package org.forester.application;
import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import org.forester.datastructures.IntMatrix;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.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 = "2.03 ALPHA";
- final static private String PRG_DATE = "2010.01.15";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org/forester/";
- final static private boolean TIME = true;
- final static private boolean VERBOSE = true;
-
- private final static void errorInCommandLine() {
- System.out.println( "\nrio: Error in command line.\n" );
- printHelp();
- System.exit( -1 );
- }
+ final static private String PRG_NAME = "rio";
+ final static private String PRG_VERSION = "4.000 beta 3";
+ final static private String PRG_DATE = "2012.12.17";
+ 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 USE_SDIR = "b";
public static void main( final String[] args ) {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
- File species_tree_file = null;
- File multiple_trees_file = null;
- File outfile = null;
- String seq_name = "";
- String arg = "";
- boolean output_ultraparalogs = false;
- double t_orthologs = 0.0;
- double t_orthologs_dc = 0.0;
- double threshold_ultra_paralogs = 0.0;
- int sort = 13;
- Phylogeny species_tree = null;
- RIO rio_instance = null;
- PrintWriter out = null;
- long time = 0;
- if ( args.length < 2 ) {
+ 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( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
printHelp();
- System.exit( 0 );
}
- else if ( ( args.length < 3 ) || ( args.length > 18 ) ) {
- errorInCommandLine();
+ if ( ( args.length < 3 ) || ( args.length > 8 ) ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
}
- for( final String arg2 : args ) {
- if ( arg2.trim().charAt( 0 ) != 'p' ) {
- if ( arg2.trim().length() < 3 ) {
- errorInCommandLine();
- }
- else {
- arg = arg2.trim().substring( 2 );
- }
- }
- try {
- switch ( arg2.trim().charAt( 0 ) ) {
- case 'M':
- multiple_trees_file = new File( arg );
- break;
- case 'N':
- seq_name = arg;
- break;
- case 'S':
- species_tree_file = new File( arg );
- break;
- case 'O':
- outfile = new File( arg );
- break;
- case 'p':
- output_ultraparalogs = true;
- break;
- case 'P':
- sort = Integer.parseInt( arg );
- if ( ( sort < 0 ) || ( sort > 17 ) ) {
- errorInCommandLine();
- }
- break;
- case 'L':
- t_orthologs = Double.parseDouble( arg );
- break;
- case 'v':
- threshold_ultra_paralogs = Double.parseDouble( arg );
- break;
- default:
- errorInCommandLine();
- }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( USE_SDIR );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "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( PRG_NAME, "\"" + logfile + "\" already exists" );
}
- catch ( final Exception e ) {
- errorInCommandLine();
+ }
+ else {
+ logfile = null;
+ }
+ final String outgroup = "";
+ ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file );
+ ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file );
+ if ( orthology_outtable.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "\"" + orthology_outtable + "\" already exists" );
+ }
+ boolean sdir = false;
+ if ( cla.isOptionSet( USE_SDIR ) ) {
+ sdir = true;
+ if ( logfile != null ) {
+ ForesterUtil.fatalError( PRG_NAME, "logfile output only for GSDIR algorithm" );
}
}
- if ( ( seq_name == "" ) || ( species_tree_file == null ) || ( multiple_trees_file == null )
- || ( outfile == null ) ) {
- errorInCommandLine();
- }
- if ( ( sort < 0 ) || ( sort > 2 ) ) {
- errorInCommandLine();
- }
- if ( VERBOSE ) {
- System.out.println( "\nMultiple trees file: " + multiple_trees_file );
- System.out.println( "Seq name: " + seq_name );
- System.out.println( "Species tree file: " + species_tree_file );
- System.out.println( "Outfile: " + outfile );
- System.out.println( "Sort: " + sort );
- System.out.println( "Threshold orthologs: " + t_orthologs );
- System.out.println( "Threshold orthologs for distance calc.: " + t_orthologs_dc );
- if ( output_ultraparalogs ) {
- System.out.println( "Threshold ultra paralogs: " + threshold_ultra_paralogs );
+ 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 ( !sdir ) {
+ if ( logfile != null ) {
+ System.out.println( "Logfile : " + logfile );
}
+ System.out.println( "Non binary species tree : allowed (GSDIR algorithm)" );
}
- if ( TIME && VERBOSE ) {
- time = System.currentTimeMillis();
+ else {
+ System.out.println( "Non binary species tree : disallowed (SDIR algorithm)" );
}
+ time = System.currentTimeMillis();
+ Phylogeny species_tree = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
System.exit( -1 );
}
if ( !species_tree.isRooted() ) {
- ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" );
- System.exit( -1 );
+ ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
}
- if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" );
- System.exit( -1 );
+ final int o = PhylogenyMethods.countNumberOfOneDescendantNodes( species_tree );
+ if ( o > 0 ) {
+ ForesterUtil.printWarningMessage( PRG_NAME, "species tree has " + o
+ + " internal nodes with only one descendent! Going to strip them." );
+ PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree );
+ if ( PhylogenyMethods.countNumberOfOneDescendantNodes( species_tree ) > 0 ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "stripping of one-desc nodes failed" );
+ }
+ }
+ final ALGORITHM algorithm;
+ if ( sdir ) {
+ algorithm = ALGORITHM.SDIR;
+ }
+ else {
+ algorithm = ALGORITHM.GSDIR;
}
- rio_instance = new RIO();
- final StringBuffer output = new StringBuffer();
try {
- rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name );
- output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs ) );
- if ( output_ultraparalogs ) {
- output.append( "\n\nUltra paralogs:\n" );
- output.append( rio_instance.inferredUltraParalogsToString( seq_name, threshold_ultra_paralogs ) );
+ final RIO rio = RIO.executeAnalysis( gene_trees_file,
+ species_tree,
+ algorithm,
+ REROOTING.BY_ALGORITHM,
+ outgroup,
+ logfile != null,
+ true );
+ if ( algorithm == ALGORITHM.GSDIR ) {
+ ForesterUtil.programMessage( PRG_NAME, "taxonomy linking based on: " + rio.getGSDIRtaxCompBase() );
+ }
+ tableOutput( orthology_outtable, rio );
+ 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() );
}
- output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
- output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() );
- output.append( "\nSamples : " + rio_instance.getNumberOfSamples() + "\n" );
- out = new PrintWriter( new FileWriter( outfile ), true );
+ final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics();
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
+ ForesterUtil.programMessage( PRG_NAME,
+ "Mean number of duplications : " + df.format( stats.arithmeticMean() )
+ + " (sd: " + df.format( stats.sampleStandardDeviation() ) + ")" );
+ if ( stats.getN() > 3 ) {
+ ForesterUtil.programMessage( PRG_NAME, "Median number of duplications: " + df.format( stats.median() ) );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Minimum duplications : " + ( int ) stats.getMin() );
+ ForesterUtil.programMessage( PRG_NAME, "Maximum duplications : " + ( int ) stats.getMax() );
}
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() );
- e.printStackTrace();
- System.exit( -1 );
+ catch ( final RIOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
}
- out.println( output );
- out.close();
- ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
- if ( TIME && VERBOSE ) {
- time = System.currentTimeMillis() - time;
- ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
+ catch ( final SDIException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, e );
}
- ForesterUtil.programMessage( PRG_NAME, "OK." );
+ time = System.currentTimeMillis() - time;
+ ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
System.exit( 0 );
}
private final static void printHelp() {
- System.out.println( "M= (String) Multiple gene tree file (mandatory)" );
- System.out.println( "N= (String) Query sequence name (mandatory)" );
- System.out.println( "S= (String) Species tree file (mandatory)" );
- System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" );
- System.out.println( "P= (int) Sort priority" );
- System.out.println( "L= (double) Threshold orthologs for output" );
- System.out.println( " Sort priority (\"P=\"):" );
- System.out.println( RIO.getOrderHelp().toString() );
+ 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( " -" + USE_SDIR
+ + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed)" );
System.out.println();
+ System.out.println( " Formats" );
+ System.out.println( " The species tree is expected to be in phyloXML format." );
System.out
- .println( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=out\"" );
+ .println( " The gene trees ideally are in phyloXML as well, but can also be in New Hamphshire (Newick)" );
+ System.out.println( " or Nexus format as long as species information can be extracted from the gene names" );
+ System.out.println( " (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." );
System.out.println();
+ System.out.println( " Examples" );
+ System.out.println( " \"rio gene_trees.nh species.xml 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 tableOutput( final File table_outfile, final RIO rio ) throws IOException, RIOException {
+ final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+ writeTable( table_outfile, rio, m );
+ }
+
+ 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();
+ ForesterUtil.programMessage( PRG_NAME, "wrote log to \"" + logfile + "\"" );
+ }
+
+ 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.getAnalyzedGeneTrees().length ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "diagonal value is off" );
+ }
+ w.print( "-" );
+ }
+ else {
+ w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getAnalyzedGeneTrees().length ) );
+ }
+ }
+ w.println();
+ }
+ w.close();
+ ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" );
}
}
git://source.jalview.org / jalview.git / blobdiff