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|
// $Id:
// 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
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// 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: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
import java.io.File;
import java.io.IOException;
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.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 = "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,
"resampled inference of orthologs",
PRG_VERSION,
PRG_DATE,
E_MAIL,
WWW,
ForesterUtil.getForesterLibraryInformation() );
CommandLineArguments cla = null;
try {
cla = new CommandLineArguments( args );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( e.getMessage() );
}
if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
printHelp();
}
if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
System.out.println();
System.out.println( "error: incorrect number of arguments" );
System.out.println();
printHelp();
}
final List<String> allowed_options = new ArrayList<String>();
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( "unknown option(s): " + dissallowed_options );
}
final File gene_trees_file = cla.getFile( 0 );
final File species_tree_file = cla.getFile( 1 );
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" );
}
}
else {
logfile = null;
}
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" );
}
}
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 );
}
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)" );
}
}
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 ( sdir ) {
ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
}
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 );
}
}
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 ( ( ( 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 );
}
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" );
}
}
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 );
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;
}
}
System.out.println( "Re-rooting : " + rerooting_str );
if ( !sdir ) {
System.out.println( "Non binary species tree : allowed" );
}
else {
System.out.println( "Non binary species tree : disallowed" );
}
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 );
}
time = System.currentTimeMillis();
final ALGORITHM algorithm;
if ( sdir ) {
algorithm = ALGORITHM.SDIR;
}
else {
algorithm = ALGORITHM.GSDIR;
}
try {
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 {
iterating = true;
if ( p instanceof NHXParser ) {
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
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 ( 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.unexpectedFatalError( e );
}
catch ( final Error e ) {
ForesterUtil.unexpectedFatalError( e );
}
time = System.currentTimeMillis() - time;
System.out.println( "Time: " + time + "ms" );
System.out.println( "OK" );
System.exit( 0 );
}
private final static void printHelp() {
System.out.println( "Usage" );
System.out.println();
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( " 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( " -" + 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( " -" + RETURN_SPECIES_TREE + "=<outfile> : to write the (stripped) species tree to file" );
System.out.println( " -" + RETURN_BEST_GENE_TREE
+ "=<outfile> : 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 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.####" );
df.setDecimalSeparatorAlwaysShown( false );
df.setRoundingMode( RoundingMode.HALF_UP );
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 ) != gene_trees_analyzed ) {
ForesterUtil.unexpectedFatalError( "diagonal value is off" );
}
w.print( "-" );
}
else {
w.print( df.format( ( ( double ) m.get( x, y ) ) / gene_trees_analyzed ) );
}
}
w.println();
}
w.close();
System.out.println( "Wrote table to \"" + table_outfile + "\"" );
}
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 + "\"" );
}
}
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