_dup_gene_tree,
- final boolean transfer_taxonomy,
- final ALGORITHM algorithm,
- final boolean use_gene_trees_dir,
- final EasyWriter log,
- final double ortholog_group_cutoff ) {
- try {
- 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 {
- throw new RuntimeException( "unknown parser type: " + p );
- }
- 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,
- !use_gene_trees_dir,
- transfer_taxonomy );
- }
- if ( !use_gene_trees_dir ) {
- if ( algorithm == ALGORITHM.GSDIR ) {
- System.out.println( "Taxonomy linking based on :\t" + 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, !use_gene_trees_dir );
- final int ortholog_groups = writeOrtologGroups( orthology_groups_outfile,
- ortholog_group_cutoff,
- stats.getN(),
- m,
- !use_gene_trees_dir,
- false );
- final int ortholog_groups_005 = writeOrtologGroups( null, 0.05, stats.getN(), m, false, true );
- final int ortholog_groups_025 = writeOrtologGroups( null, 0.25, stats.getN(), m, false, true );
- final int ortholog_groups_05 = writeOrtologGroups( null, 0.5, stats.getN(), m, false, true );
- final int ortholog_groups_075 = writeOrtologGroups( null, 0.75, stats.getN(), m, false, true );
- final int ortholog_groups_095 = writeOrtologGroups( null, 0.95, stats.getN(), m, false, true );
- 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(),
- !use_gene_trees_dir );
- }
- if ( return_species_tree != null ) {
- writeTree( rio.getSpeciesTree(),
- return_species_tree,
- use_gene_trees_dir ? null : "Wrote (stripped) species tree to :\t" );
- }
- if ( return_min_dup_gene_tree != null && rio.getMinDuplicationsGeneTree() != null ) {
- final int min = ( int ) rio.getDuplicationsStatistics().getMin();
- writeTree( rio.getMinDuplicationsGeneTree(),
- new File( return_min_dup_gene_tree.toString() + min + ".xml" ),
- use_gene_trees_dir ? null : "Wrote one min duplication gene tree :\t" );
- }
- if ( return_median_dup_gene_tree != null && rio.getDuplicationsToTreeMap() != null ) {
- final int med = ( int ) rio.getDuplicationsStatistics().median();
- writeTree( rio.getDuplicationsToTreeMap().get( med ),
- new File( return_median_dup_gene_tree.toString() + med + ".xml" ),
- use_gene_trees_dir ? null : "Wrote one med duplication gene tree :\t" );
- }
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.##" );
- final int min = ( int ) stats.getMin();
- final int max = ( int ) stats.getMax();
- final int median = ( int ) stats.median();
- int min_count = 0;
- int max_count = 0;
- int median_count = 0;
- for( double d : stats.getData() ) {
- if ( ( ( int ) d ) == min ) {
- ++min_count;
- }
- if ( ( ( int ) d ) == max ) {
- ++max_count;
- }
- if ( ( ( int ) d ) == median ) {
- ++median_count;
- }
- }
- final double min_count_percentage = ( 100.0 * min_count ) / stats.getN();
- final double max_count_percentage = ( 100.0 * max_count ) / stats.getN();
- final double median_count_percentage = ( 100.0 * median_count ) / stats.getN();
- if ( use_gene_trees_dir ) {
- String name = gene_trees_file.getName();
- if ( name.indexOf( "." ) > 0 ) {
- name = name.substring( 0, name.lastIndexOf( "." ) );
- }
- log.print( name );
- log.print( "\t" );
- log.print( Integer.toString( rio.getExtNodesOfAnalyzedGeneTrees() ) );
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups ) );
- //
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups_005 ) );
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups_025 ) );
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups_05 ) );
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups_075 ) );
- log.print( "\t" );
- log.print( Integer.toString( ortholog_groups_095 ) );
- //
- log.print( "\t" );
- if ( stats.getN() > 3 ) {
- log.print( df.format( median ) );
- }
- else {
- log.print( "" );
- }
- log.print( "\t" );
- log.print( df.format( stats.arithmeticMean() ) );
- log.print( "\t" );
- if ( stats.getN() > 3 ) {
- log.print( df.format( stats.sampleStandardDeviation() ) );
- }
- else {
- log.print( "" );
- }
- log.print( "\t" );
- log.print( Integer.toString( min ) );
- log.print( "\t" );
- log.print( Integer.toString( max ) );
- log.print( "\t" );
- log.print( Integer.toString( rio.getRemovedGeneTreeNodes().size() ) );
- log.print( "\t" );
- log.print( Integer.toString( stats.getN() ) );
- log.println();
- }
- else {
- System.out.println( "Gene tree internal nodes :\t" + rio.getIntNodesOfAnalyzedGeneTrees() );
- System.out.println( "Gene tree external nodes :\t" + rio.getExtNodesOfAnalyzedGeneTrees() );
- System.out.println( "Mean number of duplications :\t" + df.format( stats.arithmeticMean() )
- + "\t" + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() )
- + "%\t(sd: " + df.format( stats.sampleStandardDeviation() ) + ")" );
- if ( stats.getN() > 3 ) {
- System.out.println( "Median number of duplications :\t" + df.format( median ) + "\t"
- + df.format( ( 100.0 * median ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
- }
- System.out.println( "Minimum duplications :\t" + min + "\t"
- + df.format( ( 100.0 * min ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
- System.out.println( "Maximum duplications :\t" + ( int ) max + "\t"
- + df.format( ( 100.0 * max ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
- System.out.println( "Gene trees with median duplications :\t" + median_count + "\t"
- + df.format( median_count_percentage ) + "%" );
- System.out.println( "Gene trees with minimum duplications:\t" + min_count + "\t"
- + df.format( min_count_percentage ) + "%" );
- System.out.println( "Gene trees with maximum duplications:\t" + max_count + "\t"
- + df.format( max_count_percentage ) + "%" );
- if ( algorithm == ALGORITHM.GSDIR ) {
- System.out.println( "Removed ext gene tree nodes :\t"
- + rio.getRemovedGeneTreeNodes().size() );
- }
- }
- }
- 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.unexpectedFatalError( e );
- }
- catch ( final Error e ) {
- ForesterUtil.unexpectedFatalError( e );
- }
- }
-
private final static void printHelp() {
System.out.println( "Usage" );
System.out.println();
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,
- final boolean verbose )
- 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 :\t" + gene_trees_file.getCanonicalPath() );
- out.println( "Species tree :\t" + species_tree_file.getCanonicalPath() );
- out.println( "All vs all orthology table :\t" + outtable.getCanonicalPath() );
- out.flush();
- out.println( rio.getLog().toString() );
- out.close();
- if ( verbose ) {
- System.out.println( "Wrote log to :\t" + logfile.getCanonicalPath() );
- }
- }
-
- private static final void writeTable( final File table_outfile,
- final int gene_trees_analyzed,
- final IntMatrix m,
- final boolean verbose )
- 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();
- if ( verbose ) {
- System.out.println( "Wrote table to :\t" + table_outfile.getCanonicalPath() );
- }
- }
-
- private static final int writeOrtologGroups( final File outfile,
- final double cutoff,
- final int gene_trees_analyzed,
- final IntMatrix m,
- final boolean verbose,
- final boolean calc_conly )
- throws IOException {
- List<SortedSet<String>> groups = new ArrayList<SortedSet<String>>();
- BasicDescriptiveStatistics stats = new BasicDescriptiveStatistics();
- int below_075 = 0;
- int below_05 = 0;
- int below_025 = 0;
- for( int x = 1; x < m.size(); ++x ) {
- final String a = m.getLabel( x );
- for( int y = 0; y < x; ++y ) {
- final String b = m.getLabel( y );
- final double s = ( ( double ) m.get( x, y ) ) / gene_trees_analyzed;
- stats.addValue( s );
- if ( s < 0.75 ) {
- below_075++;
- if ( s < 0.5 ) {
- below_05++;
- if ( s < 0.25 ) {
- below_025++;
- }
- }
- }
- if ( s >= cutoff ) {
- boolean found = false;
- for( final SortedSet<String> group : groups ) {
- if ( group.contains( a ) ) {
- group.add( b );
- found = true;
- }
- if ( group.contains( b ) ) {
- group.add( a );
- found = true;
- }
- }
- if ( !found ) {
- final SortedSet<String> new_group = new TreeSet<String>();
- new_group.add( a );
- new_group.add( b );
- groups.add( new_group );
- }
- }
- }
- }
- //Deal with singlets:
- for( int x = 0; x < m.size(); ++x ) {
- final String a = m.getLabel( x );
- boolean found = false;
- for( final SortedSet<String> group : groups ) {
- if ( group.contains( a ) ) {
- found = true;
- break;
- }
- }
- if ( !found ) {
- final SortedSet<String> new_group = new TreeSet<String>();
- new_group.add( a );
- groups.add( new_group );
- }
- }
- if ( calc_conly ) {
- return groups.size();
- }
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
- df.setDecimalSeparatorAlwaysShown( false );
- df.setRoundingMode( RoundingMode.HALF_UP );
- final EasyWriter w = ForesterUtil.createEasyWriter( outfile );
- int counter = 1;
- for( final SortedSet<String> group : groups ) {
- w.print( Integer.toString( counter++ ) );
- for( final String s : group ) {
- w.print( "\t" );
- w.print( s );
- }
- w.println();
- }
- w.println();
- w.println( "# Cutoff\t" + df.format( cutoff ) );
- w.println();
- w.println( "# Orthology support statistics:" );
- if ( stats.getN() > 3 ) {
- w.println( "# Median\t" + df.format( stats.median() ) );
- }
- w.println( "# Mean\t" + df.format( stats.arithmeticMean() ) );
- if ( stats.getN() > 3 ) {
- w.println( "# SD\t" + df.format( stats.sampleStandardDeviation() ) );
- }
- w.println( "# Min\t" + df.format( stats.getMin() ) );
- w.println( "# Max\t" + df.format( stats.getMax() ) );
- w.println( "# Total\t" + df.format( stats.getN() ) );
- w.println( "# Below 0.75\t" + below_075 + "\t" + df.format( ( 100.0 * below_075 / stats.getN() ) ) + "%" );
- w.println( "# Below 0.5\t" + below_05 + "\t" + df.format( ( 100.0 * below_05 / stats.getN() ) ) + "%" );
- w.println( "# Below 0.25\t" + below_025 + "\t" + df.format( ( 100.0 * below_025 / stats.getN() ) ) + "%" );
- w.close();
- if ( verbose ) {
- System.out.println( "Number of ortholog groups :\t" + groups.size() );
- System.out.println( "Wrote orthologs groups table to :\t" + outfile.getCanonicalPath() );
- }
- return groups.size();
- }
-
- 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 );
- if ( comment != null ) {
- System.out.println( comment + f.getCanonicalPath() );
- }
- }
}
--- /dev/null
+
+package org.forester.rio;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.math.RoundingMode;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+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.rio.RIO.REROOTING;
+import org.forester.sdi.SDIException;
+import org.forester.sdi.SDIutil.ALGORITHM;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.EasyWriter;
+import org.forester.util.ForesterUtil;
+
+public final class RIOUtil {
+
+ public static final void executeAnalysis( final File gene_trees_file,
+ final File species_tree_file,
+ final File orthology_outtable,
+ final File orthology_groups_outfile,
+ final File logfile,
+ final String outgroup,
+ final REROOTING rerooting,
+ final int gt_first,
+ final int gt_last,
+ final File return_species_tree,
+ final File return_min_dup_gene_tree,
+ final File return_median_dup_gene_tree,
+ final boolean transfer_taxonomy,
+ final ALGORITHM algorithm,
+ final boolean use_gene_trees_dir,
+ final EasyWriter log,
+ final double ortholog_group_cutoff ) {
+ try {
+ 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 {
+ throw new RuntimeException( "unknown parser type: " + p );
+ }
+ 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,
+ !use_gene_trees_dir,
+ transfer_taxonomy );
+ }
+ if ( !use_gene_trees_dir ) {
+ if ( algorithm == ALGORITHM.GSDIR ) {
+ System.out.println( "Taxonomy linking based on :\t" + 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, !use_gene_trees_dir );
+ final int ortholog_groups = writeOrtologGroups( orthology_groups_outfile,
+ ortholog_group_cutoff,
+ stats.getN(),
+ m,
+ !use_gene_trees_dir,
+ false );
+ final int ortholog_groups_005 = writeOrtologGroups( null, 0.05, stats.getN(), m, false, true );
+ final int ortholog_groups_025 = writeOrtologGroups( null, 0.25, stats.getN(), m, false, true );
+ final int ortholog_groups_05 = writeOrtologGroups( null, 0.5, stats.getN(), m, false, true );
+ final int ortholog_groups_075 = writeOrtologGroups( null, 0.75, stats.getN(), m, false, true );
+ final int ortholog_groups_095 = writeOrtologGroups( null, 0.95, stats.getN(), m, false, true );
+ if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) {
+ writeLogFile( logfile,
+ rio,
+ species_tree_file,
+ gene_trees_file,
+ orthology_outtable,
+ org.forester.application.rio.PRG_NAME,
+ org.forester.application.rio.PRG_VERSION,
+ org.forester.application.rio.PRG_DATE,
+ ForesterUtil.getForesterLibraryInformation(),
+ !use_gene_trees_dir );
+ }
+ if ( return_species_tree != null ) {
+ writeTree( rio.getSpeciesTree(),
+ return_species_tree,
+ use_gene_trees_dir ? null : "Wrote (stripped) species tree to :\t" );
+ }
+ if ( return_min_dup_gene_tree != null && rio.getMinDuplicationsGeneTree() != null ) {
+ final int min = ( int ) rio.getDuplicationsStatistics().getMin();
+ writeTree( rio.getMinDuplicationsGeneTree(),
+ new File( return_min_dup_gene_tree.toString() + min + ".xml" ),
+ use_gene_trees_dir ? null : "Wrote one min duplication gene tree :\t" );
+ }
+ if ( return_median_dup_gene_tree != null && rio.getDuplicationsToTreeMap() != null ) {
+ final int med = ( int ) rio.getDuplicationsStatistics().median();
+ writeTree( rio.getDuplicationsToTreeMap().get( med ),
+ new File( return_median_dup_gene_tree.toString() + med + ".xml" ),
+ use_gene_trees_dir ? null : "Wrote one med duplication gene tree :\t" );
+ }
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.##" );
+ final int min = ( int ) stats.getMin();
+ final int max = ( int ) stats.getMax();
+ final int median = ( int ) stats.median();
+ int min_count = 0;
+ int max_count = 0;
+ int median_count = 0;
+ for( double d : stats.getData() ) {
+ if ( ( ( int ) d ) == min ) {
+ ++min_count;
+ }
+ if ( ( ( int ) d ) == max ) {
+ ++max_count;
+ }
+ if ( ( ( int ) d ) == median ) {
+ ++median_count;
+ }
+ }
+ final double min_count_percentage = ( 100.0 * min_count ) / stats.getN();
+ final double max_count_percentage = ( 100.0 * max_count ) / stats.getN();
+ final double median_count_percentage = ( 100.0 * median_count ) / stats.getN();
+ if ( use_gene_trees_dir ) {
+ String name = gene_trees_file.getName();
+ if ( name.indexOf( "." ) > 0 ) {
+ name = name.substring( 0, name.lastIndexOf( "." ) );
+ }
+ log.print( name );
+ log.print( "\t" );
+ log.print( Integer.toString( rio.getExtNodesOfAnalyzedGeneTrees() ) );
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups ) );
+ //
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups_005 ) );
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups_025 ) );
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups_05 ) );
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups_075 ) );
+ log.print( "\t" );
+ log.print( Integer.toString( ortholog_groups_095 ) );
+ //
+ log.print( "\t" );
+ if ( stats.getN() > 3 ) {
+ log.print( df.format( median ) );
+ }
+ else {
+ log.print( "" );
+ }
+ log.print( "\t" );
+ log.print( df.format( stats.arithmeticMean() ) );
+ log.print( "\t" );
+ if ( stats.getN() > 3 ) {
+ log.print( df.format( stats.sampleStandardDeviation() ) );
+ }
+ else {
+ log.print( "" );
+ }
+ log.print( "\t" );
+ log.print( Integer.toString( min ) );
+ log.print( "\t" );
+ log.print( Integer.toString( max ) );
+ log.print( "\t" );
+ log.print( Integer.toString( rio.getRemovedGeneTreeNodes().size() ) );
+ log.print( "\t" );
+ log.print( Integer.toString( stats.getN() ) );
+ log.println();
+ }
+ else {
+ System.out.println( "Gene tree internal nodes :\t" + rio.getIntNodesOfAnalyzedGeneTrees() );
+ System.out.println( "Gene tree external nodes :\t" + rio.getExtNodesOfAnalyzedGeneTrees() );
+ System.out.println( "Mean number of duplications :\t" + df.format( stats.arithmeticMean() )
+ + "\t" + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() )
+ + "%\t(sd: " + df.format( stats.sampleStandardDeviation() ) + ")" );
+ if ( stats.getN() > 3 ) {
+ System.out.println( "Median number of duplications :\t" + df.format( median ) + "\t"
+ + df.format( ( 100.0 * median ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ }
+ System.out.println( "Minimum duplications :\t" + min + "\t"
+ + df.format( ( 100.0 * min ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ System.out.println( "Maximum duplications :\t" + ( int ) max + "\t"
+ + df.format( ( 100.0 * max ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ System.out.println( "Gene trees with median duplications :\t" + median_count + "\t"
+ + df.format( median_count_percentage ) + "%" );
+ System.out.println( "Gene trees with minimum duplications:\t" + min_count + "\t"
+ + df.format( min_count_percentage ) + "%" );
+ System.out.println( "Gene trees with maximum duplications:\t" + max_count + "\t"
+ + df.format( max_count_percentage ) + "%" );
+ if ( algorithm == ALGORITHM.GSDIR ) {
+ System.out.println( "Removed ext gene tree nodes :\t"
+ + rio.getRemovedGeneTreeNodes().size() );
+ }
+ }
+ }
+ 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.unexpectedFatalError( e );
+ }
+ catch ( final Error e ) {
+ ForesterUtil.unexpectedFatalError( e );
+ }
+ }
+
+ private static final void writeTable( final File table_outfile,
+ final int gene_trees_analyzed,
+ final IntMatrix m,
+ final boolean verbose )
+ 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();
+ if ( verbose ) {
+ System.out.println( "Wrote table to :\t" + table_outfile.getCanonicalPath() );
+ }
+ }
+
+ private static final int writeOrtologGroups( final File outfile,
+ final double cutoff,
+ final int gene_trees_analyzed,
+ final IntMatrix m,
+ final boolean verbose,
+ final boolean calc_conly )
+ throws IOException {
+ List<SortedSet<String>> groups = new ArrayList<SortedSet<String>>();
+ BasicDescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ int below_075 = 0;
+ int below_05 = 0;
+ int below_025 = 0;
+ for( int x = 1; x < m.size(); ++x ) {
+ final String a = m.getLabel( x );
+ for( int y = 0; y < x; ++y ) {
+ final String b = m.getLabel( y );
+ final double s = ( ( double ) m.get( x, y ) ) / gene_trees_analyzed;
+ stats.addValue( s );
+ if ( s < 0.75 ) {
+ below_075++;
+ if ( s < 0.5 ) {
+ below_05++;
+ if ( s < 0.25 ) {
+ below_025++;
+ }
+ }
+ }
+ if ( s >= cutoff ) {
+ boolean found = false;
+ for( final SortedSet<String> group : groups ) {
+ if ( group.contains( a ) ) {
+ group.add( b );
+ found = true;
+ }
+ if ( group.contains( b ) ) {
+ group.add( a );
+ found = true;
+ }
+ }
+ if ( !found ) {
+ final SortedSet<String> new_group = new TreeSet<String>();
+ new_group.add( a );
+ new_group.add( b );
+ groups.add( new_group );
+ }
+ }
+ }
+ }
+ //Deal with singlets:
+ for( int x = 0; x < m.size(); ++x ) {
+ final String a = m.getLabel( x );
+ boolean found = false;
+ for( final SortedSet<String> group : groups ) {
+ if ( group.contains( a ) ) {
+ found = true;
+ break;
+ }
+ }
+ if ( !found ) {
+ final SortedSet<String> new_group = new TreeSet<String>();
+ new_group.add( a );
+ groups.add( new_group );
+ }
+ }
+ if ( calc_conly ) {
+ return groups.size();
+ }
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
+ df.setDecimalSeparatorAlwaysShown( false );
+ df.setRoundingMode( RoundingMode.HALF_UP );
+ final EasyWriter w = ForesterUtil.createEasyWriter( outfile );
+ int counter = 1;
+ for( final SortedSet<String> group : groups ) {
+ w.print( Integer.toString( counter++ ) );
+ for( final String s : group ) {
+ w.print( "\t" );
+ w.print( s );
+ }
+ w.println();
+ }
+ w.println();
+ w.println( "# Cutoff\t" + df.format( cutoff ) );
+ w.println();
+ w.println( "# Orthology support statistics:" );
+ if ( stats.getN() > 3 ) {
+ w.println( "# Median\t" + df.format( stats.median() ) );
+ }
+ w.println( "# Mean\t" + df.format( stats.arithmeticMean() ) );
+ if ( stats.getN() > 3 ) {
+ w.println( "# SD\t" + df.format( stats.sampleStandardDeviation() ) );
+ }
+ w.println( "# Min\t" + df.format( stats.getMin() ) );
+ w.println( "# Max\t" + df.format( stats.getMax() ) );
+ w.println( "# Total\t" + df.format( stats.getN() ) );
+ w.println( "# Below 0.75\t" + below_075 + "\t" + df.format( ( 100.0 * below_075 / stats.getN() ) ) + "%" );
+ w.println( "# Below 0.5\t" + below_05 + "\t" + df.format( ( 100.0 * below_05 / stats.getN() ) ) + "%" );
+ w.println( "# Below 0.25\t" + below_025 + "\t" + df.format( ( 100.0 * below_025 / stats.getN() ) ) + "%" );
+ w.close();
+ if ( verbose ) {
+ System.out.println( "Number of ortholog groups :\t" + groups.size() );
+ System.out.println( "Wrote orthologs groups table to :\t" + outfile.getCanonicalPath() );
+ }
+ return groups.size();
+ }
+
+ 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 );
+ if ( comment != null ) {
+ System.out.println( comment + f.getCanonicalPath() );
+ }
+ }
+
+ 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,
+ final boolean verbose )
+ 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 :\t" + gene_trees_file.getCanonicalPath() );
+ out.println( "Species tree :\t" + species_tree_file.getCanonicalPath() );
+ out.println( "All vs all orthology table :\t" + outtable.getCanonicalPath() );
+ out.flush();
+ out.println( rio.getLog().toString() );
+ out.close();
+ if ( verbose ) {
+ System.out.println( "Wrote log to :\t" + logfile.getCanonicalPath() );
+ }
+ }
+
+ private final static Map<String, String> obtainMapping( final File dir, final String prefix, final String suffix )
+ throws IOException {
+ if ( !dir.exists() ) {
+ throw new IOException( "[" + dir + "] does not exist" );
+ }
+ if ( !dir.isDirectory() ) {
+ throw new IOException( "[" + dir + "] is not a directory" );
+ }
+ final File mapping_files[] = dir.listFiles( new FilenameFilter() {
+
+ @Override
+ public boolean accept( final File dir, final String name ) {
+ return ( name.endsWith( suffix ) );
+ }
+ } );
+ String my_suffix = suffix;
+ boolean done = false;
+ do {
+ int matches = 0;
+ for( File file : mapping_files ) {
+ if ( file.getName().equals( my_suffix ) ) {
+ matches++;
+ }
+ }
+ if ( matches == 1) {
+ done = true;
+ }
+ else {
+ my_suffix = my_suffix.substring( 0, my_suffix.length() - 1);
+ }
+ } while (!done );
+
+
+ if ( mapping_files.length == 0 ) {
+ throw new IOException( "file with prefix \"" + prefix + "\" and suffix \"" + suffix + "\" not found in ["
+ + dir + "] " );
+ }
+ if ( mapping_files.length > 1 ) {
+ throw new IOException( "file with prefix \"" + prefix + "\" and suffix \"" + suffix + "\" not unique in ["
+ + dir + "] " );
+ }
+ final BasicTable<String> t = BasicTableParser.parse( mapping_files[ 0 ], '\t' );
+ return t.getColumnsAsMap( 0, 1 );
+ }
+}
git://source.jalview.org / jalview.git / commitdiff