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.rio.RIO;
import org.forester.rio.RIO.REROOTING;
import org.forester.rio.RIOException;
final static private String PRG_NAME = "rio";
final static private String PRG_VERSION = "4.000 beta 3";
- final static private String PRG_DATE = "2012.12.18";
+ final static private String PRG_DATE = "2012.12.19";
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";
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 < 3 ) || ( args.length > 8 ) ) {
+ if ( ( args.length < 3 ) || ( args.length > 9 ) ) {
System.out.println();
- System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println( "error: incorrect number of arguments" );
System.out.println();
printHelp();
}
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 );
+ ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options );
}
final File gene_trees_file = cla.getFile( 0 );
final File species_tree_file = cla.getFile( 1 );
if ( cla.getNumberOfNames() > 3 ) {
logfile = cla.getFile( 3 );
if ( logfile.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "\"" + logfile + "\" already exists" );
+ ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
}
}
else {
boolean sdir = false;
if ( cla.isOptionSet( USE_SDIR ) ) {
if ( cla.isOptionHasAValue( USE_SDIR ) ) {
- ForesterUtil.fatalError( PRG_NAME, "no value allowed for -" + USE_SDIR );
+ ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR );
}
sdir = true;
if ( logfile != null ) {
- ForesterUtil.fatalError( PRG_NAME, "no logfile output for SDIR algorithm" );
+ ForesterUtil.fatalError( "no logfile output for SDIR algorithm" );
}
}
String outgroup = null;
if ( cla.isOptionSet( OUTGROUP ) ) {
if ( !cla.isOptionHasAValue( OUTGROUP ) ) {
- ForesterUtil.fatalError( PRG_NAME, "no value for -" + OUTGROUP );
+ ForesterUtil.fatalError( "no value for -" + OUTGROUP );
}
if ( sdir ) {
- ForesterUtil.fatalError( PRG_NAME, "no outgroup option for SDIR algorithm" );
+ 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( PRG_NAME, "no value for -" + REROOTING_OPT );
+ ForesterUtil.fatalError( "no value for -" + REROOTING_OPT );
}
if ( sdir ) {
- ForesterUtil.fatalError( PRG_NAME, "no re-rooting option for SDIR algorithm" );
+ ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" );
}
final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase();
if ( rerooting_str.equals( "none" ) ) {
}
else {
ForesterUtil
- .fatalError( PRG_NAME,
- "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
+ .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
}
}
if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) {
- ForesterUtil.fatalError( PRG_NAME, "selected re-rooting by outgroup, but outgroup not set" );
+ ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" );
}
if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) {
- ForesterUtil.fatalError( PRG_NAME, "outgroup set, but selected re-rooting by other approach" );
+ 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( PRG_NAME, "no value for -" + GT_FIRST );
+ ForesterUtil.fatalError( "no value for -" + GT_FIRST );
}
if ( sdir ) {
- ForesterUtil.fatalError( PRG_NAME, "no gene tree range option for SDIR algorithm" );
+ ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
}
try {
gt_first = cla.getOptionValueAsInt( GT_FIRST );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "could not parse integer for -" + GT_FIRST + " option" );
+ ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" );
}
if ( gt_first < 0 ) {
- ForesterUtil.fatalError( PRG_NAME, "attempt to set index of first tree to analyze to: " + gt_first );
+ 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( PRG_NAME, "no value for -" + GT_LAST );
+ ForesterUtil.fatalError( "no value for -" + GT_LAST );
}
if ( sdir ) {
- ForesterUtil.fatalError( PRG_NAME, "no gene tree range option for SDIR algorithm" );
+ ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
}
try {
gt_last = cla.getOptionValueAsInt( GT_LAST );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "could not parse integer for -" + GT_LAST + " option" );
+ ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" );
}
if ( gt_last < 0 ) {
- ForesterUtil.fatalError( PRG_NAME, "attempt to set index of last tree to analyze to: " + gt_last );
+ 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( PRG_NAME, "attempt to set range (0-based) of gene to analyze to: from " + gt_first
- + " to " + gt_last );
+ ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to "
+ + gt_last );
}
- ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file );
- ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file );
+ ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file );
+ ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
if ( orthology_outtable.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "\"" + orthology_outtable + "\" already exists" );
+ ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
}
long time = 0;
System.out.println( "Gene trees : " + gene_trees_file );
System.out.println( "Non binary species tree : disallowed" );
}
time = System.currentTimeMillis();
- Phylogeny species_tree = null;
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- System.exit( -1 );
- }
- if ( !species_tree.isRooted() ) {
- ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
- }
- 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" );
- }
- }
+ // Phylogeny species_tree = null;
+ // try {
+ // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ // species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ // }
+ // catch ( final Exception e ) {
+ // e.printStackTrace();
+ // System.exit( -1 );
+ // }
final ALGORITHM algorithm;
if ( sdir ) {
algorithm = ALGORITHM.SDIR;
}
try {
final RIO rio = RIO.executeAnalysis( gene_trees_file,
- species_tree,
+ species_tree_file,
algorithm,
rerooting,
outgroup,
logfile != null,
true );
if ( algorithm == ALGORITHM.GSDIR ) {
- ForesterUtil.programMessage( PRG_NAME, "taxonomy linking based on: " + rio.getGSDIRtaxCompBase() );
+ System.out.println( "Taxonomy linking based on : " + rio.getGSDIRtaxCompBase() );
}
tableOutput( orthology_outtable, rio );
if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) {
}
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() ) + ")" );
+ 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 ) {
- ForesterUtil.programMessage( PRG_NAME, "Median number of duplications: " + df.format( stats.median() ) );
+ System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " ("
+ + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
}
- ForesterUtil.programMessage( PRG_NAME, "Minimum duplications : " + ( int ) stats.getMin() );
- ForesterUtil.programMessage( PRG_NAME, "Maximum duplications : " + ( int ) stats.getMax() );
+ 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( PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
}
catch ( final SDIException e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
+ }
+ catch ( final OutOfMemoryError e ) {
+ ForesterUtil.outOfMemoryError( e );
}
catch ( final Exception e ) {
- ForesterUtil.unexpectedFatalError( PRG_NAME, e );
+ ForesterUtil.unexpectedFatalError( e );
+ }
+ catch ( final Error e ) {
+ ForesterUtil.unexpectedFatalError( e );
}
time = System.currentTimeMillis() - time;
- ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
- ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println( "Time: " + time + "ms" );
+ System.out.println( "OK" );
System.exit( 0 );
}
System.out.println( " disallowed, as are most options)" );
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 outtable.tsv log.txt\"" );
out.flush();
out.println( rio.getLog().toString() );
out.close();
- ForesterUtil.programMessage( PRG_NAME, "wrote log to \"" + logfile + "\"" );
+ System.out.println( "Wrote log to \"" + logfile + "\"" );
}
private static void writeTable( final File table_outfile, final RIO rio, final IntMatrix m ) throws IOException {
w.print( "\t" );
if ( x == y ) {
if ( m.get( x, y ) != rio.getAnalyzedGeneTrees().length ) {
- ForesterUtil.unexpectedFatalError( PRG_NAME, "diagonal value is off" );
+ ForesterUtil.unexpectedFatalError( "diagonal value is off" );
}
w.print( "-" );
}
w.println();
}
w.close();
- ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" );
+ System.out.println( "Wrote table to \"" + table_outfile + "\"" );
}
}
git://source.jalview.org / jalview.git / blobdiff