import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
import org.forester.sdi.SDI;
import org.forester.sdi.SDI.TaxonomyComparisonBase;
import org.forester.sdi.SDIException;
public final class gsdi {
private enum BASE_ALGORITHM {
- GSDI, SDI
+ GSDIR, 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 GSDIR_OPTION = "r";
+ 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 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 = "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";
public static void main( final String args[] ) {
try {
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();
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.GSDIR_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.GSDIR_OPTION ) ) {
+ base_algorithm = BASE_ALGORITHM.GSDIR;
+ }
+ else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
base_algorithm = BASE_ALGORITHM.SDI;
}
if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
- if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
+ if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with 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" );
+ if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
}
allow_stripping_of_gene_tree = true;
}
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 ( base_algorithm == BASE_ALGORITHM.SDI ) {
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 or GSDIR instead",
+ log_writer );
}
}
log_writer.println( PRG_NAME + " - " + PRG_DESC );
SDI sdi = null;
final long start_time = new Date().getTime();
try {
- if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
+ if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
+ }
+ else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+ System.out.println( "Algorithm : GSDIR" );
+ log_writer.println( "Algorithm : GSDIR" );
+ }
System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
log_writer.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
log_writer.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
log_writer.flush();
- sdi = new GSDI( gene_tree,
- species_tree,
- most_parsimonous_duplication_model,
- allow_stripping_of_gene_tree,
- true );
+ if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
+ sdi = new GSDI( gene_tree,
+ species_tree,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ true );
+ }
+ else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+ sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 );
+ }
}
else {
System.out.println();
- System.out.println( "Using SDIse algorithm" );
- log_writer.println( "Using SDIse algorithm" );
+ System.out.println( "Algorithm : SDI" );
+ log_writer.println( "Algorithm : SDI" );
log_writer.flush();
sdi = new SDIse( gene_tree, species_tree );
}
}
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" );
System.out.println( "Mapping based on : " + gsdi.getTaxCompBase() );
log_writer.println( "Mapping based on : " + gsdi.getTaxCompBase() );
}
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
+ final GSDIR gsdir = ( GSDIR ) sdi;
+ System.out.println( "Mapping based on : " + gsdir.getTaxCompBase() );
+ log_writer.println( "Mapping based on : " + gsdir.getTaxCompBase() );
+ System.out.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() );
+ log_writer.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() );
+ System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
+ log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() );
+ }
try {
final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( out_file, gene_tree, 0 );
+ if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+ writer.toPhyloXML( out_file,
+ ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(),
+ 0,
+ ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ 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() );
log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
}
- else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
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 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 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();
- 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( " -" + gsdi.GSDIR_OPTION
+ + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
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