package org.forester.application;
import java.io.File;
+import java.io.FilenameFilter;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
final static private String GSDIR_OPTION = "r";
final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ final static private String SUFFIX_FOR_DIR_OPTION = "s";
final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
final static private String TRANSFER_TAXONOMY_OPTION = "t";
final static private String HELP_OPTION_1 = "help";
final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt";
final static private String PRG_NAME = "gsdi";
final static private String PRG_VERSION = "1.001";
- final static private String PRG_DATE = "130325";
+ final static private String PRG_DATE = "170327";
final static private String PRG_DESC = "general speciation duplication inference";
- final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
public static void main( final String args[] ) {
catch ( final Exception e ) {
ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
- if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
System.out.println();
gsdi.print_help();
System.exit( 0 );
}
- else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 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.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 );
+ allowed_options.add( GSDIR_OPTION );
+ allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE );
+ allowed_options.add( MOST_PARSIMONIOUS_OPTION );
+ allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
allowed_options.add( TRANSFER_TAXONOMY_OPTION );
+ allowed_options.add( SUFFIX_FOR_DIR_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
}
execute( cla );
}
ALGORITHM base_algorithm = ALGORITHM.GSDI;
boolean most_parsimonous_duplication_model = false;
boolean allow_stripping_of_gene_tree = false;
- if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {
+ if ( cla.isOptionSet( GSDIR_OPTION ) ) {
base_algorithm = ALGORITHM.GSDIR;
}
- if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
+ if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
if ( base_algorithm == ALGORITHM.SDI ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
+ ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
}
most_parsimonous_duplication_model = true;
}
- if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
+ if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
if ( base_algorithm == ALGORITHM.SDI ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
+ ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
}
allow_stripping_of_gene_tree = true;
}
if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
transfer_taxonomy = true;
}
- Phylogeny species_tree = null;
- Phylogeny gene_tree = null;
+ boolean use_gene_tree_dir = false;
+ final String gene_tree_suffix;
+ if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) {
+ gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION );
+ use_gene_tree_dir = true;
+ }
+ else {
+ gene_tree_suffix = null;
+ }
File gene_tree_file = null;
File species_tree_file = null;
File out_file = null;
File log_file = null;
- EasyWriter log_writer = null;
try {
gene_tree_file = cla.getFile( 0 );
species_tree_file = cla.getFile( 1 );
- out_file = cla.getFile( 2 );
- log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
+ if ( cla.getNumberOfNames() == 3 ) {
+ out_file = cla.getFile( 2 );
+ log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
+ }
}
catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
}
+ if ( use_gene_tree_dir ) {
+ final File dir = new File( gene_tree_file.toString() );
+ final File gene_tree_files[] = dir.listFiles( new FilenameFilter() {
+
+ @Override
+ public boolean accept( final File dir, final String name ) {
+ return name.endsWith( gene_tree_suffix );
+ }
+ } );
+ for( final File file : gene_tree_files ) {
+ System.out.println( file );
+ }
+ execute( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_files,
+ species_tree_file );
+ }
+ else {
+ execute( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_file,
+ species_tree_file,
+ out_file,
+ log_file );
+ }
+ }
+
+ private static void execute( final ALGORITHM base_algorithm,
+ final boolean most_parsimonous_duplication_model,
+ final boolean allow_stripping_of_gene_tree,
+ final boolean transfer_taxonomy,
+ final File gene_tree_files[],
+ final File species_tree_file )
+ throws IOException {
+ for( final File gene_tree_file : gene_tree_files ) {
+ if (gene_tree_file.getName().equals( species_tree_file.getName() )) {
+ continue;
+ }
+ execute( base_algorithm,
+ most_parsimonous_duplication_model,
+ allow_stripping_of_gene_tree,
+ transfer_taxonomy,
+ gene_tree_file,
+ species_tree_file,
+ new File( gene_tree_file + "gsdi" ),
+ new File( gene_tree_file + "gsdi_log" ) );
+ }
+ }
+
+ private static void execute( final ALGORITHM base_algorithm,
+ final boolean most_parsimonous_duplication_model,
+ final boolean allow_stripping_of_gene_tree,
+ final boolean transfer_taxonomy,
+ final File gene_tree_file,
+ final File species_tree_file,
+ final File out_file,
+ final File log_file )
+ throws IOException {
if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
}
if ( ForesterUtil.isWritableFile( log_file ) != null ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
}
+ EasyWriter log_writer = null;
try {
log_writer = ForesterUtil.createEasyWriter( log_file );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
}
+ Phylogeny species_tree = null;
+ Phylogeny gene_tree = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
gene_tree.setRooted( true );
species_tree.setRooted( true );
if ( !gene_tree.isCompletelyBinary() ) {
- fatalError( "user error", "gene tree is not completely binary", log_writer );
+ fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
}
if ( base_algorithm == ALGORITHM.SDI ) {
if ( !species_tree.isCompletelyBinary() ) {
fatalError( "unexpected error", e.toString(), log_writer );
}
System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
- + "ms" );
+ + "ms" );
log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
- + "ms" );
+ + "ms" );
System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() );
log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() );
try {
System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() );
final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
- + SUFFIX_FOR_SPECIES_TREE_USED );
+ + SUFFIX_FOR_SPECIES_TREE_USED );
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
- + "]: " + 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() );
+ gsdii.getStrippedExternalGeneTreeNodes().size() );
log_writer.println( "External nodes stripped from gene tree : "
+ gsdii.getStrippedExternalGeneTreeNodes().size() );
- System.out.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
- log_writer.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
+ System.out
+ .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
+ log_writer
+ .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
System.out.println();
System.out.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
log_writer.println( "Number of speciations : " + gsdii.getSpeciationsSum() );
}
private static void print_help() {
- System.out.println( "Usage: " + gsdi.PRG_NAME
- + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
+ System.out.println( "Usage: " + PRG_NAME
+ + " [-options] <gene tree in phyloXML format, or directory with gene trees> <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" );
- 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 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.GSDIR_OPTION
- + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
+ System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " : to allow stripping of gene tree nodes without a matching species" );
+ System.out.println( " -" + 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 due to polytomies in the species tree" );
+ System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE
+ + " : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
+ System.out.println( " -" + GSDIR_OPTION
+ + " : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
- + ": to transfer taxonomic data from species tree to gene tree\n" );
+ + " : to transfer taxonomic data from species tree to gene tree" );
+ System.out.println( " -" + SUFFIX_FOR_DIR_OPTION
+ + "=<suffix>: suffix for gene trees for analyzing entire directory of trees" );
System.out.println();
- System.out.println( "Gene tree:" );
+ System.out.println();
+ System.out.println( "Gene tree(s):" );
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( " in phyloXML format (unless option -" + 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" );
+ System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
+ + " gene_tree.xml tree_of_life.xml out.xml" );
+ System.out.println( " gsdi -" + SUFFIX_FOR_DIR_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml"
+ + " gene_tree_dir tree_of_life.xml" );
System.out.println();
}
private static void writeToRemappedFile( final File out_file,
final SortedSet<String> remapped,
- final EasyWriter log_writer ) throws IOException {
+ 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 ) {
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