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 trees in-dir:\t" + best_trees_indir.getCanonicalPath() );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
+ }
+ System.out.println( "Consensus (\"best\") gene trees suffix:\t" + best_trees_suffix );
+ }
if ( use_dir ) {
System.out.println( "Out-dir :\t" + outdir );
}
log.print( "\t" );
log.print( species_tree_file.getCanonicalPath() );
log.println();
+ if ( perform_id_mapping ) {
+ log.print( "# Id mappings in-dir" );
+ log.print( "\t" );
+ log.print( id_mapping_dir.getCanonicalPath() );
+ log.println();
+ log.print( "# Id mappings suffix" );
+ log.print( "\t" );
+ log.print( id_mapping_suffix );
+ log.println();
+ }
+ if ( perform_gsdir_on_best_tree ) {
+ log.print( "# Consensus (\"best\") gene tree dir" );
+ log.print( "\t" );
+ log.print( best_trees_indir.getCanonicalPath() );
+ log.println();
+ log.print( "# Consensus (\"best\") gene tree suffix" );
+ log.print( "\t" );
+ log.print( best_trees_suffix );
+ log.println();
+ }
log.print( "# Out-dir" );
log.print( "\t" );
log.print( outdir.getCanonicalPath() );
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
- + ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
+ + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
new File( outdir.getCanonicalFile() + "/" + outname
- + ORTHOLOG_GROUPS_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ),
+ + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + 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 );
}
git://source.jalview.org / jalview.git / blobdiff