// 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.FilenameFilter;
import java.io.IOException;
+import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Date;
import java.util.List;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
-
-import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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.sdi.GSDI;
-import org.forester.sdi.SDI;
-import org.forester.sdi.SDIse;
+import org.forester.sdi.GSDII;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
+import org.forester.sdi.SDIutil;
+import org.forester.sdi.SDIutil.ALGORITHM;
import org.forester.util.CommandLineArguments;
+import org.forester.util.EasyWriter;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class gsdi {
- final static private String STRIP_OPTION = "s";
- final static private String SDI_OPTION = "b";
- final static private String MOST_PARSIMONIOUS_OPTION = "m";
- final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE = "gsdi_out.phylo.xml";
- final static private String PRG_NAME = "gsdi";
- final static private String PRG_VERSION = "0.5";
- final static private String PRG_DATE = "120608";
- final static private String PRG_DESC = "general speciation duplication inference";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "www.phylosoft.org/forester";
+ final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
+ final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
+ final static private String GSDIR_OPTION = "r";
+ final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ final static private String SUFFIX_FOR_DIR_OPTION = "s";
+ final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
+ final static private String TRANSFER_TAXONOMY_OPTION = "t";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
+ final static private String OUTTREE_SUFFIX = "_gsdir.xml";
+ final static private String LOGFILE_NAME = "00_gsdi_log.tsv";
+ final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
+ final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt";
+ final static private String PRG_NAME = "gsdi";
+ final static private String PRG_VERSION = "1.100";
+ final static private String PRG_DATE = "170403";
+ final static private String PRG_DESC = "general speciation duplication inference";
+ final static private String E_MAIL = "phyloxml@gmail.com";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
public static void main( final String args[] ) {
- ForesterUtil.printProgramInformation( PRG_NAME,
- PRG_DESC,
- PRG_VERSION,
- PRG_DATE,
- E_MAIL,
- WWW,
- ForesterUtil.getForesterLibraryInformation() );
- CommandLineArguments cla = null;
try {
- cla = new CommandLineArguments( args );
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ PRG_DESC,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ WWW,
+ ForesterUtil.getForesterLibraryInformation() );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
+ System.out.println();
+ gsdi.print_help();
+ System.exit( 0 );
+ }
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
+ System.out.println();
+ System.out.println( "Wrong number of arguments." );
+ System.out.println();
+ gsdi.print_help();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( GSDIR_OPTION );
+ allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE );
+ allowed_options.add( MOST_PARSIMONIOUS_OPTION );
+ allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
+ allowed_options.add( TRANSFER_TAXONOMY_OPTION );
+ allowed_options.add( SUFFIX_FOR_DIR_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ execute( cla );
}
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
- System.out.println();
- gsdi.print_help();
- System.exit( 0 );
- }
- else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
- System.out.println();
- System.out.println( "Wrong number of arguments." );
- System.out.println();
- gsdi.print_help();
- System.exit( -1 );
- }
- final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( gsdi.STRIP_OPTION );
- allowed_options.add( gsdi.SDI_OPTION );
- allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
- allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
- final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
- if ( dissallowed_options.length() > 0 ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
- }
- boolean use_sdise = false;
- boolean strip = false;
- boolean most_parsimonous_duplication_model = false;
- boolean species_tree_in_phyloxml = true;
- if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
- strip = true;
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
}
- if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
- use_sdise = true;
+ }
+
+ private final static void execute( final CommandLineArguments cla ) throws IOException {
+ ALGORITHM base_algorithm = ALGORITHM.GSDI;
+ boolean most_parsimonous_duplication_model = false;
+ boolean allow_stripping_of_gene_tree = false;
+ if ( cla.isOptionSet( GSDIR_OPTION ) ) {
+ base_algorithm = ALGORITHM.GSDIR;
}
- if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
- if ( use_sdise ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
+ if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
+ if ( base_algorithm == ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
}
most_parsimonous_duplication_model = true;
}
- if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
- species_tree_in_phyloxml = false;
+ if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
+ if ( base_algorithm == ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
+ }
+ allow_stripping_of_gene_tree = true;
+ }
+ boolean transfer_taxonomy = false;
+ if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
+ transfer_taxonomy = true;
+ }
+ boolean use_gene_tree_dir = false;
+ final String gene_tree_suffix;
+ if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) {
+ gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION );
+ use_gene_tree_dir = true;
+ }
+ else {
+ gene_tree_suffix = null;
}
- Phylogeny species_tree = null;
- Phylogeny gene_tree = null;
File gene_tree_file = null;
File species_tree_file = null;
File out_file = null;
+ File log_file = null;
+ File out_dir = null;
try {
gene_tree_file = cla.getFile( 0 );
species_tree_file = cla.getFile( 1 );
- if ( cla.getNumberOfNames() == 3 ) {
- out_file = cla.getFile( 2 );
+ if ( use_gene_tree_dir ) {
+ out_dir = cla.getFile( 2 );
+ if ( out_dir.exists() ) {
+ if ( !out_dir.isDirectory() ) {
+ ForesterUtil
+ .fatalError( gsdi.PRG_NAME,
+ "out-directory [" + out_dir + "] already exists but is not a directory" );
+ }
+ }
+ else {
+ final boolean success = out_dir.mkdirs();
+ if ( !success ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "could not create out-directory [" + out_dir + "]" );
+ }
+ }
}
else {
- out_file = new File( gsdi.DEFAULT_OUTFILE );
+ out_file = cla.getFile( 2 );
+ log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
}
}
catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ if ( use_gene_tree_dir ) {
+ final File indir = new File( gene_tree_file.toString() );
+ if ( !indir.exists() ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] does not exist" );
+ }
+ if ( !indir.isDirectory() ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] is not a directory" );
+ }
+ final String species_tree_file_name = species_tree_file.getName();
+ final File gene_tree_files[] = indir.listFiles( new FilenameFilter() {
+
+ @Override
+ public boolean accept( final File dir, final String name ) {
+ return ( ( name.endsWith( gene_tree_suffix ) ) && !( name.equals( species_tree_file_name ) ) );
+ }
+ } );
+ if ( gene_tree_files.length < 1 ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "in-directory [" + indir
+ + "] does not contain any gene tree files with suffix "
+ + gene_tree_suffix );
+ }
+ executeDir( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_files,
+ species_tree_file,
+ out_dir );
+ }
+ else {
+ execute( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_file,
+ species_tree_file,
+ out_file,
+ log_file );
+ }
+ }
+
+ private final static void executeDir( final ALGORITHM base_algorithm,
+ final boolean most_parsimonous_duplication_model,
+ final boolean allow_stripping_of_gene_tree,
+ final boolean transfer_taxonomy,
+ final File gene_tree_files[],
+ final File species_tree_file,
+ final File outdir )
+ throws IOException {
+ final File log_file = new File( outdir, LOGFILE_NAME );
+ if ( ForesterUtil.isWritableFile( log_file ) != null ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
}
+ EasyWriter log_writer = null;
+ try {
+ log_writer = ForesterUtil.createEasyWriter( log_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
+ }
+ log_writer.println( "# " + PRG_NAME );
+ log_writer.println( "# Version\t" + PRG_VERSION );
+ log_writer.println( "# Date\t" + PRG_DATE );
+ log_writer.println( "# Forester version\t" + ForesterConstants.FORESTER_VERSION );
+ log_writer.println( "# Species tree\t" + species_tree_file.getCanonicalPath() );
+ if ( base_algorithm == ALGORITHM.GSDI ) {
+ log_writer.println( "# Algorithm\tGSDI" );
+ }
+ else if ( base_algorithm == ALGORITHM.GSDIR ) {
+ log_writer.println( "# Algorithm\tGSDIR" );
+ }
+ log_writer.println( "# Use most parsimonous duplication model\t" + most_parsimonous_duplication_model );
+ log_writer.println( "# Allow stripping of gene tree nodes\t" + allow_stripping_of_gene_tree );
+ log_writer.println( "# Start time\t" + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ log_writer.println();
+ log_writer.print( "Gene-tree file\t" );
+ log_writer.print( "Gene-tree name/#\t" );
+ log_writer.print( "Ext. nodes\t" );
+ log_writer.print( "Speciations\t" );
+ log_writer.print( "Duplications\t" );
+ if ( !most_parsimonous_duplication_model ) {
+ log_writer.print( "Spec. or Dup.\t" );
+ }
+ if ( allow_stripping_of_gene_tree ) {
+ log_writer.print( "Stripped gene-tree ext. nodes\t" );
+ }
+ log_writer.print( "Taxonomy mapping" );
+ log_writer.println();
+ int counter = 0;
+ Arrays.sort( gene_tree_files );
+ for( final File gene_tree_file : gene_tree_files ) {
+ String outname = gene_tree_file.getName();
+ if ( outname.indexOf( "." ) > 0 ) {
+ outname = outname.substring( 0, outname.lastIndexOf( "." ) );
+ }
+ outname = outname + OUTTREE_SUFFIX;
+ counter += executeOneTreeInDir( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_file,
+ species_tree_file,
+ new File( outdir, outname ),
+ log_writer );
+ log_writer.flush();
+ System.out.print( "\r" + counter );
+ }
+ System.out.print( "\r" );
+ log_writer.close();
+ System.out.println( "Analyzed " + counter + " gene trees" );
+ System.out.println();
+ System.out.println( "Wrote log to: " + log_file.getCanonicalPath() );
+ System.out.println();
+ }
+
+ private final static int executeOneTreeInDir( final ALGORITHM base_algorithm,
+ final boolean most_parsimonous_duplication_model,
+ final boolean allow_stripping_of_gene_tree,
+ final boolean transfer_taxonomy,
+ final File gene_tree_file,
+ final File species_tree_file,
+ final File out_file,
+ final EasyWriter log_writer )
+ throws IOException {
if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
}
if ( ForesterUtil.isWritableFile( out_file ) != null ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
}
+ Phylogeny gene_trees[] = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- if ( species_tree_in_phyloxml ) {
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ gene_trees = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() );
+ }
+ catch ( final IOException e ) {
+ fatalError( "error",
+ "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
+ log_writer );
+ }
+ int counter = 0;
+ final List<Phylogeny> out_trees = new ArrayList<Phylogeny>();
+ for( final Phylogeny gene_tree : gene_trees ) {
+ if ( !gene_tree.isEmpty() && gene_tree.getNumberOfExternalNodes() > 1 ) {
+ Phylogeny species_tree = null;
+ try {
+ species_tree = SDIutil.parseSpeciesTree( gene_tree,
+ species_tree_file,
+ REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
+ true,
+ TAXONOMY_EXTRACTION.NO );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ fatalError( "user error",
+ "failed to transfer general node name, in [" + species_tree_file + "]: "
+ + e.getMessage(),
+ log_writer );
+ }
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getMessage(), log_writer );
+ }
+ catch ( final IOException e ) {
+ fatalError( "error",
+ "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
+ log_writer );
+ }
+ gene_tree.setRooted( true );
+ species_tree.setRooted( true );
+ if ( !gene_tree.isCompletelyBinary() ) {
+ fatalError( "user error",
+ "gene tree [" + gene_tree_file + "] is not completely binary",
+ log_writer );
+ }
+ if ( base_algorithm == ALGORITHM.SDI ) {
+ if ( !species_tree.isCompletelyBinary() ) {
+ fatalError( "user error",
+ "species tree is not completely binary, use GSDI or GSDIR instead",
+ log_writer );
+ }
+ }
+ log_writer.print( gene_tree_file.getName() );
+ log_writer.print( "\t" );
+ log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ if ( gene_trees.length > 1 ) {
+ log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? Integer.toString( counter )
+ : ( ":" + Integer.toString( counter ) ) ) );
+ }
+ log_writer.print( "\t" );
+ GSDII gsdii = null;
+ try {
+ if ( base_algorithm == ALGORITHM.GSDI ) {
+ gsdii = new GSDI( gene_tree,
+ species_tree,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ true,
+ transfer_taxonomy );
+ }
+ else if ( base_algorithm == ALGORITHM.GSDIR ) {
+ gsdii = new GSDIR( gene_tree,
+ species_tree,
+ allow_stripping_of_gene_tree,
+ true,
+ transfer_taxonomy );
+ }
+ }
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getLocalizedMessage(), log_writer );
+ }
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ fatalError( "unexpected error", e.toString(), log_writer );
+ }
+ if ( base_algorithm == ALGORITHM.GSDIR ) {
+ final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree();
+ gt.setRerootable( false );
+ out_trees.add( gt );
+ }
+ else {
+ gene_tree.setRerootable( false );
+ out_trees.add( gene_tree );
+ }
+ log_writer.print( gene_tree.getNumberOfExternalNodes() + "\t" );
+ log_writer.print( gsdii.getSpeciationsSum() + "\t" );
+ if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
+ final GSDIR gsdir = ( GSDIR ) gsdii;
+ log_writer.print( gsdir.getMinDuplicationsSum() + "\t" );
+ }
+ else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) gsdii;
+ log_writer.print( gsdi.getDuplicationsSum() + "\t" );
+ if ( !most_parsimonous_duplication_model ) {
+ log_writer.print( gsdi.getSpeciationOrDuplicationEventsSum() + "\t" );
+ }
+ }
+ if ( allow_stripping_of_gene_tree ) {
+ log_writer.print( gsdii.getStrippedExternalGeneTreeNodes().size() + "\t" );
+ }
+ log_writer.print( gsdii.getTaxCompBase().toString() );
+ log_writer.println();
+ ++counter;
}
- else {
- final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
-
+ }
+ if ( counter > 0 ) {
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( out_file, out_trees, 0, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
}
}
+ return counter;
+ }
+
+ private final static void execute( final ALGORITHM base_algorithm,
+ final boolean most_parsimonous_duplication_model,
+ final boolean allow_stripping_of_gene_tree,
+ final boolean transfer_taxonomy,
+ final File gene_tree_file,
+ final File species_tree_file,
+ final File out_file,
+ final File log_file )
+ throws IOException {
+ if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
+ }
+ if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
+ }
+ if ( ForesterUtil.isWritableFile( out_file ) != null ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
+ }
+ if ( ForesterUtil.isWritableFile( log_file ) != null ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
+ }
+ EasyWriter log_writer = null;
+ try {
+ log_writer = ForesterUtil.createEasyWriter( log_file );
+ }
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
}
-
+ Phylogeny species_tree = null;
+ Phylogeny gene_tree = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
+ gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ fatalError( "error",
+ "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
+ log_writer );
+ }
+ try {
+ species_tree = SDIutil.parseSpeciesTree( gene_tree,
+ species_tree_file,
+ REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
+ true,
+ TAXONOMY_EXTRACTION.NO );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ fatalError( "user error",
+ "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
+ log_writer );
+ }
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getMessage(), log_writer );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ fatalError( "error",
+ "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
+ log_writer );
}
gene_tree.setRooted( true );
species_tree.setRooted( true );
if ( !gene_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary" );
+ fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
}
- if ( use_sdise ) {
+ if ( base_algorithm == ALGORITHM.SDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
- + "\") is not completely binary" );
+ fatalError( "user error",
+ "species tree is not completely binary, use GSDI or GSDIR instead",
+ log_writer );
}
}
- // For timing.
- // gene_tree = Helper.createBalancedTree( 10 );
- // species_tree = Helper.createBalancedTree( 13 );
- // species_tree = Helper.createUnbalancedTree( 1024 );
- // gene_tree = Helper.createUnbalancedTree( 8192 );
- // species_tree = gene_tree.copyTree();
- // gene_tree = species_tree.copyTree();
- // Helper.numberSpeciesInOrder( species_tree );
- // Helper.numberSpeciesInOrder( gene_tree );
- // Helper.randomizeSpecies( 1, 8192, gene_tree );
- // Helper.intervalNumberSpecies( gene_tree, 4096 );
- // Helper.numberSpeciesInDescOrder( gene_tree );
- System.out.println();
- System.out.println( "Strip species tree: " + strip );
- SDI sdi = null;
+ log_writer.println( PRG_NAME + " - " + PRG_DESC );
+ log_writer.println( " version : " + PRG_VERSION );
+ log_writer.println( " date : " + PRG_DATE );
+ log_writer.println( " forester version: " + ForesterConstants.FORESTER_VERSION );
+ log_writer.println();
+ log_writer.println( "Start time : "
+ + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ System.out.println( "Start time : "
+ + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ log_writer.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
+ System.out.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
+ log_writer.println( "Gene tree name : "
+ + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ System.out.println( "Gene tree name : "
+ + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ log_writer.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
+ System.out.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
+ log_writer.println( "Species tree name : "
+ + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
+ System.out.println( "Species tree name : "
+ + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
+ System.out.println( "Transfer taxonomy : " + transfer_taxonomy );
+ GSDII gsdii = null;
final long start_time = new Date().getTime();
try {
- if ( use_sdise ) {
- System.out.println();
- System.out.println( "Using SDIse algorithm" );
- sdi = new SDIse( gene_tree, species_tree );
+ if ( base_algorithm == ALGORITHM.GSDI ) {
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
}
- else {
- System.out.println();
- System.out.println( "Using GSDI algorithm" );
- System.out.println();
- System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
- sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model, true );
+ else if ( base_algorithm == ALGORITHM.GSDIR ) {
+ System.out.println( "Algorithm : GSDIR" );
+ log_writer.println( "Algorithm : GSDIR" );
}
+ System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
+ System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
+ log_writer.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
+ log_writer.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
+ log_writer.flush();
+ if ( base_algorithm == ALGORITHM.GSDI ) {
+ gsdii = new GSDI( gene_tree,
+ species_tree,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ true,
+ transfer_taxonomy );
+ }
+ else if ( base_algorithm == ALGORITHM.GSDIR ) {
+ gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
+ }
+ }
+ catch ( final SDIException e ) {
+ fatalError( "user error", e.getLocalizedMessage(), log_writer );
+ }
+ catch ( final IOException e ) {
+ fatalError( "error", e.toString(), log_writer );
+ }
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ e.printStackTrace();
+ fatalError( "unexpected error", e.toString(), log_writer );
}
- System.out.println();
- System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
+ System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
+ + "ms" );
+ log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
+ + "ms" );
+ System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() );
+ log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() );
try {
final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( out_file, gene_tree, 0 );
+ if ( base_algorithm == ALGORITHM.GSDIR ) {
+ final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree();
+ gt.setRerootable( false );
+ writer.toPhyloXML( out_file, gt, 0 );
+ }
+ else {
+ gene_tree.setRerootable( false );
+ writer.toPhyloXML( out_file, gene_tree, 0 );
+ }
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
}
- System.out.println();
- System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
- System.out.println();
- if ( use_sdise ) {
- sdi.computeMappingCostL();
- System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
+ System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
+ log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
+ final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
+ + SUFFIX_FOR_SPECIES_TREE_USED );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to write to [" + species_tree_used_file.getCanonicalPath() + "]: "
+ + e.getMessage() );
+ }
+ System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() );
+ log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() );
+ if ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
+ && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
+ System.out.println( "Number of gene tree species remapped : "
+ + gsdii.getReMappedScientificNamesFromGeneTree().size() );
+ log_writer.println( "Number of gene tree species remapped : "
+ + gsdii.getReMappedScientificNamesFromGeneTree().size() );
+ writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
}
- System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- if ( !use_sdise && !most_parsimonous_duplication_model ) {
- System.out.println( "Number of potential duplications: "
- + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() );
+ System.out.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
+ log_writer.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
+ System.out.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
+ log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ System.out.println( "Number of polytomies in species tree : " + poly );
+ log_writer.println( "Number of polytomies in species tree : " + poly );
+ System.out.println( "External nodes stripped from gene tree : "
+ + gsdii.getStrippedExternalGeneTreeNodes().size() );
+ log_writer.println( "External nodes stripped from gene tree : "
+ + gsdii.getStrippedExternalGeneTreeNodes().size() );
+ System.out
+ .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
+ log_writer
+ .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
+ System.out.println();
+ System.out.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
+ log_writer.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
+ if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
+ final GSDIR gsdir = ( GSDIR ) gsdii;
+ System.out.println( "Minimal number of duplications : " + gsdir.getMinDuplicationsSum() );
+ log_writer.println( "Minimal number of duplications : " + gsdir.getMinDuplicationsSum() );
}
- if ( !use_sdise ) {
- System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
+ else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) gsdii;
+ System.out.println( "Number of duplications : " + gsdi.getDuplicationsSum() );
+ log_writer.println( "Number of duplications : " + gsdi.getDuplicationsSum() );
+ if ( !most_parsimonous_duplication_model ) {
+ final int u = gsdi.getSpeciationOrDuplicationEventsSum();
+ System.out.println( "Number of potential duplications : " + u );
+ log_writer.println( "Number of potential duplications : " + u );
+ }
}
+ log_writer.println();
+ printMappedNodesToLog( log_writer, gsdii );
+ log_writer.println();
+ printStrippedGeneTreeNodesToLog( log_writer, gsdii );
System.out.println();
+ System.out.println( "Wrote log to : " + log_file.getCanonicalPath() );
+ System.out.println();
+ log_writer.close();
+ }
+
+ private final static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
+ try {
+ log_writer.flush();
+ log_writer.println();
+ log_writer.print( type.toUpperCase() + ": " );
+ log_writer.println( msg );
+ log_writer.close();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
}
- private static void print_help() {
- System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [outfile]" );
+ private final static void print_help() {
+ System.out.println( "Usage: " + PRG_NAME
+ + " [-options] <gene tree file, or gene trees in-directory> <species tree> <outfile, or out-directory>" );
System.out.println();
System.out.println( "Options:" );
- System.out.println( " -" + gsdi.STRIP_OPTION + ": to strip the species tree prior to duplication inference" );
- System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );
- System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
- + ": use most parimonious duplication model for GSDI: " );
- System.out.println( " assign nodes as speciations which would otherwise be assiged" );
- System.out.println( " as unknown because of polytomies in the species tree" );
- System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + ": to allow species tree in other formats than" );
- System.out.println( " phyloXML (Newick, NHX, Nexus)" );
+ System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " : to allow stripping of gene tree nodes without a matching species" );
+ System.out.println( " -" + MOST_PARSIMONIOUS_OPTION
+ + " : use most parimonious duplication model for GSDI: " );
+ System.out.println( " assign nodes as speciations which would otherwise be assiged" );
+ System.out.println( " as potential duplications due to polytomies in the species tree" );
+ System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE
+ + " : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
+ System.out.println( " -" + GSDIR_OPTION
+ + " : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
+ System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
+ + " : to transfer taxonomic data from species tree to gene tree" );
+ System.out.println( " -" + SUFFIX_FOR_DIR_OPTION
+ + "=<suffix>: suffix for gene trees for analyzing entire directory of trees" );
System.out.println();
- System.out.println( "Species tree:" );
- System.out.println( " In phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
- + " is used), with taxonomy data in appropriate fields" );
System.out.println();
- System.out.println( "Gene tree:" );
- System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" );
+ System.out.println( "Gene tree(s):" );
+ System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
System.out.println();
- System.out.println( "Note -- GSDI algorithm is under development" );
+ System.out.println( "Species tree:" );
+ System.out.println( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
+ System.out.println();
+ System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " gene_tree.xml tree_of_life.xml out.xml" );
+ System.out.println( " gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + SUFFIX_FOR_DIR_OPTION
+ + "=.xml" + " gene_tree_dir tree_of_life.xml out_dir" );
+ System.out.println( " gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + MOST_PARSIMONIOUS_OPTION
+ + " -" + GSDIR_OPTION + " -" + TRANSFER_TAXONOMY_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml"
+ + " gene_tree_dir tree_of_life.xml out_dir" );
System.out.println();
}
+
+ private final static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
+ throws IOException {
+ final SortedSet<String> ss = new TreeSet<String>();
+ for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
+ ss.add( n.toString() );
+ }
+ log_writer.println( "The following " + ss.size() + " species were used: " );
+ for( final String s : ss ) {
+ log_writer.println( " " + s );
+ }
+ }
+
+ private final static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
+ throws IOException {
+ final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
+ for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
+ final String s = n.toString();
+ if ( sm.containsKey( s ) ) {
+ sm.put( s, sm.get( s ) + 1 );
+ }
+ else {
+ sm.put( s, 1 );
+ }
+ }
+ log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
+ for( final String s : sm.keySet() ) {
+ final int count = sm.get( s );
+ if ( count == 1 ) {
+ log_writer.println( " " + s );
+ }
+ else {
+ log_writer.println( " " + s + " [" + count + "]" );
+ }
+ }
+ }
+
+ private final static void writeToRemappedFile( final File out_file,
+ final SortedSet<String> remapped,
+ final EasyWriter log_writer )
+ throws IOException {
+ final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
+ final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
+ for( final String s : remapped ) {
+ remapped_writer.println( s );
+ }
+ remapped_writer.close();
+ System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ }
}
git://source.jalview.org / jalview.git / blobdiff