// 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.util.TreeMap;
import java.util.TreeSet;
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nhx.NHXParser;
+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.sdi.SDIException;
import org.forester.sdi.SDIutil;
import org.forester.sdi.SDIutil.ALGORITHM;
-import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
import org.forester.util.CommandLineArguments;
import org.forester.util.EasyWriter;
import org.forester.util.ForesterConstants;
final static private String GSDIR_OPTION = "r";
final static private String MOST_PARSIMONIOUS_OPTION = "m";
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 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 = "1.000";
- final static private String PRG_DATE = "120629";
+ final static private String PRG_VERSION = "1.001";
+ final static private String PRG_DATE = "130325";
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 private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
public static void main( final String args[] ) {
try {
allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
+ allowed_options.add( TRANSFER_TAXONOMY_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
allow_stripping_of_gene_tree = true;
}
+ boolean transfer_taxonomy = false;
+ if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
+ transfer_taxonomy = true;
+ }
Phylogeny species_tree = null;
Phylogeny gene_tree = null;
File gene_tree_file = 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(),
+ fatalError( "error",
+ "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
log_writer );
}
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
- if ( p instanceof PhyloXmlParser ) {
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- }
- else {
- if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
- ( ( NHXParser ) p ).setReplaceUnderscores( true );
- }
- species_tree = factory.create( species_tree_file, p )[ 0 ];
- final TaxonomyComparisonBase comp_base = SDIutil.determineTaxonomyComparisonBase( gene_tree );
- switch ( comp_base ) {
- case SCIENTIFIC_NAME:
- try {
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- case CODE:
- try {
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- case ID:
- try {
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
- true );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
- + species_tree_file + "]: " + e.getMessage(), log_writer );
- }
- break;
- default:
- fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
- }
- }
+ 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",
+ fatalError( "error",
"Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
log_writer );
}
+ ( 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 ( base_algorithm == ALGORITHM.GSDI ) {
- System.out.println( "Algorithm : GSDI" );
- log_writer.println( "Algorithm : GSDI" );
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
}
else if ( base_algorithm == ALGORITHM.GSDIR ) {
- System.out.println( "Algorithm : GSDIR" );
- log_writer.println( "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 );
species_tree,
most_parsimonous_duplication_model,
allow_stripping_of_gene_tree,
- true );
+ true,
+ transfer_taxonomy );
}
else if ( base_algorithm == ALGORITHM.GSDIR ) {
- gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true );
+ gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
}
}
catch ( final SDIException e ) {
catch ( final IOException e ) {
fatalError( "error", e.toString(), log_writer );
}
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
+ }
catch ( final Exception e ) {
e.printStackTrace();
fatalError( "unexpected error", e.toString(), log_writer );
}
System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
- + "ms" );
+ + "ms" );
log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
- + "ms" );
+ + "ms" );
System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() );
log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() );
- if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
- final GSDIR gsdir = ( GSDIR ) gsdii;
- System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
- log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
- }
try {
final PhylogenyWriter writer = new PhylogenyWriter();
if ( base_algorithm == ALGORITHM.GSDIR ) {
- writer.toPhyloXML( out_file,
- ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTrees(),
- 0,
- ForesterUtil.LINE_SEPARATOR );
+ writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
}
else {
writer.toPhyloXML( out_file, gene_tree, 0 );
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 );
+ + 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() );
+ + "]: " + 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() );
log_writer.close();
}
- private 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() );
- }
-
- private 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 static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
try {
log_writer.flush();
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> <outfile>" );
+ System.out.println();
+ System.out.println( "Options:" );
+ System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + ": to allow stripping of gene tree nodes without a matching species" );
+ 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 potential duplications due to polytomies in the species tree" );
+ System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
+ + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
+ System.out.println( " -" + gsdi.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\n" );
+ 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();
+ System.out.println( "Species tree:" );
+ System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
+ System.out.println();
+ System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " gene_tree.xml tree_of_life.xml out.xml" );
+ System.out.println();
+ }
+
+ private 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 static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
throws IOException {
final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
}
}
- private static void print_help() {
- System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
- System.out.println();
- System.out.println( "Options:" );
- System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
- + ": to allow stripping of gene tree nodes without a matching species" );
- 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 potential duplications due to polytomies in the species tree" );
- System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
- + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
- System.out.println( " -" + gsdi.GSDIR_OPTION
- + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
- 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();
- System.out.println( "Species tree:" );
- System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
- System.out.println();
- System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
- + " gene_tree.xml tree_of_life.xml out.xml" );
- System.out.println();
+ private 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