private enum BASE_ALGORITHM {
GSDI, SDI
}
- final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
- final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
- final static private String SDI_OPTION = "b";
- final static private String MOST_PARSIMONIOUS_OPTION = "m";
- 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_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
- 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 PRG_NAME = "gsdi";
- final static private String PRG_VERSION = "0.901";
- final static private String PRG_DATE = "120608";
- 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";
+ final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
+ final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
+ final static private String SDISE_OPTION = "b";
+ final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ 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 PRG_NAME = "gsdi";
+ final static private String PRG_VERSION = "1.000";
+ final static private String PRG_DATE = "120608";
+ 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";
public static void main( final String args[] ) {
try {
System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( gsdi.SDI_OPTION );
+ allowed_options.add( gsdi.SDISE_OPTION );
allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
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.SDI_OPTION ) ) {
+ if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
base_algorithm = BASE_ALGORITHM.SDI;
}
if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
}
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 {
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 );
}
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 );
- log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file );
+ 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() );
}
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() );
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 print_help() {
System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [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 + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + );
- System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
+ System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + ": to allow stripping of gene tree nodes without a matching species" );
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 unknown because of polytomies in the species tree" );
+ System.out.println( " as potential duplications dueof 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();
- System.out.println( "Species tree:" );
- System.out
- .println( " In phyloXML format (unless option -"
- + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
- + " is used, in which case the species matching between gene tree and species tree must be via scientific name), with taxonomy data in appropriate fields" );
+ System.out.println( " -" + gsdi.SDISE_OPTION
+ + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" );
System.out.println();
System.out.println( "Gene tree:" );
- System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" );
+ System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
+ System.out.println();
+ System.out.println( "Species tree:" );
+ System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
System.out.println();
- System.out.println( "Example:" );
- // System.out.println( "gsdi
- // System.out.println();
- System.out.println( "Note -- GSDI algorithm is under development" );
+ System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " gene_tree.xml tree_of_life.xml out.xml" );
System.out.println();
}
}
git://source.jalview.org / jalview.git / blobdiff