X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=7d7632cd043c5efae3270d71d9052364e4b91c72;hb=5c494e04b1cb40db2f1ac11c9dd9f459c9fab7f5;hp=99f034e496c960f0525da07a01226e6e3b206bae;hpb=862ca59d36af9ccbed3ef284b497f9c04263ba97;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 99f034e..7d7632c 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -32,360 +32,148 @@ import java.io.FileWriter; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.HashMap; -import java.util.Vector; +import java.util.List; +import org.forester.datastructures.IntMatrix; import org.forester.io.parsers.phyloxml.PhyloXmlParser; 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.phylogeny.iterators.PreorderTreeIterator; -import org.forester.sdi.DistanceCalculator; -import org.forester.sdi.RIO; +import org.forester.rio.RIO; +import org.forester.rio.RIOException; import org.forester.sdi.SDIException; -import org.forester.sdi.SDIR; +import org.forester.util.CommandLineArguments; +import org.forester.util.EasyWriter; import org.forester.util.ForesterUtil; public class rio { - final static private String PRG_NAME = "RIO"; - final static private String PRG_VERSION = "2.03 ALPHA"; - final static private String PRG_DATE = "2010.01.15"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/"; - final static private boolean TIME = true; - final static private boolean VERBOSE = true; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_COST = false; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_DUPS = true; - // For method getDistances -- calculation of distances. - final static private boolean MINIMIZE_HEIGHT = true; - final static private int WARN_NO_ORTHOS_DEFAULT = 2; - final static private int - // How many sd away from mean to root. - WARN_MORE_THAN_ONE_ORTHO_DEFAULT = 2; - // How many sd away from mean to LCA of orthos. - final static private double THRESHOLD_ULTRA_PARALOGS_DEFAULT = 50; - // How many sd away from mean to LCA of orthos. - final static private double WARN_ONE_ORTHO_DEFAULT = 2; + final static private String PRG_NAME = "rio"; + final static private String PRG_VERSION = "3.00 beta 3"; + final static private String PRG_DATE = "2012.12.05"; + final static private String E_MAIL = "czmasek@burnham.org"; + final static private String WWW = "www.phylosoft.org/forester/"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String QUERY_OPTION = "q"; + final static private String SORT_OPTION = "s"; + final static private String OUTPUT_ULTRA_P_OPTION = "u"; + final static private String CUTOFF_ULTRA_P_OPTION = "cu"; + final static private String CUTOFF_ORTHO_OPTION = "co"; + final static private String TABLE_OUTPUT_OPTION = "t"; - // Factor between the two distances to their LCA - // (larger/smaller). - // Factor between the two distances to their LCA - // (larger/smaller). - /** - * Calculates the mean and standard deviation of all nodes of Phylogeny t - * which have a bootstrap values zero or more. Returns null in case of - * failure (e.g t has no bootstrap values, or just one). - *

- * - * @param t - * reference to a tree with bootstrap values - * @return Array of doubles, [0] is the mean, [1] the standard deviation - */ - private static double[] calculateMeanBoostrapValue( final Phylogeny t ) { - double b = 0; - int n = 0; - long sum = 0; - double x = 0.0, mean = 0.0; - final double[] da = new double[ 2 ]; - final Vector bv = new Vector(); - PhylogenyNode node = null; - PreorderTreeIterator i = null; - i = new PreorderTreeIterator( t ); - // Calculates the mean. - while ( i.hasNext() ) { - node = i.next(); - if ( !( ( node.getParent() != null ) && node.getParent().isRoot() - && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode1() ) > 0 ) - && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode2() ) > 0 ) && ( node - .getParent().getChildNode2() == node ) ) ) { - b = PhylogenyMethods.getConfidenceValue( node ); - if ( b > 0 ) { - sum += b; - bv.addElement( new Double( b ) ); - n++; - } - } - // i.next(); + public static void main( final String[] args ) { + ForesterUtil.printProgramInformation( PRG_NAME, + "resampled inference of orthologs", + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + CommandLineArguments cla = null; + try { + cla = new CommandLineArguments( args ); } - if ( n < 2 ) { - return null; + catch ( final Exception e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); } - mean = ( double ) sum / n; - // Calculates the standard deviation. - sum = 0; - for( int j = 0; j < n; ++j ) { - b = ( bv.elementAt( j ) ).intValue(); - x = b - mean; - sum += ( x * x ); + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { + printHelp(); } - da[ 0 ] = mean; - da[ 1 ] = java.lang.Math.sqrt( sum / ( n - 1.0 ) ); - return da; - } - - private final static void errorInCommandLine() { - System.out.println( "\nrio: Error in command line.\n" ); - printHelp(); - System.exit( -1 ); - } - - // Uses DistanceCalculator to calculate distances. - private final static StringBuffer getDistances( final File tree_file_for_dist_val, - final File outfile, - final Phylogeny species_tree, - final String seq_name, - final ArrayList al_ortholog_names_for_dc, - final HashMap ortholog_hashmap, - final HashMap super_ortholog_hashmap, - final int warn_more_than_one_ortho, - final int warn_no_orthos, - final double warn_one_ortho, - final int bootstraps, - final double t_orthologs_dc ) throws IOException, SDIException { - Phylogeny consensus_tree = null; - Phylogeny - // to be a consensus tree. - assigned_cons_tree = null; - final SDIR sdiunrooted = new SDIR(); - final ArrayList al_ortholog_nodes = new ArrayList(); - double m = 0.0; - double sd = 0.0; - double d = 0.0; - int n = 0; - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - consensus_tree = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ]; - PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, consensus_tree ); - assigned_cons_tree = sdiunrooted.infer( consensus_tree, - species_tree, - rio.MINIMIZE_COST, - rio.MINIMIZE_DUPS, - rio.MINIMIZE_HEIGHT, - true, - 1 )[ 0 ]; - final DistanceCalculator dc = new DistanceCalculator(); - final StringBuffer sb = new StringBuffer(); - sb.append( "Given the threshold for distance calculations (" + ForesterUtil.roundToInt( t_orthologs_dc ) - + "): " ); - // No orthologs. - if ( al_ortholog_names_for_dc.size() == 0 ) { - dc.setTree( assigned_cons_tree ); - // Remark. Calculation of mean and sd _does_ include the node - // with seq_name. - m = dc.getMean(); - sd = dc.getStandardDeviation(); - d = dc.getDistanceToRoot( seq_name ); - n = dc.getN(); - sb.append( "No sequence is considered orthologous to query." - + "\ndistance of query to root = " + ForesterUtil.FORMATTER_06.format( d ) - + "\nmean of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( m ) - + "\nsd of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( sd ) - + "\nn (sum of sequences in alignment plus query) = " + n ); - if ( !( ( ( m - ( warn_no_orthos * sd ) ) < d ) && ( ( m + ( warn_no_orthos * sd ) ) > d ) ) ) { - sb.append( "\nWARNING: distance of query to root is outside of mean+/-" + warn_no_orthos + "*sd!" ); - } + if ( ( args.length < 2 ) || ( args.length > 10 ) ) { + System.out.println(); + System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" ); + System.out.println(); + printHelp(); } - // One ortholog. - else if ( al_ortholog_names_for_dc.size() == 1 ) { - final String name_of_ortholog = al_ortholog_names_for_dc.get( 0 ); - al_ortholog_nodes.add( assigned_cons_tree.getNode( name_of_ortholog ) ); - al_ortholog_nodes.add( assigned_cons_tree.getNode( seq_name ) ); - dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes ); - // Remark. Calculation of mean _does_ include the node - // with seq_name. - d = dc.getDistanceToLCA( seq_name ); - final double d_o = dc.getDistanceToLCA( name_of_ortholog ); - sb.append( "One sequence is considered orthologous to query." + "\nLCA is LCA of query and its ortholog." - + "\ndistance of query to LCA = " + ForesterUtil.FORMATTER_06.format( d ) - + "\ndistance of ortholog to LCA = " + ForesterUtil.FORMATTER_06.format( d_o ) ); - if ( ( d_o > 0.0 ) - && ( d > 0.0 ) - && ( ( ( d_o >= d ) && ( ( d_o / d ) > warn_one_ortho ) ) || ( ( d_o < d ) && ( ( d / d_o ) > warn_one_ortho ) ) ) ) { - sb.append( "\nWARNING: Ratio of distances to LCA is greater than " + warn_one_ortho + "!" ); - } - else if ( ( ( d_o == 0.0 ) || ( d == 0.0 ) ) && ( ( d_o != 0.0 ) || ( d != 0.0 ) ) ) { - sb.append( "\nWARNING: Ratio could not be calculated, " + " one distance is 0.0!" ); - } + final List allowed_options = new ArrayList(); + allowed_options.add( QUERY_OPTION ); + allowed_options.add( SORT_OPTION ); + allowed_options.add( CUTOFF_ULTRA_P_OPTION ); + allowed_options.add( CUTOFF_ORTHO_OPTION ); + allowed_options.add( TABLE_OUTPUT_OPTION ); + allowed_options.add( OUTPUT_ULTRA_P_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); } - // More than one ortholog. - else { - for( int i = 0; i < al_ortholog_names_for_dc.size(); ++i ) { - al_ortholog_nodes.add( assigned_cons_tree.getNodeViaSequenceName( al_ortholog_names_for_dc.get( i ) ) ); - } - al_ortholog_nodes.add( assigned_cons_tree.getNodesViaSequenceName( seq_name ).get( 0 ) ); - dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes ); - // Remark. Calculation of mean and sd _does_ include the node - // with seq_name. - m = dc.getMean(); - sd = dc.getStandardDeviation(); - d = dc.getDistanceToLCA( seq_name ); - n = dc.getN(); - sb.append( "More than one sequence is considered orthologous to query." - + "\nLCA is LCA of query and its orthologs." - + "\ndistance of query to LCA = " - + ForesterUtil.FORMATTER_06.format( d ) - + "\nmean of distances (for query and its orthologs) to LCA = " - + ForesterUtil.FORMATTER_06.format( m ) - + "\nsd of distances (for query and its orthologs) to LCA = " - + ForesterUtil.FORMATTER_06.format( sd ) - + "\nn (sum of orthologs plus query) = " + n ); - if ( !( ( ( m - ( warn_more_than_one_ortho * sd ) ) < d ) && ( ( m + ( warn_more_than_one_ortho * sd ) ) > d ) ) ) { - sb.append( "\n!WARNING: distance of query to LCA is outside of mean+/-" + warn_more_than_one_ortho - + "*sd!" ); + final File gene_trees_file = cla.getFile( 0 ); + final File species_tree_file = cla.getFile( 1 ); + File outfile = null; + if ( cla.getNumberOfNames() > 2 ) { + outfile = cla.getFile( 2 ); + } + ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file ); + ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file ); + if ( ( outfile != null ) && outfile.exists() ) { + ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" ); + } + String query = null; + if ( cla.isOptionSet( QUERY_OPTION ) ) { + query = cla.getOptionValue( QUERY_OPTION ); + } + File table_outfile = null; + if ( cla.isOptionSet( TABLE_OUTPUT_OPTION ) ) { + table_outfile = new File( cla.getOptionValue( TABLE_OUTPUT_OPTION ) ); + if ( table_outfile.exists() ) { + ForesterUtil.fatalError( PRG_NAME, "[" + table_outfile + "] already exists" ); } } - return sb; - } - - public static void main( final String[] args ) { - ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW ); - File species_tree_file = null; - File multiple_trees_file = null; - File outfile = null; - File distance_matrix_file = null; - File tree_file_for_dist_val = null; - File tree_file_for_avg_bs = null; - String seq_name = ""; - String arg = ""; boolean output_ultraparalogs = false; - ArrayList orthologs_al_for_dc = null; - double t_orthologs = 0.0; - double t_sn = 0.0; - double t_orthologs_dc = 0.0; - double[] bs_mean_sd = null; - int sort = 13; - Phylogeny species_tree = null; - RIO rio_instance = null; - PrintWriter out = null; - long time = 0; - int warn_no_orthos = WARN_NO_ORTHOS_DEFAULT; - int warn_more_than_one_ortho = WARN_MORE_THAN_ONE_ORTHO_DEFAULT; - double warn_one_ortho = WARN_ONE_ORTHO_DEFAULT; - double threshold_ultra_paralogs = THRESHOLD_ULTRA_PARALOGS_DEFAULT; - if ( args.length < 2 ) { - printHelp(); - System.exit( 0 ); + if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) { + output_ultraparalogs = true; } - else if ( ( args.length < 3 ) || ( args.length > 18 ) ) { - errorInCommandLine(); - } - for( int i = 0; i < args.length; ++i ) { - if ( args[ i ].trim().charAt( 0 ) != 'p' ) { - if ( args[ i ].trim().length() < 3 ) { - errorInCommandLine(); + double cutoff_for_orthologs = 50; + double cutoff_for_ultra_paralogs = 50; + int sort = 1; + try { + if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) { + cutoff_for_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION ); + if ( query == null ) { + ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" ); } - else { - arg = args[ i ].trim().substring( 2 ); + if ( outfile == null ) { + ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); } } - try { - switch ( args[ i ].trim().charAt( 0 ) ) { - case 'M': - multiple_trees_file = new File( arg ); - break; - case 'N': - seq_name = arg; - break; - case 'S': - species_tree_file = new File( arg ); - break; - case 'O': - outfile = new File( arg ); - break; - case 'D': - distance_matrix_file = new File( arg ); - break; - case 'T': - tree_file_for_dist_val = new File( arg ); - break; - case 't': - tree_file_for_avg_bs = new File( arg ); - break; - case 'p': - output_ultraparalogs = true; - break; - case 'P': - sort = Integer.parseInt( arg ); - if ( ( sort < 0 ) || ( sort > 17 ) ) { - errorInCommandLine(); - } - break; - case 'L': - t_orthologs = Double.parseDouble( arg ); - break; - case 'B': - t_sn = Double.parseDouble( arg ); - break; - case 'U': - t_orthologs_dc = Double.parseDouble( arg ); - break; - case 'v': - threshold_ultra_paralogs = Double.parseDouble( arg ); - break; - case 'X': - warn_more_than_one_ortho = Integer.parseInt( arg ); - break; - case 'Y': - warn_no_orthos = Integer.parseInt( arg ); - break; - case 'Z': - warn_one_ortho = Double.parseDouble( arg ); - break; - default: - errorInCommandLine(); - } + if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) { + cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION ); + output_ultraparalogs = true; } - catch ( final Exception e ) { - errorInCommandLine(); + if ( cla.isOptionSet( SORT_OPTION ) ) { + sort = cla.getOptionValueAsInt( SORT_OPTION ); } } - if ( ( seq_name == "" ) || ( species_tree_file == null ) || ( multiple_trees_file == null ) - || ( outfile == null ) ) { - errorInCommandLine(); + catch ( final Exception e ) { + ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() ); } - if ( ( sort < 0 ) || ( sort > 17 ) ) { - errorInCommandLine(); + if ( ( cutoff_for_orthologs < 0 ) || ( cutoff_for_ultra_paralogs < 0 ) || ( sort < 0 ) || ( sort > 2 ) ) { + ForesterUtil.fatalError( PRG_NAME, "numberical option out of range, type \"rio -h\" for help" ); } - if ( ( sort > 2 ) && ( distance_matrix_file == null ) ) { - errorInCommandLine(); + if ( ( ( query == null ) && ( ( outfile != null ) || output_ultraparalogs ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" ); } - if ( VERBOSE ) { - System.out.println( "\nMultiple trees file: " + multiple_trees_file ); - System.out.println( "Seq name: " + seq_name ); - System.out.println( "Species tree file: " + species_tree_file ); - System.out.println( "Outfile: " + outfile ); - if ( distance_matrix_file != null ) { - System.out.println( "Distance matrix file: " + distance_matrix_file ); - } - if ( tree_file_for_dist_val != null ) { - if ( tree_file_for_avg_bs == null ) { - System.out.println( "Phy to read dists and calc mean support from: " + tree_file_for_dist_val ); - } - else { - System.out.println( "Phylogeny to read dist values from: " + tree_file_for_dist_val ); - } - } - if ( tree_file_for_avg_bs != null ) { - System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs ); - } - System.out.println( "Sort: " + sort ); - System.out.println( "Threshold orthologs: " + t_orthologs ); - System.out.println( "Threshold subtree neighborings: " + t_sn ); - System.out.println( "Threshold orthologs for distance calc.: " + t_orthologs_dc ); + if ( ( output_ultraparalogs && ( outfile == null ) ) || ( ( query != null ) && ( outfile == null ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); + } + long time = 0; + System.out.println( "Gene trees : " + gene_trees_file ); + System.out.println( "Species tree : " + species_tree_file ); + if ( query != null ) { + System.out.println( "Query : " + query ); + System.out.println( "Outfile : " + outfile ); + System.out.println( "Sort : " + sort ); + System.out.println( "Cutoff for orthologs : " + cutoff_for_orthologs ); if ( output_ultraparalogs ) { - System.out.println( "Threshold ultra paralogs: " + threshold_ultra_paralogs ); + System.out.println( "Cutoff for ultra paralogs : " + cutoff_for_ultra_paralogs ); } - System.out.println( "More than one ortholog sd diff: " + warn_more_than_one_ortho ); - System.out.println( "No orthologs sd diff: " + warn_no_orthos ); - System.out.println( "One ortholog factor : " + warn_one_ortho + "\n" ); } - if ( TIME && VERBOSE ) { - time = System.currentTimeMillis(); + if ( table_outfile != null ) { + System.out.println( "Table output : " + table_outfile ); } + System.out.println(); + time = System.currentTimeMillis(); + Phylogeny species_tree = null; try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; @@ -395,109 +183,127 @@ public class rio { System.exit( -1 ); } if ( !species_tree.isRooted() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" ); - System.exit( -1 ); + ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" ); } if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" ); - System.exit( -1 ); + ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary" ); } - rio_instance = new RIO(); - final StringBuffer output = new StringBuffer(); try { - if ( distance_matrix_file != null ) { - rio_instance.readDistanceMatrix( distance_matrix_file ); + final RIO rio; + if ( ForesterUtil.isEmpty( query ) ) { + rio = new RIO( gene_trees_file, species_tree ); } - rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name ); - output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs, t_sn ) ); - if ( tree_file_for_dist_val != null ) { - orthologs_al_for_dc = rio_instance.inferredOrthologsToArrayList( seq_name, t_orthologs_dc ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - if ( tree_file_for_avg_bs != null ) { - final Phylogeny p = factory.create( tree_file_for_avg_bs, new PhyloXmlParser() )[ 0 ]; - bs_mean_sd = calculateMeanBoostrapValue( p ); - } - else { - final Phylogeny p = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ]; - bs_mean_sd = calculateMeanBoostrapValue( p ); - } - if ( ( bs_mean_sd != null ) && ( bs_mean_sd.length == 2 ) ) { - final double bs_mean = bs_mean_sd[ 0 ]; - final double bs_sd = bs_mean_sd[ 1 ]; - output.append( "\n\nMean bootstrap value of consensus tree (sd): " - + ForesterUtil.roundToInt( ( bs_mean * 100.0 ) / rio_instance.getBootstraps() ) + "% (+/-" - + ForesterUtil.roundToInt( ( bs_sd * 100.0 ) / rio_instance.getBootstraps() ) + "%)\n" ); + else { + rio = new RIO( gene_trees_file, species_tree, query ); + } + if ( outfile != null ) { + final StringBuilder output = new StringBuilder(); + output.append( rio.inferredOrthologsToString( query, sort, cutoff_for_orthologs ) ); + if ( output_ultraparalogs ) { + output.append( "\n\nUltra paralogs:\n" ); + output.append( rio.inferredUltraParalogsToString( query, cutoff_for_ultra_paralogs ) ); } - output.append( "\n\nDistance values:\n" ); - output.append( getDistances( tree_file_for_dist_val, - outfile, - species_tree, - seq_name, - orthologs_al_for_dc, - rio_instance.getInferredOrthologs( seq_name ), - rio_instance.getInferredSuperOrthologs( seq_name ), - warn_more_than_one_ortho, - warn_no_orthos, - warn_one_ortho, - rio_instance.getBootstraps(), - t_orthologs_dc ) ); + output.append( "\n\nSort priority: " + RIO.getOrder( sort ) ); + output.append( "\nExt nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() ); + output.append( "\nSamples : " + rio.getNumberOfSamples() + "\n" ); + final PrintWriter out = new PrintWriter( new FileWriter( outfile ), true ); + out.println( output ); + out.close(); } - if ( output_ultraparalogs ) { - output.append( "\n\nUltra paralogs:\n" ); - output.append( rio_instance - .inferredUltraParalogsToString( seq_name, sort > 2, threshold_ultra_paralogs ) ); + if ( table_outfile != null ) { + tableOutput( table_outfile, rio ); } - rio_instance.inferredOrthologTableToFile( new File( "table" ) ); - output.append( "\n\nSort priority: " + RIO.getOrder( sort ) ); - output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() ); - output.append( "\nSamples : " + rio_instance.getBootstraps() + "\n" ); - out = new PrintWriter( new FileWriter( outfile ), true ); + } + catch ( final RIOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + catch ( final SDIException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); } catch ( final Exception e ) { - ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() ); - e.printStackTrace(); - System.exit( -1 ); + ForesterUtil.unexpectedFatalError( PRG_NAME, e ); } - out.println( output ); - out.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); - if ( TIME && VERBOSE ) { - time = System.currentTimeMillis() - time; - ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); + if ( outfile != null ) { + ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); } - ForesterUtil.programMessage( PRG_NAME, "OK." ); + time = System.currentTimeMillis() - time; + ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); + ForesterUtil.programMessage( PRG_NAME, "OK" ); System.exit( 0 ); } + private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException, RIOException { + final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees() ); + writeTable( table_outfile, rio, m ); + } + + private static void writeTable( final File table_outfile, final RIO rio, final IntMatrix m ) throws IOException { + final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile ); + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" ); + df.setDecimalSeparatorAlwaysShown( false ); + for( int i = 0; i < m.size(); ++i ) { + w.print( "\t" ); + w.print( m.getLabel( i ) ); + } + w.println(); + for( int x = 0; x < m.size(); ++x ) { + w.print( m.getLabel( x ) ); + for( int y = 0; y < m.size(); ++y ) { + w.print( "\t" ); + if ( x == y ) { + if ( m.get( x, y ) != rio.getNumberOfSamples() ) { + ForesterUtil.unexpectedFatalError( PRG_NAME, "diagonal value is off" ); + } + w.print( "-" ); + } + else { + w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getNumberOfSamples() ) ); + } + } + w.println(); + } + w.close(); + ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" ); + } + private final static void printHelp() { - System.out.println( "M= (String) Multiple gene tree file (mandatory)" ); - System.out.println( "N= (String) Query sequence name (mandatory)" ); - System.out.println( "S= (String) Species tree file (mandatory)" ); - System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" ); - System.out.println( "D= (String) Distance matrix file for pairwise distances" ); - System.out.println( "T= (String) Phylogeny file for distances of query to LCA" ); - System.out.println( " of orthologs and for mean bootstrap value (if t= is not used)," ); - System.out.println( " must be binary )" ); - System.out.println( "t= (String) Phylogeny file for mean bootstrap value (if this option is used," ); - System.out.println( " the mean bootstrap value is not calculated from the tree read in" ); - System.out.println( " with T=), not necessary binary" ); - System.out.println( "p To output ultra paralogs" ); - System.out.println( "P= (int) Sort priority" ); - System.out.println( "L= (double) Threshold orthologs for output" ); - System.out.println( "U= (double) Threshold orthologs for distance calculation" ); - System.out.println( "X= (int) More than one ortholog: " ); - System.out.println( " numbers of sd the dist. to LCA has to differ from mean to generate a warning" ); - System.out.println( "Y= (int) No orthologs:" ); - System.out.println( " Numbers of sd the dist to root has to differ from mean to generate a warning" ); - System.out.println( "Z= (double) One ortholog:" ); - System.out.println( " threshold for factor between the two distances to their LCA (larger/smaller)" ); - System.out.println( " to generate a warning" ); + System.out.println( "Usage" ); System.out.println(); - System.out.println( " Sort priority (\"P=\"):" ); - System.out.println( RIO.getOrderHelp().toString() ); + System.out.println( PRG_NAME + " [options] [outfile]" ); + System.out.println(); + System.out.println( " Options" ); + System.out.println( " -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" ); + System.out.println( " -" + TABLE_OUTPUT_OPTION + + " : file-name for output table of all vs. all ortholgy support" ); + System.out.println( " -" + QUERY_OPTION + + " : name for query (sequence/node), if this is used, [outfile] is required as well" ); + System.out.println( " -" + SORT_OPTION + " : sort (default: 1)" ); + System.out.println( " -" + OUTPUT_ULTRA_P_OPTION + + " : to output ultra-paralogs (species specific expansions/paralogs)" ); + System.out.println( " -" + CUTOFF_ULTRA_P_OPTION + " : cutoff for ultra-paralog output (default: 50)" ); + System.out.println(); + System.out.println( " Note" ); + System.out.println( " Either output of all vs. all ortholgy support with -t= and/or output for" ); + System.out.println( " one query sequence with -q= and a [outfile] are required." ); System.out.println(); + System.out.println( " Sort" ); + System.out.println( RIO.getOrderHelp().toString() ); + System.out.println( " Formats" ); + System.out.println( " The species tree is expected to be in phyloXML format." ); System.out - .println( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=out\"" ); + .println( " The gene trees ideally are in phyloXML as well, but can also be in New Hamphshire (Newick)" ); + System.out.println( " or Nexus format as long as species information can be extracted from the gene names" ); + System.out.println( " (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." ); + System.out.println(); + System.out.println( " Examples" ); + System.out.println( " \"rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60\"" ); + System.out.println( " \"rio gene_trees.nh species.xml -t=outtable\"" ); System.out.println(); + System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" ); + System.out.println(); + System.exit( -1 ); } }