final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
final static private String HELP_OPTION_1 = "help";
- final static private String LOGFILE_SUFFIX = "_RIO_log.tsv";
- final static private String STRIPPED_SPECIES_TREE_SUFFIX = "_RIO_sst.xml";
- final static private String ORTHO_OUTTABLE_SUFFIX = "_RIO_orthologies.tsv";
- final static private String ORTHO_OUTTABLE_WITH_MAP_SUFFIX = "_RIO_orthologies_ext_map.tsv";
- final static private String OUT_MIN_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_min_dup_";
- final static private String OUT_MED_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_med_dup_";
- final static private String ORTHOLOG_GROUPS_SUFFIX = "_RIO_ortholog_groups.tsv";
final static private String HELP_OPTION_2 = "h";
final static private String GT_FIRST = "f";
final static private String GT_LAST = "l";
final static private String GENE_TREES_SUFFIX_OPTION = "g";
final static private String MAPPINGS_DIR_OPTION = "m";
final static private String MAPPINGS_SUFFIX_OPTION = "ms";
+ final static private String CONSENSUS_TREES_DIR_OPTION = "co";
+ final static private String CONSENSUS_TREES_SUFFIX_OPTION = "cos";
final static private String MAPPINGS_SUFFIX_DEFAULT = ".nim";
+ final static private String CONSENSUS_TREE_SUFFIX_DEFAULT = ".xml";
final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION = "c";
final static private String GENE_TREES_SUFFIX_DEFAULT = ".mlt";
final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5;
allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION );
allowed_options.add( MAPPINGS_DIR_OPTION );
allowed_options.add( MAPPINGS_SUFFIX_OPTION );
+ allowed_options.add( CONSENSUS_TREES_DIR_OPTION );
+ allowed_options.add( CONSENSUS_TREES_SUFFIX_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options );
else {
id_mapping_suffix = MAPPINGS_SUFFIX_DEFAULT;
}
+ boolean perform_gsdir_on_best_tree;
+ final File best_trees_indir;
+ if ( cla.isOptionSet( CONSENSUS_TREES_DIR_OPTION ) ) {
+ best_trees_indir = new File( cla.getOptionValue( CONSENSUS_TREES_DIR_OPTION ) );
+ perform_gsdir_on_best_tree = true;
+ if ( !use_dir ) {
+ ForesterUtil
+ .fatalError( "no consensus (\"best\") gene tree GSDIR analysis when operating on individual gene trees" );
+ }
+ if ( !best_trees_indir.exists() ) {
+ ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir
+ + "\" does not exist" );
+ }
+ if ( !best_trees_indir.isDirectory() ) {
+ ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir
+ + "\" is not a directory" );
+ }
+ if ( best_trees_indir.listFiles().length < 1 ) {
+ ForesterUtil
+ .fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + "\" is empty" );
+ }
+ }
+ else {
+ best_trees_indir = null;
+ perform_gsdir_on_best_tree = false;
+ }
+ final String best_trees_suffix;
+ if ( cla.isOptionSet( CONSENSUS_TREES_SUFFIX_OPTION ) ) {
+ if ( !use_dir ) {
+ ForesterUtil
+ .fatalError( "no consensus (\"best\") gene tree suffix option when operating on individual gene trees" );
+ }
+ if ( !perform_gsdir_on_best_tree ) {
+ ForesterUtil.fatalError( "no consensus (\"best\") gene tree directory given" );
+ }
+ if ( !cla.isOptionHasAValue( CONSENSUS_TREES_SUFFIX_OPTION ) ) {
+ ForesterUtil.fatalError( "no value for -" + CONSENSUS_TREES_SUFFIX_OPTION );
+ }
+ best_trees_suffix = cla.getOptionValueAsCleanString( CONSENSUS_TREES_SUFFIX_OPTION );
+ }
+ else {
+ best_trees_suffix = CONSENSUS_TREE_SUFFIX_DEFAULT;
+ }
+ ////////////////////////////////
ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
if ( !use_dir && orthology_outtable.exists() ) {
ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
}
System.out.println( "Id mappings suffix :\t" + id_mapping_suffix );
}
+ if ( perform_gsdir_on_best_tree ) {
+ try {
+ System.out.println( "Consensus (\"best\") gene tree dir :\t" + best_trees_indir.getCanonicalPath() );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
+ }
+ System.out.println( "Consensus (\"best\") gene tree suffix :\t" + best_trees_suffix );
+ }
if ( use_dir ) {
System.out.println( "Out-dir :\t" + outdir );
}
log.print( "\t" );
log.print( "0.95 O GROUPS" );
log.print( "\t" );
- if ( true ) { //TODO
+ if ( perform_gsdir_on_best_tree ) {
log.print( "BEST TREE DUP" );
log.print( "\t" );
+ log.print( "MEDIAN DUP - BEST TREE DUP" );
+ log.print( "\t" );
}
log.print( "MEDIAN DUP" );
log.print( "\t" );
RIOUtil.executeAnalysis( gf,
species_tree_file,
new File( outdir.getCanonicalFile() + "/" + outname
- + ORTHO_OUTTABLE_SUFFIX ),
+ + RIOUtil.ORTHO_OUTTABLE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname
- + ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
+ + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname
- + ORTHOLOG_GROUPS_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ),
+ + RIOUtil.LOGFILE_SUFFIX ),
outgroup,
rerooting,
gt_first,
gt_last,
new File( outdir.getCanonicalFile() + "/" + outname
- + STRIPPED_SPECIES_TREE_SUFFIX ),
+ + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname
- + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
+ + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname
- + OUT_MED_DUP_GENE_TREE_SUFFIX ),
+ + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ),
true,
algorithm,
true,
ortholog_group_cutoff,
perform_id_mapping,
id_mapping_dir,
- id_mapping_suffix );
+ id_mapping_suffix,
+ perform_gsdir_on_best_tree,
+ outdir,
+ best_trees_indir,
+ best_trees_suffix );
}
catch ( IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
System.out.println();
}
else {
- String outname = orthology_outtable.toString();
- if ( outname.indexOf( "." ) > 0 ) {
- outname = outname.substring( 0, outname.lastIndexOf( "." ) );
- }
+ String outname = ForesterUtil.removeFileExtension( orthology_outtable.toString() );
RIOUtil.executeAnalysis( gene_trees_file,
species_tree_file,
orthology_outtable,
null,
- new File( outname + ORTHOLOG_GROUPS_SUFFIX ),
+ new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
logfile,
outgroup,
rerooting,
gt_first,
gt_last,
- new File( outname + STRIPPED_SPECIES_TREE_SUFFIX ),
- new File( outname + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
- new File( outname + OUT_MED_DUP_GENE_TREE_SUFFIX ),
+ new File( outname + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ),
+ new File( outname + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ),
+ new File( outname + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ),
algorithm == ALGORITHM.GSDIR,
algorithm,
false,
ortholog_group_cutoff,
false,
null,
+ null,
+ false,
+ null,
+ null,
null );
}
if ( !use_dir ) {
System.out.println( " -" + MAPPINGS_DIR_OPTION + "=<dir> : directory for id mapping files" );
System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "=<suffix> : suffix for id mapping files (default: "
+ MAPPINGS_SUFFIX_DEFAULT + ")" );
+ System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION
+ + "=<dir> : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" );
+ System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION
+ + "=<suffix> : suffix for consenus (\"best\") gene trees (default: " + CONSENSUS_TREE_SUFFIX_DEFAULT
+ + ")" );
+ ///
System.out.println();
System.out.println( " Formats" );
System.out
System.out.println( " rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" );
System.out.println( " rio -g=.mlt -m=id_maps_dir -ms=.nim -c=0.8 gene_trees_dir species.xml out_dir log.tsv" );
System.out.println( " rio -m=id_maps_dir -c=0.8 gene_trees_dir species.xml out_dir log.tsv" );
+ System.out
+ .println( " rio -m=id_maps_dir -co=consensus_dir -cos=.xml -c=0.8 gene_trees_dir species.xml out_dir log.tsv" );
System.out.println();
System.exit( -1 );
}
package org.forester.rio;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.math.RoundingMode;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeSet;
-import javax.swing.JOptionPane;
-
-import org.forester.archaeopteryx.AptxUtil;
import org.forester.datastructures.IntMatrix;
import org.forester.io.parsers.IteratingPhylogenyParser;
import org.forester.io.parsers.PhylogenyParser;
public final class RIOUtil {
+ public final static String STRIPPED_SPECIES_TREE_SUFFIX = "_RIO_stripped_species_tree.xml";
+ public final static String ORTHO_OUTTABLE_SUFFIX = "_RIO_orthologies.tsv";
+ public final static String ORTHO_OUTTABLE_WITH_MAP_SUFFIX = "_RIO_orthologies_ext_map.tsv";
+ public final static String OUT_MIN_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_min_dup_";
+ public final static String OUT_MED_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_med_dup_";
+ public final static String BEST_TREE_SUFFIX = "_RIO_consensus_gene_tree_dup_";
+ public final static String ORTHOLOG_GROUPS_SUFFIX = "_RIO_ortholog_groups.tsv";
+ public final static String LOGFILE_SUFFIX = "_RIO_log.tsv";
+
public static final void executeAnalysis( final File gene_trees_file,
final File species_tree_file,
final File orthology_outtable,
final double ortholog_group_cutoff,
final boolean perform_id_mapping,
final File id_mapping_dir,
- final String id_mapping_suffix ) {
+ final String id_mapping_suffix,
+ final boolean perform_gsdir_on_best_tree,
+ final File outdir,
+ final File best_trees_indir,
+ final String best_trees_suffix ) {
try {
final SortedMap<String, String> id_map;
if ( perform_id_mapping ) {
else {
m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
}
- ////////////////////////////////////////////
- ////////////////////////////////////////////
- //TODO
- final boolean perform_gsdir_on_best_tree = true;
- final File best_trees_dir = new File( "best_trees" );
- final String best_trees_suffix = ".xml";
final GSDIR gsdir_for_best_tree;
if ( perform_gsdir_on_best_tree ) {
- final Phylogeny best_tree = obtainTree( best_trees_dir, gene_trees_file.getName(), best_trees_suffix );
- final Phylogeny species_tree = SDIutil
- .parseSpeciesTree( best_tree, species_tree_file, false, true, TAXONOMY_EXTRACTION.NO );
- PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree );
- best_tree.setRooted( true );
- species_tree.setRooted( true );
- if ( !best_tree.isCompletelyBinaryAllow3ChildrenAtRoot() ) {
- throw new IOException( "gene tree matching to ["
- + ForesterUtil.removeFileExtension( gene_trees_file.getName() )
- + "] is not completely binary" );
- }
- final PhylogenyNodeIterator it = best_tree.iteratorExternalForward();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- final String name = n.getName().trim();
- if ( !ForesterUtil.isEmpty( name ) ) {
- try {
- ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE );
- }
- catch ( final PhyloXmlDataFormatException e ) {
- // Ignore.
- }
- }
- }
- gsdir_for_best_tree = new GSDIR( best_tree, species_tree, true, true, true );
- final Phylogeny result_gene_tree = gsdir_for_best_tree.getMinDuplicationsSumGeneTree();
- System.out.println( gsdir_for_best_tree.getMinDuplicationsSum() );
- result_gene_tree.setRerootable( false );
- PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(),
- true,
- true,
- DESCENDANT_SORT_PRIORITY.NODE_NAME );
- writeTree( result_gene_tree, new File( gene_trees_file.getName() + "____.xml" ), null, id_map );
+ gsdir_for_best_tree = analyzeConsensusTree( gene_trees_file,
+ species_tree_file,
+ outdir,
+ best_trees_indir,
+ id_map,
+ best_trees_suffix );
}
else {
gsdir_for_best_tree = null;
}
- ////////////////////////////////////////////
- ////////////////////////////////////////////
final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics();
if ( perform_id_mapping ) {
writeOrthologyTable( orthology_outtable, stats.getN(), m, !use_gene_trees_dir, id_map, true );
log.print( "\t" );
log.print( Integer.toString( ortholog_groups_095 ) );
//
+ if ( true ) {
+ log.print( "\t" );
+ log.print( Integer.toString( gsdir_for_best_tree.getMinDuplicationsSum() ) );
+ log.print( "\t" );
+ log.print( df.format( median - gsdir_for_best_tree.getMinDuplicationsSum() ) );
+ }
+ //
log.print( "\t" );
if ( stats.getN() > 3 ) {
log.print( df.format( median ) );
}
}
+ private final static GSDIR analyzeConsensusTree( final File gene_trees_file,
+ final File species_tree_file,
+ final File outdir,
+ final File best_trees_indir,
+ final SortedMap<String, String> id_map,
+ final String best_trees_suffix )
+ throws IOException, FileNotFoundException, PhyloXmlDataFormatException, SDIException {
+ final File the_one = ForesterUtil.getMatchingFile( best_trees_indir,
+ gene_trees_file.getName(),
+ best_trees_suffix );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny best_tree = factory.create( the_one, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
+ final Phylogeny species_tree = SDIutil
+ .parseSpeciesTree( best_tree, species_tree_file, false, true, TAXONOMY_EXTRACTION.NO );
+ PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree );
+ best_tree.setRooted( true );
+ species_tree.setRooted( true );
+ if ( !best_tree.isCompletelyBinaryAllow3ChildrenAtRoot() ) {
+ throw new IOException( "gene tree matching to ["
+ + ForesterUtil.removeFileExtension( gene_trees_file.getName() ) + "] is not completely binary" );
+ }
+ final PhylogenyNodeIterator it = best_tree.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ try {
+ ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ // Ignore.
+ }
+ }
+ }
+ final GSDIR gsdir_for_best_tree = new GSDIR( best_tree, species_tree, true, true, true );
+ final Phylogeny result_gene_tree = gsdir_for_best_tree.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ final String outname = ForesterUtil.removeFileExtension( the_one.getName() );
+ final File outfile = new File( outdir.getCanonicalFile() + "/" + outname + RIOUtil.BEST_TREE_SUFFIX
+ + gsdir_for_best_tree.getMinDuplicationsSum() + ".xml" );
+ writeTree( result_gene_tree, outfile, null, id_map );
+ return gsdir_for_best_tree;
+ }
+
private static final void writeOrthologyTable( final File table_outfile,
final int gene_trees_analyzed,
final IntMatrix m,
final BasicTable<String> t = BasicTableParser.parse( the_one, '\t' );
return t.getColumnsAsMap( 0, 1 );
}
-
- private final static Phylogeny obtainTree( final File dir, final String prefix, final String suffix )
- throws IOException {
- final File the_one = ForesterUtil.getMatchingFile( dir, prefix, suffix );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- return factory.create( the_one, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
- }
}
git://source.jalview.org / jalview.git / commitdiff