import org.forester.util.ForesterUtil;
public class rio {
+ //
- public final static String PRG_NAME = "rio";
- public final static String PRG_VERSION = "5.000";
- public final static String PRG_DATE = "170411";
+ public final static String PRG_NAME = "rio";
+ public final static String PRG_VERSION = "5.900";
+ public final static String PRG_DATE = "170420";
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 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 OUTGROUP = "o";
final static private String USE_SDIR = "s";
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;
public static void main( final String[] args ) {
allowed_options.add( USE_SDIR );
allowed_options.add( GENE_TREES_SUFFIX_OPTION );
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 );
if ( !gene_trees_file.exists() ) {
ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" does not exist" );
}
+ if ( gene_trees_file.listFiles().length < 1 ) {
+ ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" is empty" );
+ }
use_dir = true;
indir = gene_trees_file;
}
gene_trees_suffix = cla.getOptionValueAsCleanString( GENE_TREES_SUFFIX_OPTION );
}
else {
- gene_trees_suffix = ".mlt";
+ gene_trees_suffix = GENE_TREES_SUFFIX_DEFAULT;
+ }
+ final boolean perform_id_mapping;
+ final File id_mapping_dir;
+ if ( cla.isOptionSet( MAPPINGS_DIR_OPTION ) ) {
+ id_mapping_dir = new File( cla.getOptionValue( MAPPINGS_DIR_OPTION ) );
+ perform_id_mapping = true;
+ if ( !use_dir ) {
+ ForesterUtil.fatalError( "no id mapping when operating on indivual gene trees" );
+ }
+ if ( !id_mapping_dir.exists() ) {
+ ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" does not exist" );
+ }
+ if ( !id_mapping_dir.isDirectory() ) {
+ ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is not a directory" );
+ }
+ if ( id_mapping_dir.listFiles().length < 1 ) {
+ ForesterUtil.fatalError( "id mappings directory \"" + id_mapping_dir + "\" is empty" );
+ }
+ }
+ else {
+ id_mapping_dir = null;
+ perform_id_mapping = false;
+ }
+ final String id_mapping_suffix;
+ if ( cla.isOptionSet( MAPPINGS_SUFFIX_OPTION ) ) {
+ if ( !use_dir ) {
+ ForesterUtil.fatalError( "no id mapping file suffix option when operating on indivual gene trees" );
+ }
+ if ( !perform_id_mapping ) {
+ ForesterUtil.fatalError( "no id mapping directory given" );
+ }
+ if ( !cla.isOptionHasAValue( MAPPINGS_SUFFIX_OPTION ) ) {
+ ForesterUtil.fatalError( "no value for -" + MAPPINGS_SUFFIX_OPTION );
+ }
+ id_mapping_suffix = cla.getOptionValueAsCleanString( MAPPINGS_SUFFIX_OPTION );
+ }
+ 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() ) {
catch ( final IOException e ) {
ForesterUtil.fatalError( e.getLocalizedMessage() );
}
+ if ( perform_id_mapping ) {
+ try {
+ System.out.println( "Id mappings in-dir :\t" + id_mapping_dir.getCanonicalPath() );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
+ }
+ 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( "EXT NODES" );
log.print( "\t" );
- log.print( ortholog_group_cutoff + " O GROUPS" );
+ log.print( ortholog_group_cutoff + " O GROUPS" );
log.print( "\t" );
log.print( "0.05 O GROUPS" );
log.print( "\t" );
log.print( "\t" );
log.print( "0.95 O GROUPS" );
log.print( "\t" );
+ 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" );
log.print( "MEAN DUP" );
}
try {
RIOUtil.executeAnalysis( gf,
- species_tree_file,
- new File( outdir.getCanonicalFile() + "/" + outname + ORTHO_OUTTABLE_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname + ORTHOLOG_GROUPS_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ),
- outgroup,
- rerooting,
- gt_first,
- gt_last,
- new File( outdir.getCanonicalFile() + "/" + outname
- + STRIPPED_SPECIES_TREE_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname
- + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
- new File( outdir.getCanonicalFile() + "/" + outname
- + OUT_MED_DUP_GENE_TREE_SUFFIX ),
- true,
- algorithm,
- true,
- log,
- ortholog_group_cutoff );
+ species_tree_file,
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHO_OUTTABLE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.LOGFILE_SUFFIX ),
+ outgroup,
+ rerooting,
+ gt_first,
+ gt_last,
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ),
+ true,
+ algorithm,
+ true,
+ log,
+ ortholog_group_cutoff,
+ perform_id_mapping,
+ id_mapping_dir,
+ 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,
- new File( outname + 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 ),
- algorithm == ALGORITHM.GSDIR,
- algorithm,
- false,
- null,
- ortholog_group_cutoff );
+ species_tree_file,
+ orthology_outtable,
+ null,
+ new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
+ logfile,
+ outgroup,
+ rerooting,
+ gt_first,
+ gt_last,
+ 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,
+ null,
+ ortholog_group_cutoff,
+ false,
+ null,
+ null,
+ false,
+ null,
+ null,
+ null );
}
if ( !use_dir ) {
time = System.currentTimeMillis() - time;
+ " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
System.out.println( " disallowed, as are most options)" );
System.out.println( " -" + GENE_TREES_SUFFIX_OPTION
- + "=<suffix> : suffix for gene trees when operating on gene tree directories (default: .mlt)" );
+ + "=<suffix> : suffix for gene trees when operating on gene tree directories (default: "
+ + GENE_TREES_SUFFIX_DEFAULT + ")" );
+ 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 gene_trees.nh species.xml outtable.tsv log.txt" );
System.out.println( " rio -c=0.9 -f=10 -l=100 -r=none gene_trees.xml species.xml outtable.tsv log.txt" );
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