// 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
// 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.sdi.RIO;
+import org.forester.rio.RIO;
+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 2";
- final static private String PRG_DATE = "2012.11.30";
- 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";
+ 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,
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<String> allowed_options = new ArrayList<String>();
- 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( 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 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;
+ }
+ else {
+ use_dir = false;
+ }
final File species_tree_file = cla.getFile( 1 );
- File outfile = null;
- if ( cla.getNumberOfNames() > 2 ) {
- outfile = cla.getFile( 2 );
+ File orthology_outtable = null;
+ if ( use_dir ) {
+ outdir = 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" );
+ else {
+ orthology_outtable = cla.getFile( 2 );
}
- String query = null;
- if ( cla.isOptionSet( QUERY_OPTION ) ) {
- query = cla.getOptionValue( QUERY_OPTION );
+ 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" );
+ }
}
- 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 {
+ if ( cla.getNumberOfNames() > 3 ) {
+ logfile = cla.getFile( 3 );
+ if ( logfile.exists() ) {
+ ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
+ }
+ }
+ else {
+ logfile = null;
}
}
- boolean output_ultraparalogs = false;
- if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
- output_ultraparalogs = 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 ( use_dir ) {
+ ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" );
+ }
+ if ( !cla.isOptionHasAValue( OUTGROUP ) ) {
+ ForesterUtil.fatalError( "no value for -" + OUTGROUP );
+ }
+ outgroup = cla.getOptionValueAsCleanString( OUTGROUP );
+ }
+ 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;
}
- if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) {
- cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION );
- output_ultraparalogs = true;
+ else {
+ ForesterUtil
+ .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
}
- if ( cla.isOptionSet( SORT_OPTION ) ) {
- sort = cla.getOptionValueAsInt( SORT_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 ( 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 );
}
}
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() );
+ 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 );
+ }
}
- 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 ( ( ( 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 ) || output_ultraparalogs ) ) ) {
- ForesterUtil.fatalError( PRG_NAME, "missing query name, type \"rio -h\" for help" );
+ 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 ( ( output_ultraparalogs && ( outfile == null ) ) || ( ( query != null ) && ( outfile == null ) ) ) {
- ForesterUtil.fatalError( PRG_NAME, "missing outfile, type \"rio -h\" for help" );
+ if ( !use_dir ) {
+ ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file );
}
- 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 );
+ 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 );
}
- if ( table_outfile != null ) {
- System.out.println( "Table output : " + table_outfile );
+ else {
+ gene_trees_suffix = GENE_TREES_SUFFIX_DEFAULT;
}
- 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 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" );
+ }
}
- catch ( final Exception e ) {
- e.printStackTrace();
- System.exit( -1 );
+ else {
+ id_mapping_dir = null;
+ perform_id_mapping = false;
+ }
+ 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 {
+ 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;
}
- if ( !species_tree.isRooted() ) {
- ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
+ 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;
}
- if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary" );
+ ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
+ if ( !use_dir && orthology_outtable.exists() ) {
+ ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
}
+ long time = 0;
try {
- RIO rio;
- if ( ForesterUtil.isEmpty( query ) ) {
- rio = new RIO( gene_trees_file, species_tree );
+ 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 );
- }
- 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() );
+ }
+ 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() );
}
- if ( table_outfile != null ) {
- tableOutput( table_outfile, rio );
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
}
+ System.out.println( "Id mappings suffix :\t" + id_mapping_suffix );
}
- catch ( final IllegalArgumentException 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 Exception e ) {
- ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() );
- e.printStackTrace();
- System.exit( -1 );
+ if ( use_dir ) {
+ System.out.println( "Out-dir :\t" + outdir );
}
- if ( outfile != null ) {
- ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
+ else {
+ System.out.println( "All vs all orthology results table :\t" + orthology_outtable );
}
- 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 {
- final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees() );
- writeTable( table_outfile, rio, m );
- }
+ if ( logfile != null ) {
+ System.out.println( "Logfile :\t" + logfile );
+ }
+ 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 );
+ }
+ 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 );
- w.print( "\t" );
- 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 ) );
- 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" );
- }
- 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();
}
- w.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" );
}
- w.close();
- ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" );
+ else {
+ try {
+ log.close();
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ time = System.currentTimeMillis() - time;
+ System.out.println( "Time :\t" + time + "ms" );
+ }
+ System.exit( 0 );
}
private final static void printHelp() {
System.out.println( "Usage" );
System.out.println();
- System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
+ System.out.println( PRG_NAME
+ + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
+ System.out.println();
+ System.out.println( PRG_NAME + " [options] <gene trees indir> <species tree infile> <outdir> <logfile>" );
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=<output table> and/or output for" );
- System.out.println( " one query sequence with -q=<query name> and a [outfile] are required." );
+ System.out.println( " Options" );
+ System.out.println( " -" + GT_FIRST + "=<first> : first gene tree to analyze (0-based index)" );
+ System.out.println( " -" + GT_LAST + "=<last> : last gene tree to analyze (0-based index)" );
+ System.out.println( " -" + ORTHOLOG_GROUPS_CUTOFF_OPTION
+ + "=<cutoff> : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" );
+ System.out.println( " -" + REROOTING_OPT
+ + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
+ System.out.println( " or 'outgroup' (default: by minizming duplications)" );
+ System.out.println( " -" + OUTGROUP
+ + "=<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> : suffix for gene trees when operating on gene tree directories (default: "
+ + GENE_TREES_SUFFIX_DEFAULT + ")" );
+ System.out.println( " -" + MAPPINGS_DIR_OPTION + "=<dir> : directory for id mapping files" );
+ System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "=<suffix> : suffix for id mapping files (default: "
+ + MAPPINGS_SUFFIX_DEFAULT + ")" );
+ System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION
+ + "=<dir> : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" );
+ System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION
+ + "=<suffix> : suffix for consenus (\"best\") gene trees (default: " + CONSENSUS_TREE_SUFFIX_DEFAULT
+ + ")" );
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\")." );
+ .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 );
}
git://source.jalview.org / jalview.git / blobdiff