X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=4c5d0cd84bdd40d503c3a7b9f5bee9bcab3c577b;hb=a1faf8469197d44197c70d2eeb529f22e8e396b4;hp=e97b504fb40f85d2a1a26fcbb5d478dfe6a5c0c4;hpb=f95ddfc23b184985166c2838f452c20b1a2c8307;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index e97b504..4c5d0cd 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -27,89 +27,109 @@ package org.forester.application; import java.io.File; import java.io.IOException; +import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Date; import java.util.List; - import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nhx.NHXParser; +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.SDI.TaxonomyComparisonBase; import org.forester.sdi.SDIse; +import org.forester.sdi.SdiException; 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"; + private enum BASE_ALGORITHM { + GSDI, SDI + } + 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 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_SUFFIX = "_gsdi_out.xml"; + final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt"; + 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 PRG_NAME = "gsdi"; + final static private String PRG_VERSION = "0.901"; + 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"; 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 ); - } - 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 ); + 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( 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 allowed_options = new ArrayList(); + allowed_options.add( gsdi.SDI_OPTION ); + 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 ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options ); + } + execute( cla ); } - final List allowed_options = new ArrayList(); - 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 ); + catch ( final IOException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() ); } - boolean use_sdise = false; - boolean strip = false; + } + + private static void execute( final CommandLineArguments cla ) throws IOException { + BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI; boolean most_parsimonous_duplication_model = false; boolean species_tree_in_phyloxml = true; - if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) { - strip = true; - } + boolean allow_stripping_of_gene_tree = false; if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) { - use_sdise = true; + base_algorithm = BASE_ALGORITHM.SDI; } if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { - if ( use_sdise ) { + if ( base_algorithm != BASE_ALGORITHM.GSDI ) { ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" ); } most_parsimonous_duplication_model = true; @@ -117,11 +137,19 @@ public final class gsdi { if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) { species_tree_in_phyloxml = false; } + if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { + if ( base_algorithm != BASE_ALGORITHM.GSDI ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" ); + } + allow_stripping_of_gene_tree = true; + } 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; + EasyWriter log_writer = null; try { gene_tree_file = cla.getFile( 0 ); species_tree_file = cla.getFile( 1 ); @@ -129,8 +157,9 @@ public final class gsdi { out_file = cla.getFile( 2 ); } else { - out_file = new File( gsdi.DEFAULT_OUTFILE ); + out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX ); } + 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() ); @@ -144,24 +173,15 @@ public final class gsdi { 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 ) ); + } try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - if ( species_tree_in_phyloxml ) { - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; - } - 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 ); - - } + 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() ); } - try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ]; @@ -170,15 +190,78 @@ public final class gsdi { ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() ); } + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + if ( species_tree_in_phyloxml ) { + species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; + } + else { + final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true ); + 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 = GSDI.determineTaxonomyComparisonBase( gene_tree ); + switch ( comp_base ) { + case SCIENTIFIC_NAME: + try { + PhylogenyMethods + .transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, + "Failed to transfer general node name to scientific name, in [" + + species_tree_file + "]: " + e.getMessage() ); + } + break; + case CODE: + try { + PhylogenyMethods + .transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, + "Failed to transfer general node name to taxonomy code, in [" + + species_tree_file + "]: " + e.getMessage() ); + } + break; + case ID: + try { + PhylogenyMethods.transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID, + true ); + } + catch ( final PhyloXmlDataFormatException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, + "Failed to transfer general node name to taxonomy id, in [" + + species_tree_file + "]: " + e.getMessage() ); + } + break; + default: + ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" ); + } + } + } + catch ( final IOException e ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: " + + e.getMessage() ); + } 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" ); + log_writer.println( "User Error: gene tree is not completely binary" ); + log_writer.close(); + ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" ); } - if ( use_sdise ) { + if ( base_algorithm != BASE_ALGORITHM.GSDI ) { if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file - + "\") is not completely binary" ); + log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" ); + log_writer.close(); + ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" ); } } // For timing. @@ -193,29 +276,61 @@ public final class gsdi { // Helper.randomizeSpecies( 1, 8192, gene_tree ); // Helper.intervalNumberSpecies( gene_tree, 4096 ); // Helper.numberSpeciesInDescOrder( gene_tree ); + 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( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) ); + log_writer.println( "Gene tree file: " + gene_tree_file.getCanonicalPath() ); + log_writer.println( "Gene tree name: " + + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) ); + log_writer.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(); - System.out.println( "Strip species tree: " + strip ); SDI sdi = null; final long start_time = new Date().getTime(); try { - if ( use_sdise ) { + if ( base_algorithm == BASE_ALGORITHM.GSDI ) { System.out.println(); - System.out.println( "Using SDIse algorithm" ); - sdi = new SDIse( gene_tree, species_tree ); + 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.write( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree ); + log_writer.flush(); + sdi = new GSDI( gene_tree, + species_tree, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + true ); } 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 ); + System.out.println( "Using SDIse algorithm" ); + log_writer.println( "Using SDIse algorithm" ); + log_writer.flush(); + sdi = new SDIse( gene_tree, species_tree ); } } - catch ( final Exception e ) { + catch ( final SdiException e ) { + log_writer.println( "User Error: " + e.getLocalizedMessage() ); + log_writer.close(); ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); } + catch ( final IOException e ) { + log_writer.println( "Error: " + e ); + log_writer.close(); + ForesterUtil.fatalError( PRG_NAME, e.toString() ); + } + catch ( final Exception e ) { + log_writer.println( "Error: " + e ); + log_writer.close(); + e.printStackTrace(); + System.exit( -1 ); + } System.out.println(); 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" ); try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toPhyloXML( out_file, gene_tree, 0 ); @@ -224,21 +339,56 @@ public final class gsdi { ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() ); } System.out.println(); - System.out.println( "Successfully wrote resulting gene tree to: " + out_file ); + System.out.println( "Wrote resulting gene tree to: " + out_file ); System.out.println(); - if ( use_sdise ) { + log_writer.println( "Wrote resulting gene tree to: " + out_file ); + if ( base_algorithm == BASE_ALGORITHM.SDI ) { sdi.computeMappingCostL(); System.out.println( "Mapping cost : " + sdi.computeMappingCostL() ); + log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() ); } 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() ); - } - if ( !use_sdise ) { - System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() ); + log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() ); + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) { + final GSDI gsdi = ( GSDI ) sdi; + final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED ); + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( PRG_NAME, + "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() ); + } + System.out.println(); + System.out.println( "Wrote used species tree to: " + species_tree_used_file ); + System.out.println(); + log_writer.println( "Wrote used species tree to: " + species_tree_used_file ); + if ( !most_parsimonous_duplication_model ) { + final int duplications = gsdi.getSpeciationOrDuplicationEventsSum(); + System.out.println( "Number of potential duplications: " + duplications ); + log_writer.println( "Number of potential duplications: " + duplications ); + } + final int spec = gsdi.getSpeciationsSum(); + System.out.println( "Number of speciations : " + spec ); + log_writer.println( "Number of speciations : " + spec ); + for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) { + System.out.println( n.toString() ); + } } System.out.println(); + log_writer.close(); + // some stat on gene tree: + // filename, name + // number of external nodes, strppided nodes + // some stats on sepcies tree, external nodes, + // filename, name + // internal nodes + // how many of which are polytomies + //wrote log file to + // if ( allow_stripping_of_gene_tree ) { + // stripped x nodes, y external nodes remain + // } } private static void print_help() { @@ -246,22 +396,27 @@ public final class gsdi { + " [-options] [outfile]" ); 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.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + ); + System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed 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( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); 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( " In phyloXML format (unless option -" + + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + + " is used, in which case the species matching between gene tree and species tree must be via scientific name), 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(); + System.out.println( "Example:" ); + // System.out.println( "gsdi + // System.out.println(); System.out.println( "Note -- GSDI algorithm is under development" ); System.out.println(); }