// 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;
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",
+ ( 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() );
private static void print_help() {
System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
+ + " [-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" );
+ + ": 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: " );
+ + ": 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)" );
+ + ": 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)" );
+ + ": 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( " 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" );
+ + " gene_tree.xml tree_of_life.xml out.xml" );
System.out.println();
}
git://source.jalview.org / jalview.git / blobdiff