final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
final static private String HELP_OPTION_1 = "help";
final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml";
final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
+ final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt";
final static private String PRG_NAME = "gsdi";
final static private String PRG_VERSION = "1.000";
- final static private String PRG_DATE = "120608";
+ final static private String PRG_DATE = "120629";
final static private String PRG_DESC = "general speciation duplication inference";
final static private String E_MAIL = "phylosoft@gmail.com";
final static private String WWW = "www.phylosoft.org/forester";
gsdi.print_help();
System.exit( 0 );
}
- else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
System.out.println();
System.out.println( "Wrong number of arguments." );
System.out.println();
private static void execute( final CommandLineArguments cla ) throws IOException {
BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
boolean most_parsimonous_duplication_model = false;
- boolean species_tree_in_phyloxml = true;
boolean allow_stripping_of_gene_tree = false;
if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
base_algorithm = BASE_ALGORITHM.SDI;
}
most_parsimonous_duplication_model = true;
}
- if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
- species_tree_in_phyloxml = false;
- }
if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
try {
gene_tree_file = cla.getFile( 0 );
species_tree_file = cla.getFile( 1 );
- if ( cla.getNumberOfNames() == 3 ) {
- out_file = cla.getFile( 2 );
- }
- else {
- out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
- }
+ out_file = cla.getFile( 2 );
log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
}
catch ( final IllegalArgumentException e ) {
gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ fatalError( "ERROR",
+ "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
+ log_writer );
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- if ( species_tree_in_phyloxml ) {
- species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
+ if ( p instanceof PhyloXmlParser ) {
+ species_tree = factory.create( species_tree_file, p )[ 0 ];
}
else {
- final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
( ( NHXParser ) p ).setReplaceUnderscores( true );
}
true );
}
catch ( final PhyloXmlDataFormatException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to transfer general node name to scientific name, in ["
- + species_tree_file + "]: " + e.getMessage() );
+ fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
+ + species_tree_file + "]: " + e.getMessage(), log_writer );
}
break;
case CODE:
true );
}
catch ( final PhyloXmlDataFormatException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to transfer general node name to taxonomy code, in ["
- + species_tree_file + "]: " + e.getMessage() );
+ fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
+ + species_tree_file + "]: " + e.getMessage(), log_writer );
}
break;
case ID:
true );
}
catch ( final PhyloXmlDataFormatException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to transfer general node name to taxonomy id, in ["
- + species_tree_file + "]: " + e.getMessage() );
+ fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
+ + species_tree_file + "]: " + e.getMessage(), log_writer );
}
break;
default:
- ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
+ fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
}
}
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: "
- + e.getMessage() );
+ fatalError( "ERROR",
+ "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
+ log_writer );
}
gene_tree.setRooted( true );
species_tree.setRooted( true );
if ( !gene_tree.isCompletelyBinary() ) {
- log_writer.println( "User Error: gene tree is not completely binary" );
- log_writer.close();
- ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
+ fatalError( "user error", "gene tree is not completely binary", log_writer );
}
if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
- log_writer.close();
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
+ fatalError( "user error", "species tree is not completely binary, use GSDI instead", log_writer );
}
}
log_writer.println( PRG_NAME + " - " + PRG_DESC );
}
}
catch ( final SDIException e ) {
- log_writer.println( "User Error: " + e.getLocalizedMessage() );
- log_writer.close();
- ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ fatalError( "user error", e.getLocalizedMessage(), log_writer );
}
catch ( final IOException e ) {
- log_writer.println( "Error: " + e );
- log_writer.close();
- ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ fatalError( "error", e.toString(), log_writer );
}
catch ( final Exception e ) {
- log_writer.println( "Error: " + e );
- log_writer.close();
e.printStackTrace();
- System.exit( -1 );
+ fatalError( "unexpected error", e.toString(), log_writer );
}
System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
+ "ms" );
writer.toPhyloXML( out_file, gene_tree, 0 );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
}
- System.out.println( "Wrote resulting gene tree to : " + out_file );
- log_writer.println( "Wrote resulting gene tree to : " + out_file );
+ System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
+ log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
if ( base_algorithm == BASE_ALGORITHM.SDI ) {
sdi.computeMappingCostL();
System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
}
else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
final GSDI gsdi = ( GSDI ) sdi;
- final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
+ final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
+ + SUFFIX_FOR_SPECIES_TREE_USED );
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME,
- "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
+ + "]: " + e.getMessage() );
+ }
+ System.out.println( "Wrote (stripped) species tree to : "
+ + species_tree_used_file.getCanonicalPath() );
+ log_writer.println( "Wrote (stripped) species tree to : "
+ + species_tree_used_file.getCanonicalPath() );
+ if ( ( gsdi.getReMappedScientificNamesFromGeneTree() != null )
+ && !gsdi.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
+ System.out.println( "Number of gene tree species remapped : "
+ + gsdi.getReMappedScientificNamesFromGeneTree().size() );
+ log_writer.println( "Number of gene tree species remapped : "
+ + gsdi.getReMappedScientificNamesFromGeneTree().size() );
+ writeToRemappedFile( out_file, gsdi.getReMappedScientificNamesFromGeneTree(), log_writer );
}
- System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file );
- log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file );
}
System.out.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
log_writer.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
printMappedNodesToLog( log_writer, gsdi );
log_writer.println();
printStrippedGeneTreeNodesToLog( log_writer, gsdi );
- log_writer.println();
- printStrippedSpeciesTreeNodesToLog( log_writer, gsdi );
}
System.out.println();
- System.out.println( "Wrote log to : " + log_file );
+ System.out.println( "Wrote log to : " + log_file.getCanonicalPath() );
System.out.println();
log_writer.close();
}
+ private static void writeToRemappedFile( final File out_file,
+ final SortedSet<String> remapped,
+ final EasyWriter log_writer ) throws IOException {
+ final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
+ final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
+ for( final String s : remapped ) {
+ remapped_writer.println( s );
+ }
+ remapped_writer.close();
+ System.out.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ log_writer.println( "Wrote remapped gene tree species to : " + file.getCanonicalPath() );
+ }
+
private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
final SortedSet<String> ss = new TreeSet<String>();
for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
}
}
+ private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
+ try {
+ log_writer.flush();
+ log_writer.println();
+ log_writer.print( type.toUpperCase() + ": " );
+ log_writer.println( msg );
+ log_writer.close();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
+ }
+
private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
throws IOException {
final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
}
}
- private static void printStrippedSpeciesTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
- throws IOException {
- final SortedSet<String> ss = new TreeSet<String>();
- for( final PhylogenyNode n : gsdi.getStrippedSpeciesTreeNodes() ) {
- ss.add( n.toString() );
- }
- log_writer.println( "The following " + ss.size() + " nodes were stripped from the species tree: " );
- for( final String n : ss ) {
- log_writer.println( " " + n );
- }
- }
-
private static void print_help() {
System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree> [outfile]" );
+ + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
System.out.println();
System.out.println( "Options:" );
System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
+ ": use most parimonious duplication model for GSDI: " );
System.out.println( " assign nodes as speciations which would otherwise be assiged" );
- System.out.println( " as potential duplications dueof polytomies in the species tree" );
+ System.out.println( " as potential duplications due to polytomies in the species tree" );
System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
+ ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
System.out.println( " -" + gsdi.SDISE_OPTION
System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
System.out.println();
System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
- + " gene_tree.xml tree_of_life.xml out.xml" );
+ + " gene_tree.xml tree_of_life.xml out.xml" );
System.out.println();
}
}