X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=fd0127e432cd7cf73537285f65341a7933db438e;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=5564763580233c619c0fe7f3e127f640448b9834;hpb=ecc5f5b302af9d2708b2b0077c9a78bb195eb02e;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 5564763..fd0127e 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -23,42 +23,53 @@ // 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.io.File; -import java.io.FileWriter; import java.io.IOException; -import java.io.PrintWriter; +import java.math.RoundingMode; import java.util.ArrayList; import java.util.List; import org.forester.datastructures.IntMatrix; +import org.forester.io.parsers.IteratingPhylogenyParser; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; 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.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.sdi.RIO; +import org.forester.rio.RIO; +import org.forester.rio.RIO.REROOTING; +import org.forester.rio.RIOException; +import org.forester.sdi.SDIException; +import org.forester.sdi.SDIutil.ALGORITHM; +import org.forester.util.BasicDescriptiveStatistics; 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 = "3.00 beta 1"; - final static private String PRG_DATE = "2012.11.27"; - 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"; + final static private String PRG_NAME = "rio"; + final static private String PRG_VERSION = "4.000 beta 10"; + final static private String PRG_DATE = "140211"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String GT_FIRST = "f"; + final static private String GT_LAST = "l"; + final static private String REROOTING_OPT = "r"; + final static private String OUTGROUP = "o"; + final static private String RETURN_SPECIES_TREE = "s"; + final static private String RETURN_BEST_GENE_TREE = "g"; + final static private String USE_SDIR = "b"; + final static private String TRANSFER_TAXONOMY_OPTION = "t"; public static void main( final String[] args ) { ForesterUtil.printProgramInformation( PRG_NAME, @@ -73,167 +84,415 @@ public class rio { cla = new CommandLineArguments( args ); } catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( e.getMessage() ); } if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { printHelp(); } - if ( ( args.length < 2 ) || ( args.length > 10 ) ) { + if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) { System.out.println(); - System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" ); + System.out.println( "error: incorrect number of arguments" ); System.out.println(); printHelp(); } 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 ); + allowed_options.add( GT_FIRST ); + allowed_options.add( GT_LAST ); + allowed_options.add( REROOTING_OPT ); + allowed_options.add( OUTGROUP ); + allowed_options.add( USE_SDIR ); + allowed_options.add( RETURN_SPECIES_TREE ); + allowed_options.add( RETURN_BEST_GENE_TREE ); + allowed_options.add( TRANSFER_TAXONOMY_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); + ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options ); } 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 ); + final File orthology_outtable = cla.getFile( 2 ); + final File logfile; + if ( cla.getNumberOfNames() > 3 ) { + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); + } } - ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file ); - ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file ); - if ( outfile.exists() ) { - ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" ); + else { + logfile = null; } - String query = null; - if ( cla.isOptionSet( QUERY_OPTION ) ) { - query = cla.getOptionValue( QUERY_OPTION ); + boolean sdir = false; + if ( cla.isOptionSet( USE_SDIR ) ) { + if ( cla.isOptionHasAValue( USE_SDIR ) ) { + ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR ); + } + sdir = true; + if ( logfile != null ) { + ForesterUtil.fatalError( "no logfile output for SDIR algorithm" ); + } } - 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" ); + String outgroup = null; + if ( cla.isOptionSet( OUTGROUP ) ) { + if ( !cla.isOptionHasAValue( OUTGROUP ) ) { + ForesterUtil.fatalError( "no value for -" + OUTGROUP ); } + if ( sdir ) { + ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" ); + } + outgroup = cla.getOptionValueAsCleanString( OUTGROUP ); } - boolean output_ultraparalogs = false; - if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) { - output_ultraparalogs = true; + REROOTING rerooting = REROOTING.BY_ALGORITHM; + if ( cla.isOptionSet( REROOTING_OPT ) ) { + if ( !cla.isOptionHasAValue( REROOTING_OPT ) ) { + ForesterUtil.fatalError( "no value for -" + REROOTING_OPT ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" ); + } + final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase(); + if ( rerooting_str.equals( "none" ) ) { + rerooting = REROOTING.NONE; + } + else if ( rerooting_str.equals( "midpoint" ) ) { + rerooting = REROOTING.MIDPOINT; + } + else if ( rerooting_str.equals( "outgroup" ) ) { + rerooting = REROOTING.OUTGROUP; + } + else { + ForesterUtil + .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); + } } - double cutoff_for_orthologs = 50; - double cutoff_for_ultra_paralogs = 50; - int sort = 2; - try { - if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) { - cutoff_for_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION ); + if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" ); + } + if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" ); + } + int gt_first = RIO.DEFAULT_RANGE; + int gt_last = RIO.DEFAULT_RANGE; + if ( cla.isOptionSet( GT_FIRST ) ) { + if ( !cla.isOptionHasAValue( GT_FIRST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_FIRST ); } - if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) { - cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION ); - if ( !output_ultraparalogs ) { - printHelp(); - } + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); } - if ( cla.isOptionSet( SORT_OPTION ) ) { - sort = cla.getOptionValueAsInt( SORT_OPTION ); + try { + gt_first = cla.getOptionValueAsInt( GT_FIRST ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" ); + } + if ( gt_first < 0 ) { + ForesterUtil.fatalError( "attempt to set index of first tree to analyze to: " + gt_first ); } } - catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() ); + if ( cla.isOptionSet( GT_LAST ) ) { + if ( !cla.isOptionHasAValue( GT_LAST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_LAST ); + } + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + try { + gt_last = cla.getOptionValueAsInt( GT_LAST ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" ); + } + if ( gt_last < 0 ) { + ForesterUtil.fatalError( "attempt to set index of last tree to analyze to: " + gt_last ); + } } - if ( ( cutoff_for_orthologs < 0 ) || ( cutoff_for_ultra_paralogs < 0 ) || ( sort < 0 ) || ( sort > 2 ) ) { - printHelp(); + if ( ( ( gt_last != RIO.DEFAULT_RANGE ) && ( gt_first != RIO.DEFAULT_RANGE ) ) && ( ( gt_last < gt_first ) ) ) { + ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to " + + gt_last ); } - if ( ( ( query == null ) && ( outfile != null ) ) || ( ( query != null ) && ( outfile == null ) ) ) { - printHelp(); + File return_species_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_SPECIES_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_SPECIES_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_SPECIES_TREE ); + } + final String s = cla.getOptionValueAsCleanString( RETURN_SPECIES_TREE ); + return_species_tree = new File( s ); + if ( return_species_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_species_tree + "\" already exists" ); + } } - if ( output_ultraparalogs && ( outfile == null ) ) { - printHelp(); + File return_gene_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_BEST_GENE_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_BEST_GENE_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_BEST_GENE_TREE ); + } + final String s = cla.getOptionValueAsCleanString( RETURN_BEST_GENE_TREE ); + return_gene_tree = new File( s ); + if ( return_gene_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_gene_tree + "\" already exists" ); + } + } + boolean transfer_taxonomy = false; + if ( !sdir && cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) { + if ( return_gene_tree == null ) { + ForesterUtil.fatalError( "no point in transferring taxonomy data without returning best gene tree" ); + } + transfer_taxonomy = true; + } + ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file ); + ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); + if ( orthology_outtable.exists() ) { + ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); } 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( "Cutoff for ultra paralogs : " + cutoff_for_ultra_paralogs ); + System.out.println( "All vs all orthology table: " + orthology_outtable ); + if ( logfile != null ) { + System.out.println( "Logfile : " + logfile ); + } + if ( gt_first != RIO.DEFAULT_RANGE ) { + System.out.println( "First gene tree to analyze: " + gt_first ); + } + if ( gt_last != RIO.DEFAULT_RANGE ) { + System.out.println( "Last gene tree to analyze : " + gt_last ); + } + String rerooting_str = ""; + switch ( rerooting ) { + case BY_ALGORITHM: { + rerooting_str = "by minimizing duplications"; + break; + } + case MIDPOINT: { + rerooting_str = "by midpoint method"; + break; + } + case OUTGROUP: { + rerooting_str = "by outgroup: " + outgroup; + break; + } + case NONE: { + rerooting_str = "none"; + break; } } - if ( table_outfile != null ) { - System.out.println( "Table output : " + table_outfile ); + System.out.println( "Re-rooting : " + rerooting_str ); + if ( !sdir ) { + System.out.println( "Non binary species tree : allowed" ); } - 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 ]; + else { + System.out.println( "Non binary species tree : disallowed" ); } - catch ( final Exception e ) { - e.printStackTrace(); - System.exit( -1 ); + if ( return_species_tree != null ) { + System.out.println( "Write used species tree to: " + return_species_tree ); + } + if ( return_gene_tree != null ) { + System.out.println( "Write best gene tree to : " + return_gene_tree ); + System.out.println( "Transfer taxonomic data : " + transfer_taxonomy ); } - if ( !species_tree.isRooted() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not rooted" ); - System.exit( -1 ); + time = System.currentTimeMillis(); + final ALGORITHM algorithm; + if ( sdir ) { + algorithm = ALGORITHM.SDIR; } - if ( !species_tree.isCompletelyBinary() ) { - ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not completely binary" ); - System.exit( -1 ); + else { + algorithm = ALGORITHM.GSDIR; } try { - RIO rio; - if ( ForesterUtil.isEmpty( query ) ) { - rio = new RIO( gene_trees_file, species_tree ); + final RIO rio; + boolean iterating = false; + final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true ); + if ( p instanceof PhyloXmlParser ) { + rio = RIO.executeAnalysis( gene_trees_file, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); } 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 ) ); + iterating = true; + if ( p instanceof NHXParser ) { + final NHXParser nhx = ( NHXParser ) p; + nhx.setReplaceUnderscores( false ); + nhx.setIgnoreQuotes( true ); + nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } - 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(); + else if ( p instanceof NexusPhylogeniesParser ) { + final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p; + nex.setReplaceUnderscores( false ); + nex.setIgnoreQuotes( true ); + nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); + } + else { + throw new RuntimeException( "unknown parser type: " + p ); + } + final IteratingPhylogenyParser ip = ( IteratingPhylogenyParser ) p; + ip.setSource( gene_trees_file ); + rio = RIO.executeAnalysis( ip, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); + } + if ( algorithm == ALGORITHM.GSDIR ) { + System.out.println( "Taxonomy linking based on : " + rio.getGSDIRtaxCompBase() ); + } + final IntMatrix m; + if ( iterating ) { + m = rio.getOrthologTable(); + } + else { + m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); + } + final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics(); + writeTable( orthology_outtable, stats.getN(), m ); + if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) { + writeLogFile( logfile, + rio, + species_tree_file, + gene_trees_file, + orthology_outtable, + PRG_NAME, + PRG_VERSION, + PRG_DATE, + ForesterUtil.getForesterLibraryInformation() ); } - if ( table_outfile != null ) { - tableOutput( table_outfile, rio ); + if ( return_species_tree != null ) { + writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" ); } + if ( return_gene_tree != null ) { + String tt = ""; + if ( transfer_taxonomy ) { + tt = "(with transferred taxonomic data) "; + } + writeTree( rio.getMinDuplicationsGeneTree(), + return_gene_tree, + "Wrote (one) minimal duplication gene tree " + tt + "to" ); + } + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" ); + System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: " + + df.format( stats.sampleStandardDeviation() ) + ") (" + + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + if ( stats.getN() > 3 ) { + System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " (" + + df.format( ( 100.0 * stats.median() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + } + System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " (" + + df.format( ( 100.0 * stats.getMin() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " (" + + df.format( ( 100.0 * stats.getMax() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + System.out.println( "Gene tree internal nodes : " + rio.getIntNodesOfAnalyzedGeneTrees() ); + System.out.println( "Gene tree external nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() ); + } + catch ( final RIOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final SDIException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final OutOfMemoryError e ) { + ForesterUtil.outOfMemoryError( e ); } catch ( final Exception e ) { - ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() ); - e.printStackTrace(); - System.exit( -1 ); + ForesterUtil.unexpectedFatalError( e ); } - if ( outfile != null ) { - ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); + catch ( final Error e ) { + ForesterUtil.unexpectedFatalError( e ); } time = System.currentTimeMillis() - time; - ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); - ForesterUtil.programMessage( PRG_NAME, "OK" ); + System.out.println( "Time: " + time + "ms" ); + System.out.println( "OK" ); System.exit( 0 ); } - private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException { - final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees() ); - writeTable( table_outfile, rio, m ); + private final static void printHelp() { + System.out.println( "Usage" ); + System.out.println(); + System.out + .println( PRG_NAME + + " [options] [logfile]" ); + System.out.println(); + System.out.println( " Options" ); + System.out.println( " -" + GT_FIRST + "= : first gene tree to analyze (0-based index)" ); + System.out.println( " -" + GT_LAST + "= : last gene tree to analyze (0-based index)" ); + System.out.println( " -" + REROOTING_OPT + + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); + System.out.println( " or 'outgroup' (default: by minizming duplications)" ); + System.out.println( " -" + OUTGROUP + + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); + System.out + .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); + System.out.println( " -" + RETURN_BEST_GENE_TREE + + "= : to write (one) minimal duplication gene tree to file" ); + System.out + .println( " -" + + TRANSFER_TAXONOMY_OPTION + + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" + + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); + System.out.println( " -" + USE_SDIR + + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); + System.out.println( " disallowed, as are most options)" ); + System.out.println(); + System.out.println( " Formats" ); + System.out + .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); + System.out + .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); + System.out + .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); + System.out.println( " in the species tree." ); + System.out.println(); + System.out.println( " Examples" ); + System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" ); + System.out.println(); + System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" ); + System.out.println(); + System.exit( -1 ); + } + + private static void writeLogFile( final File logfile, + final RIO rio, + final File species_tree_file, + final File gene_trees_file, + final File outtable, + final String prg_name, + final String prg_v, + final String prg_date, + final String f ) throws IOException { + final EasyWriter out = ForesterUtil.createEasyWriter( logfile ); + out.println( prg_name ); + out.println( "version : " + prg_v ); + out.println( "date : " + prg_date ); + out.println( "based on: " + f ); + out.println( "----------------------------------" ); + out.println( "Gene trees : " + gene_trees_file ); + out.println( "Species tree : " + species_tree_file ); + out.println( "All vs all orthology table : " + outtable ); + out.flush(); + out.println( rio.getLog().toString() ); + out.close(); + System.out.println( "Wrote log to \"" + logfile + "\"" ); } - private static void writeTable( final File table_outfile, final RIO rio, final IntMatrix m ) throws IOException { + private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m ) + throws IOException { final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile ); - final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" ); + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" ); df.setDecimalSeparatorAlwaysShown( false ); - w.print( "\t" ); + df.setRoundingMode( RoundingMode.HALF_UP ); for( int i = 0; i < m.size(); ++i ) { w.print( "\t" ); w.print( m.getLabel( i ) ); @@ -241,52 +500,27 @@ public class rio { w.println(); for( int x = 0; x < m.size(); ++x ) { w.print( m.getLabel( x ) ); - w.print( "\t" ); 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" ); + if ( m.get( x, y ) != gene_trees_analyzed ) { + ForesterUtil.unexpectedFatalError( "diagonal value is off" ); } w.print( "-" ); } else { - w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getNumberOfSamples() ) ); + w.print( df.format( ( ( double ) m.get( x, y ) ) / gene_trees_analyzed ) ); } } w.println(); } w.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" ); + System.out.println( "Wrote table to \"" + table_outfile + "\"" ); } - private final static void printHelp() { - System.out.println( "Usage" ); - System.out.println(); - 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" ); - System.out.println( " -" + QUERY_OPTION + " : name for query (sequence/node)" ); - System.out.println( " -" + SORT_OPTION + " : sort (default: 2)" ); - 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( " 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( " 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.exit( -1 ); + private static void writeTree( final Phylogeny p, final File f, final String comment ) throws IOException { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( f, p, 0 ); + System.out.println( comment + " \"" + f + "\"" ); } }