X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=7e2d51418d973c67c252ab7994980c42379c1d20;hb=90e29ddfe15f6c44f3e3ba419a67c3e267e279bd;hp=71bd6d9a2608485a55293be74f8e62aae8719cfa;hpb=03001eb3d298d53e97e4194787fa21bcbc43c5d8;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 71bd6d9..7e2d514 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -21,7 +21,7 @@ // 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; @@ -36,11 +36,9 @@ 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; +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; @@ -53,7 +51,6 @@ import org.forester.sdi.GSDIR; 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; @@ -66,17 +63,18 @@ public final class gsdi { 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 { @@ -111,6 +109,7 @@ public final class gsdi { 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 ); @@ -141,6 +140,10 @@ public final class gsdi { } 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; @@ -177,71 +180,30 @@ public final class gsdi { } 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 ); } @@ -278,16 +240,17 @@ public final class gsdi { + ( 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 ); @@ -299,10 +262,11 @@ public final class gsdi { 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 ) { @@ -311,6 +275,9 @@ public final class gsdi { 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 ); @@ -321,18 +288,10 @@ public final class gsdi { + "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 ); @@ -405,30 +364,6 @@ public final class gsdi { log_writer.close(); } - private static void writeToRemappedFile( final File out_file, - final SortedSet 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 ss = new TreeSet(); - 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(); @@ -443,30 +378,6 @@ public final class gsdi { ForesterUtil.fatalError( gsdi.PRG_NAME, msg ); } - private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) - throws IOException { - final SortedMap sm = new TreeMap(); - 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 static void print_help() { System.out.println( "Usage: " + gsdi.PRG_NAME + " [-options] " ); @@ -482,6 +393,8 @@ public final class gsdi { + ": 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" ); @@ -493,4 +406,52 @@ public final class gsdi { + " 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 ss = new TreeSet(); + 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 sm = new TreeMap(); + 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 static void writeToRemappedFile( final File out_file, + final SortedSet 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() ); + } }