X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=24acfe8b3d51fb09a41c4f93f38b7ebaff572017;hb=b5fe992f707cdad84255eb85040effbee97d61b3;hp=80a34abe214f9837c4b3e0e8cfe77a1c9e765321;hpb=9a9e40a5768c100cbbb70e32a2637c82890d2d53;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 80a34ab..24acfe8 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -2,10 +2,7 @@ // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // -// Copyright (C) 2008-2009 Christian M. Zmasek -// Copyright (C) 2008-2009 Burnham Institute for Medical Research -// Copyright (C) 2000-2001 Washington University School of Medicine -// and Howard Hughes Medical Institute +// Copyright (C) 2017 Christian M. Zmasek // All rights reserved // // This library is free software; you can redistribute it and/or @@ -22,48 +19,50 @@ // License along with this library; if not, write to the Free Software // 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.FilenameFilter; import java.io.IOException; -import java.io.PrintWriter; import java.util.ArrayList; +import java.util.Arrays; 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.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.rio.RIO; -import org.forester.rio.RIOException; -import org.forester.sdi.SDI; -import org.forester.sdi.SDI.ALGORITHM; -import org.forester.sdi.SDIException; +import org.forester.rio.RIO.REROOTING; +import org.forester.rio.RIOUtil; +import org.forester.sdi.SDIutil.ALGORITHM; 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 4"; - final static private String PRG_DATE = "2012.12.10"; - 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 ALLOW_NON_BIN_SPECIES_TREE_OPTION = "g"; - 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"; + public final static String PRG_NAME = "rio"; + public final static String PRG_VERSION = "5.900"; + public final static String PRG_DATE = "170420"; + 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 USE_SDIR = "s"; + final static private String GENE_TREES_SUFFIX_OPTION = "g"; + final static private String MAPPINGS_DIR_OPTION = "m"; + final static private String MAPPINGS_SUFFIX_OPTION = "ms"; + final static private String CONSENSUS_TREES_DIR_OPTION = "co"; + final static private String CONSENSUS_TREES_SUFFIX_OPTION = "cos"; + final static private String MAPPINGS_SUFFIX_DEFAULT = ".nim"; + final static private String CONSENSUS_TREE_SUFFIX_DEFAULT = ".xml"; + final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION = "c"; + final static private String GENE_TREES_SUFFIX_DEFAULT = ".mlt"; + final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5; public static void main( final String[] args ) { ForesterUtil.printProgramInformation( PRG_NAME, @@ -78,250 +77,692 @@ 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( ALLOW_NON_BIN_SPECIES_TREE_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( GENE_TREES_SUFFIX_OPTION ); + allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION ); + allowed_options.add( MAPPINGS_DIR_OPTION ); + allowed_options.add( MAPPINGS_SUFFIX_OPTION ); + allowed_options.add( CONSENSUS_TREES_DIR_OPTION ); + allowed_options.add( CONSENSUS_TREES_SUFFIX_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 boolean use_dir; + File indir = null; + File outdir = null; + if ( gene_trees_file.isDirectory() ) { + if ( !gene_trees_file.exists() ) { + ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" does not exist" ); + } + if ( gene_trees_file.listFiles().length < 1 ) { + ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" is empty" ); + } + use_dir = true; + indir = gene_trees_file; } - 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" ); + else { + use_dir = false; } - String query = null; - if ( cla.isOptionSet( QUERY_OPTION ) ) { - query = cla.getOptionValue( QUERY_OPTION ); + final File species_tree_file = cla.getFile( 1 ); + File orthology_outtable = null; + if ( use_dir ) { + outdir = cla.getFile( 2 ); } - 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" ); + else { + orthology_outtable = cla.getFile( 2 ); + } + File logfile; + if ( use_dir ) { + if ( ( cla.getNumberOfNames() < 4 ) ) { + System.out.println(); + System.out.println( "error: incorrect number of arguments" ); + System.out.println(); + printHelp(); + } + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); } } - boolean output_ultraparalogs = false; - if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) { - output_ultraparalogs = true; + else { + if ( cla.getNumberOfNames() > 3 ) { + logfile = cla.getFile( 3 ); + if ( logfile.exists() ) { + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); + } + } + else { + logfile = null; + } } - boolean gsdir = false; - if ( cla.isOptionSet( ALLOW_NON_BIN_SPECIES_TREE_OPTION ) ) { - gsdir = true; + boolean sdir = false; + if ( cla.isOptionSet( USE_SDIR ) ) { + if ( cla.isOptionHasAValue( USE_SDIR ) ) { + ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR ); + } + sdir = true; + if ( !use_dir && logfile != null ) { + ForesterUtil.fatalError( "no logfile output for SDIR algorithm" ); + } } - 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" ); - } - if ( outfile == null ) { - ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); - } + String outgroup = null; + if ( cla.isOptionSet( OUTGROUP ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" ); } - if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) { - cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION ); - output_ultraparalogs = true; + if ( use_dir ) { + ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" ); } - if ( cla.isOptionSet( SORT_OPTION ) ) { - sort = cla.getOptionValueAsInt( SORT_OPTION ); + if ( !cla.isOptionHasAValue( OUTGROUP ) ) { + ForesterUtil.fatalError( "no value for -" + OUTGROUP ); } + outgroup = cla.getOptionValueAsCleanString( OUTGROUP ); } - catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() ); + 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" ) ) { + if ( use_dir ) { + ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" ); + } + rerooting = REROOTING.OUTGROUP; + } + else { + ForesterUtil + .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); + } } - 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 ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" ); } - if ( ( ( query == null ) && ( ( outfile != null ) || output_ultraparalogs ) ) ) { - ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" ); + if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) { + ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" ); } - if ( ( output_ultraparalogs && ( outfile == null ) ) || ( ( query != null ) && ( outfile == null ) ) ) { - ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" ); + int gt_first = RIO.DEFAULT_RANGE; + int gt_last = RIO.DEFAULT_RANGE; + if ( cla.isOptionSet( GT_FIRST ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( GT_FIRST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_FIRST ); + } + 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 ); + } } - long time = 0; - System.out.println( "Gene trees : " + gene_trees_file ); - System.out.println( "Species tree : " + species_tree_file ); - if ( gsdir ) { - System.out.println( "Non binary species tree : allowed (GSDIR algorithm)" ); + if ( cla.isOptionSet( GT_LAST ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( GT_LAST ) ) { + ForesterUtil.fatalError( "no value for -" + GT_LAST ); + } + 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 ); + } } - else { - System.out.println( "Non binary species tree : disallowed (SDIR algorithm)" ); + 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 ) { - 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 ); + double ortholog_group_cutoff = ORTHOLOG_GROUPS_CUTOFF_DEFAULT; + if ( cla.isOptionSet( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) { + if ( sdir ) { + ForesterUtil.fatalError( "ortholog groups cutoff for SDIR algorithm" ); + } + if ( !cla.isOptionHasAValue( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION ); + } + try { + ortholog_group_cutoff = cla.getOptionValueAsDouble( ORTHOLOG_GROUPS_CUTOFF_OPTION ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( "could not parse double for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + " option" ); + } + if ( ortholog_group_cutoff < 0 ) { + ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff ); + } + if ( ortholog_group_cutoff > 1 ) { + ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff ); } } - if ( table_outfile != null ) { - System.out.println( "Table output : " + table_outfile ); + if ( !use_dir ) { + ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file ); } - 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 ]; + final String gene_trees_suffix; + if ( cla.isOptionSet( GENE_TREES_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil.fatalError( "no gene tree suffix option when operating on indivual gene trees" ); + } + if ( !cla.isOptionHasAValue( GENE_TREES_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + GENE_TREES_SUFFIX_OPTION ); + } + gene_trees_suffix = cla.getOptionValueAsCleanString( GENE_TREES_SUFFIX_OPTION ); } - catch ( final Exception e ) { - e.printStackTrace(); - System.exit( -1 ); + else { + gene_trees_suffix = GENE_TREES_SUFFIX_DEFAULT; + } + final boolean perform_id_mapping; + final File id_mapping_dir; + if ( cla.isOptionSet( MAPPINGS_DIR_OPTION ) ) { + id_mapping_dir = new File( cla.getOptionValue( MAPPINGS_DIR_OPTION ) ); + perform_id_mapping = true; + if ( !use_dir ) { + ForesterUtil.fatalError( "no id mapping when operating on indivual gene trees" ); + } + if ( !id_mapping_dir.exists() ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" does not exist" ); + } + if ( !id_mapping_dir.isDirectory() ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is not a directory" ); + } + if ( id_mapping_dir.listFiles().length < 1 ) { + ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is empty" ); + } } - if ( !species_tree.isRooted() ) { - ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" ); + else { + id_mapping_dir = null; + perform_id_mapping = false; } - final SDI.ALGORITHM algorithm; - if ( gsdir ) { - algorithm = ALGORITHM.GSDIR; + final String id_mapping_suffix; + if ( cla.isOptionSet( MAPPINGS_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil.fatalError( "no id mapping file suffix option when operating on indivual gene trees" ); + } + if ( !perform_id_mapping ) { + ForesterUtil.fatalError( "no id mapping directory given" ); + } + if ( !cla.isOptionHasAValue( MAPPINGS_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + MAPPINGS_SUFFIX_OPTION ); + } + id_mapping_suffix = cla.getOptionValueAsCleanString( MAPPINGS_SUFFIX_OPTION ); } else { - algorithm = ALGORITHM.SDIR; + id_mapping_suffix = MAPPINGS_SUFFIX_DEFAULT; + } + boolean perform_gsdir_on_best_tree; + final File best_trees_indir; + if ( cla.isOptionSet( CONSENSUS_TREES_DIR_OPTION ) ) { + best_trees_indir = new File( cla.getOptionValue( CONSENSUS_TREES_DIR_OPTION ) ); + perform_gsdir_on_best_tree = true; + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree GSDIR analysis when operating on individual gene trees" ); + } + if ( !best_trees_indir.exists() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" does not exist" ); + } + if ( !best_trees_indir.isDirectory() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" is not a directory" ); + } + if ( best_trees_indir.listFiles().length < 1 ) { + ForesterUtil + .fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + "\" is empty" ); + } + } + else { + best_trees_indir = null; + perform_gsdir_on_best_tree = false; + } + final String best_trees_suffix; + if ( cla.isOptionSet( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree suffix option when operating on individual gene trees" ); + } + if ( !perform_gsdir_on_best_tree ) { + ForesterUtil.fatalError( "no consensus (\"best\") gene tree directory given" ); + } + if ( !cla.isOptionHasAValue( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + CONSENSUS_TREES_SUFFIX_OPTION ); + } + best_trees_suffix = cla.getOptionValueAsCleanString( CONSENSUS_TREES_SUFFIX_OPTION ); + } + else { + best_trees_suffix = CONSENSUS_TREE_SUFFIX_DEFAULT; } + ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); + if ( !use_dir && orthology_outtable.exists() ) { + ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); + } + long time = 0; try { - final RIO rio; - if ( ForesterUtil.isEmpty( query ) ) { - rio = new RIO( gene_trees_file, species_tree, algorithm ); + if ( use_dir ) { + System.out.println( "Gene trees in-dir :\t" + indir.getCanonicalPath() ); + System.out.println( "Gene trees suffix :\t" + gene_trees_suffix ); } else { - rio = new RIO( gene_trees_file, species_tree, query, algorithm ); - } - 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\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(); + System.out.println( "Gene trees :\t" + gene_trees_file.getCanonicalPath() ); } - if ( table_outfile != null ) { - tableOutput( table_outfile, rio ); + System.out.println( "Species tree :\t" + species_tree_file.getCanonicalPath() ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + if ( perform_id_mapping ) { + try { + System.out.println( "Id mappings in-dir :\t" + id_mapping_dir.getCanonicalPath() ); } + catch ( IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + System.out.println( "Id mappings suffix :\t" + id_mapping_suffix ); } - catch ( final RIOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + if ( perform_gsdir_on_best_tree ) { + try { + System.out.println( "Consensus (\"best\") gene trees in-dir:\t" + best_trees_indir.getCanonicalPath() ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + System.out.println( "Consensus (\"best\") gene trees suffix:\t" + best_trees_suffix ); } - catch ( final SDIException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + if ( use_dir ) { + System.out.println( "Out-dir :\t" + outdir ); } - catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + else { + System.out.println( "All vs all orthology results table :\t" + orthology_outtable ); } - catch ( final Exception e ) { - ForesterUtil.unexpectedFatalError( PRG_NAME, e ); + if ( logfile != null ) { + System.out.println( "Logfile :\t" + logfile ); } - if ( outfile != null ) { - ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" ); + System.out.println( "Ortholog groups cutoff :\t" + ortholog_group_cutoff ); + if ( gt_first != RIO.DEFAULT_RANGE ) { + System.out.println( "First gene tree to analyze :\t" + gt_first ); } - 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(), true ); - writeTable( table_outfile, rio, m ); - } + if ( gt_last != RIO.DEFAULT_RANGE ) { + System.out.println( "Last gene tree to analyze :\t" + 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; + } + } + System.out.println( "Re-rooting : \t" + rerooting_str ); + if ( !sdir ) { + System.out.println( "Non binary species tree :\tallowed" ); + } + else { + System.out.println( "Non binary species tree :\tdisallowed" ); + } + time = System.currentTimeMillis(); + final ALGORITHM algorithm; + if ( sdir ) { + algorithm = ALGORITHM.SDIR; + } + else { + algorithm = ALGORITHM.GSDIR; + } + EasyWriter log = null; + if ( use_dir ) { + if ( outdir.exists() ) { + if ( !outdir.isDirectory() ) { + ForesterUtil.fatalError( PRG_NAME, + "out-directory [" + outdir + "] already exists but is not a directory" ); + } + } + else { + final boolean success = outdir.mkdirs(); + if ( !success ) { + ForesterUtil.fatalError( PRG_NAME, "could not create out-directory [" + outdir + "]" ); + } + } + final String species_tree_file_name = species_tree_file.getName(); + final File gene_trees_files[] = indir.listFiles( new FilenameFilter() { - 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( "-" ); + @Override + public boolean accept( final File dir, final String name ) { + return ( ( name.endsWith( gene_trees_suffix ) ) && !( name.equals( species_tree_file_name ) ) ); + } + } ); + if ( gene_trees_files.length < 1 ) { + ForesterUtil.fatalError( PRG_NAME, + "in-directory [" + indir + + "] does not contain any gene tree files with suffix " + + gene_trees_suffix ); + } + try { + log = ForesterUtil.createEasyWriter( logfile ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( PRG_NAME, "could not create [" + logfile + "]" ); + } + Arrays.sort( gene_trees_files ); + try { + log.print( "# program" ); + log.print( "\t" ); + log.print( PRG_NAME ); + log.println(); + log.print( "# version" ); + log.print( "\t" ); + log.print( PRG_VERSION ); + log.println(); + log.print( "# date" ); + log.print( "\t" ); + log.print( PRG_DATE ); + log.println(); + log.print( "# Algorithm " ); + log.print( "\t" ); + log.print( algorithm.toString() ); + log.println(); + log.print( "# Gene trees in-dir" ); + log.print( "\t" ); + log.print( indir.getCanonicalPath() ); + log.println(); + log.print( "# Gene trees suffix" ); + log.print( "\t" ); + log.print( gene_trees_suffix ); + log.println(); + log.print( "# Species tree" ); + log.print( "\t" ); + log.print( species_tree_file.getCanonicalPath() ); + log.println(); + if ( perform_id_mapping ) { + log.print( "# Id mappings in-dir" ); + log.print( "\t" ); + log.print( id_mapping_dir.getCanonicalPath() ); + log.println(); + log.print( "# Id mappings suffix" ); + log.print( "\t" ); + log.print( id_mapping_suffix ); + log.println(); + } + if ( perform_gsdir_on_best_tree ) { + log.print( "# Consensus (\"best\") gene tree dir" ); + log.print( "\t" ); + log.print( best_trees_indir.getCanonicalPath() ); + log.println(); + log.print( "# Consensus (\"best\") gene tree suffix" ); + log.print( "\t" ); + log.print( best_trees_suffix ); + log.println(); + } + log.print( "# Out-dir" ); + log.print( "\t" ); + log.print( outdir.getCanonicalPath() ); + log.println(); + log.print( "# Logfile" ); + log.print( "\t" ); + log.print( logfile.getCanonicalPath() ); + log.println(); + log.print( "# Ortholog groups cutoff" ); + log.print( "\t" ); + log.print( Double.toString( ortholog_group_cutoff ) ); + log.println(); + if ( gt_first != RIO.DEFAULT_RANGE ) { + log.print( "# First gene tree to analyze" ); + log.print( "\t" ); + log.print( Integer.toString( gt_first ) ); + log.println(); + } + if ( gt_last != RIO.DEFAULT_RANGE ) { + log.print( "# Last gene tree to analyze" ); + log.print( "\t" ); + log.print( Integer.toString( gt_last ) ); + log.println(); + } + log.print( "# Re-rooting" ); + log.print( "\t" ); + log.print( rerooting_str ); + log.println(); + log.print( "# Non binary species tree" ); + log.print( "\t" ); + if ( !sdir ) { + log.print( "allowed" ); } else { - w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getNumberOfSamples() ) ); + log.print( "disallowed" ); + } + log.println(); + log.println(); + log.print( "NAME" ); + log.print( "\t" ); + log.print( "EXT NODES" ); + log.print( "\t" ); + log.print( ortholog_group_cutoff + " O GROUPS" ); + log.print( "\t" ); + log.print( "0.05 O GROUPS" ); + log.print( "\t" ); + log.print( "0.25 O GROUPS" ); + log.print( "\t" ); + log.print( "0.5 O GROUPS" ); + log.print( "\t" ); + log.print( "0.75 O GROUPS" ); + log.print( "\t" ); + log.print( "0.95 O GROUPS" ); + log.print( "\t" ); + if ( perform_gsdir_on_best_tree ) { + log.print( "BEST TREE DUP" ); + log.print( "\t" ); + log.print( "MEDIAN DUP - BEST TREE DUP" ); + log.print( "\t" ); + } + log.print( "MEDIAN DUP" ); + log.print( "\t" ); + log.print( "MEAN DUP" ); + log.print( "\t" ); + log.print( "MEAN DUP SD" ); + log.print( "\t" ); + log.print( "MIN DUP" ); + log.print( "\t" ); + log.print( "MAX DUP" ); + log.print( "\t" ); + log.print( "REMOVED EXT NODES" ); + log.print( "\t" ); + log.print( "N" ); + log.println(); + } + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + int counter = 1; + for( final File gf : gene_trees_files ) { + String outname = gf.getName(); + System.out + .print( "\r " ); + System.out.print( "\r" + counter + "/" + gene_trees_files.length + ": " + outname ); + counter++; + if ( outname.indexOf( "." ) > 0 ) { + outname = outname.substring( 0, outname.lastIndexOf( "." ) ); } + try { + RIOUtil.executeAnalysis( gf, + species_tree_file, + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHO_OUTTABLE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.LOGFILE_SUFFIX ), + outgroup, + rerooting, + gt_first, + gt_last, + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), + true, + algorithm, + true, + log, + ortholog_group_cutoff, + perform_id_mapping, + id_mapping_dir, + id_mapping_suffix, + perform_gsdir_on_best_tree, + outdir, + best_trees_indir, + best_trees_suffix ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + } + } + System.out + .print( "\r " ); + System.out.println(); + } + else { + String outname = ForesterUtil.removeFileExtension( orthology_outtable.toString() ); + RIOUtil.executeAnalysis( gene_trees_file, + species_tree_file, + orthology_outtable, + null, + new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), + logfile, + outgroup, + rerooting, + gt_first, + gt_last, + new File( outname + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), + algorithm == ALGORITHM.GSDIR, + algorithm, + false, + null, + ortholog_group_cutoff, + false, + null, + null, + false, + null, + null, + null ); + } + if ( !use_dir ) { + time = System.currentTimeMillis() - time; + System.out.println( "Time :\t" + time + "ms" ); + } + else { + try { + log.close(); + } + catch ( IOException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); } - w.println(); + time = System.currentTimeMillis() - time; + System.out.println( "Time :\t" + time + "ms" ); } - w.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" ); + System.exit( 0 ); } private final static void printHelp() { System.out.println( "Usage" ); System.out.println(); - System.out.println( PRG_NAME + " [options] [outfile]" ); + System.out.println( PRG_NAME + + " [options] [logfile]" ); System.out.println(); - System.out.println( " Options" ); - System.out.println( " -" + ALLOW_NON_BIN_SPECIES_TREE_OPTION + " : to allow non-binary species tree" ); - 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( PRG_NAME + " [options] " ); 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( " 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( " -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + + "= : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" ); + 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( " -" + 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( " -" + GENE_TREES_SUFFIX_OPTION + + "= : suffix for gene trees when operating on gene tree directories (default: " + + GENE_TREES_SUFFIX_DEFAULT + ")" ); + System.out.println( " -" + MAPPINGS_DIR_OPTION + "= : directory for id mapping files" ); + System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "= : suffix for id mapping files (default: " + + MAPPINGS_SUFFIX_DEFAULT + ")" ); + System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION + + "= : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" ); + System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION + + "= : suffix for consenus (\"best\") gene trees (default: " + CONSENSUS_TREE_SUFFIX_DEFAULT + + ")" ); + System.out.println(); 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\")." ); + .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 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( " rio -s gene_trees.nh species.xml outtable.tsv" ); + System.out.println( " rio gene_trees.nh species.xml outtable.tsv log.txt" ); + System.out.println( " rio -c=0.9 -f=10 -l=100 -r=none gene_trees.xml species.xml outtable.tsv log.txt" ); + System.out.println( " rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" ); + System.out.println( " rio -g=.mlt -m=id_maps_dir -ms=.nim -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); + System.out.println( " rio -m=id_maps_dir -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); + System.out + .println( " rio -m=id_maps_dir -co=consensus_dir -cos=.xml -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); System.out.println(); System.exit( -1 ); }