import java.io.File;
import java.io.IOException;
+import java.math.RoundingMode;
import java.util.ArrayList;
import java.util.List;
public class rio {
- final static private String PRG_NAME = "rio";
- final static private String PRG_VERSION = "4.000 beta 8";
- final static private String PRG_DATE = "2013.01.11";
- 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 HELP_OPTION_2 = "h";
- final static private String GT_FIRST = "f";
- final static private String GT_LAST = "l";
- final static private String REROOTING_OPT = "r";
- final static private String OUTGROUP = "o";
- final static private String RETURN_SPECIES_TREE = "s";
- final static private String RETURN_BEST_GENE_TREE = "g";
- final static private String USE_SDIR = "b";
+ final static private String PRG_NAME = "rio";
+ final static private String PRG_VERSION = "4.000 beta 11";
+ final static private String PRG_DATE = "170417";
+ 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 HELP_OPTION_2 = "h";
+ final static private String GT_FIRST = "f";
+ final static private String GT_LAST = "l";
+ final static private String REROOTING_OPT = "r";
+ final static private String OUTGROUP = "o";
+ final static private String RETURN_SPECIES_TREE = "s";
+ final static private String RETURN_BEST_GENE_TREE = "g";
+ final static private String USE_SDIR = "b";
+ final static private String TRANSFER_TAXONOMY_OPTION = "t";
public static void main( final String[] args ) {
ForesterUtil.printProgramInformation( PRG_NAME,
if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
printHelp();
}
- if ( ( args.length < 3 ) || ( args.length > 11 ) ) {
+ if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
System.out.println();
System.out.println( "error: incorrect number of arguments" );
System.out.println();
allowed_options.add( USE_SDIR );
allowed_options.add( RETURN_SPECIES_TREE );
allowed_options.add( RETURN_BEST_GENE_TREE );
+ allowed_options.add( TRANSFER_TAXONOMY_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options );
ForesterUtil.fatalError( "\"" + return_gene_tree + "\" already exists" );
}
}
+ boolean transfer_taxonomy = false;
+ if ( !sdir && cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
+ if ( return_gene_tree == null ) {
+ ForesterUtil.fatalError( "no point in transferring taxonomy data without returning best gene tree" );
+ }
+ transfer_taxonomy = true;
+ }
ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file );
ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
if ( orthology_outtable.exists() ) {
ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
}
long time = 0;
- System.out.println( "Gene trees : " + gene_trees_file );
- System.out.println( "Species tree : " + species_tree_file );
- System.out.println( "All vs all orthology table: " + orthology_outtable );
+ try {
+ System.out.println( "Gene trees :\t" + gene_trees_file.getCanonicalPath() );
+ System.out.println( "Species tree :\t" + species_tree_file.getCanonicalPath() );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( e.getLocalizedMessage() );
+ }
+ System.out.println( "All vs all orthology results table :\t" + orthology_outtable );
if ( logfile != null ) {
- System.out.println( "Logfile : " + logfile );
+ System.out.println( "Logfile :\t" + logfile );
}
if ( gt_first != RIO.DEFAULT_RANGE ) {
- System.out.println( "First gene tree to analyze: " + gt_first );
+ System.out.println( "First gene tree to analyze :\t" + gt_first );
}
if ( gt_last != RIO.DEFAULT_RANGE ) {
- System.out.println( "Last gene tree to analyze : " + gt_last );
+ System.out.println( "Last gene tree to analyze :\t" + gt_last );
}
String rerooting_str = "";
switch ( rerooting ) {
break;
}
}
- System.out.println( "Re-rooting : " + rerooting_str );
+ System.out.println( "Re-rooting : \t" + rerooting_str );
if ( !sdir ) {
- System.out.println( "Non binary species tree : allowed" );
+ System.out.println( "Non binary species tree :\tallowed" );
}
else {
- System.out.println( "Non binary species tree : disallowed" );
+ System.out.println( "Non binary species tree :\tdisallowed" );
}
if ( return_species_tree != null ) {
- System.out.println( "Write used species tree to: " + return_species_tree );
+ System.out.println( "Write used species tree to :\t" + return_species_tree );
}
if ( return_gene_tree != null ) {
- System.out.println( "Write best gene tree to : " + return_gene_tree );
+ System.out.println( "Write best gene tree to :\t" + return_gene_tree );
+ System.out.println( "Transfer taxonomic data :\t" + transfer_taxonomy );
}
time = System.currentTimeMillis();
final ALGORITHM algorithm;
gt_first,
gt_last,
logfile != null,
- true );
+ true,
+ transfer_taxonomy );
}
else {
iterating = true;
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( false );
nhx.setIgnoreQuotes( true );
- nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+ nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( p instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
nex.setReplaceUnderscores( false );
nex.setIgnoreQuotes( true );
- nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+ nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else {
throw new RuntimeException( "unknown parser type: " + p );
gt_first,
gt_last,
logfile != null,
- true );
+ true,
+ transfer_taxonomy );
}
if ( algorithm == ALGORITHM.GSDIR ) {
- System.out.println( "Taxonomy linking based on : " + rio.getGSDIRtaxCompBase() );
+ System.out.println( "Taxonomy linking based on :\t" + rio.getGSDIRtaxCompBase() );
}
final IntMatrix m;
if ( iterating ) {
ForesterUtil.getForesterLibraryInformation() );
}
if ( return_species_tree != null ) {
- writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" );
+ writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to :\t" );
}
if ( return_gene_tree != null ) {
writeTree( rio.getMinDuplicationsGeneTree(),
return_gene_tree,
- "Wrote (one) minimal duplication gene tree to" );
+ "Wrote one min duplication gene tree :\t" );
}
final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
- System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: "
- + df.format( stats.sampleStandardDeviation() ) + ") ("
- + df.format( 100.0 * stats.arithmeticMean() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
- if ( stats.getN() > 3 ) {
- System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " ("
- + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+ final int min = ( int ) stats.getMin();
+ final int max = ( int ) stats.getMax();
+ final int median = ( int ) stats.median();
+ int min_count = 0;
+ int max_count = 0;
+ int median_count = 0;
+ for( double d : stats.getData() ) {
+ if ( ( ( int ) d ) == min ) {
+ ++min_count;
+ }
+ if ( ( ( int ) d ) == max ) {
+ ++max_count;
+ }
+ if ( ( ( int ) d ) == median ) {
+ ++median_count;
+ }
}
- System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " ("
- + df.format( 100.0 * stats.getMin() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
- System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " ("
- + df.format( 100.0 * stats.getMax() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
- System.out.println( "Gene tree internal nodes : " + rio.getIntNodesOfAnalyzedGeneTrees() );
- System.out.println( "Gene tree external nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() );
+ final double min_count_percentage = ( 100.0 * min_count ) / stats.getN();
+ final double max_count_percentage = ( 100.0 * max_count ) / stats.getN();
+ final double median_count_percentage = ( 100.0 * median_count ) / stats.getN();
+ System.out.println( "Gene tree internal nodes :\t" + rio.getIntNodesOfAnalyzedGeneTrees() );
+ System.out.println( "Gene tree external nodes :\t" + rio.getExtNodesOfAnalyzedGeneTrees() );
+ System.out.println( "Mean number of duplications :\t" + df.format( stats.arithmeticMean() ) + "\t"
+ + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() )
+ + "%\t(sd: " + df.format( stats.sampleStandardDeviation() ) + ")" );
+ if ( stats.getN() > 3 ) {
+ System.out.println( "Median number of duplications :\t" + df.format( median ) + "\t"
+ + df.format( ( 100.0 * median ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ }
+ System.out.println( "Minimum duplications :\t" + min + "\t"
+ + df.format( ( 100.0 * min ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ System.out.println( "Maximum duplications :\t" + ( int ) max + "\t"
+ + df.format( ( 100.0 * max ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
+ System.out.println( "Gene trees with median duplications :\t" + median_count + "\t"
+ + df.format( median_count_percentage ) + "%" );
+ System.out.println( "Gene trees with minimum duplications:\t" + min_count + "\t"
+ + df.format( min_count_percentage ) + "%" );
+ System.out.println( "Gene trees with maximum duplications:\t" + max_count + "\t"
+ + df.format( max_count_percentage ) + "%" );
}
catch ( final RIOException e ) {
ForesterUtil.fatalError( e.getLocalizedMessage() );
ForesterUtil.unexpectedFatalError( e );
}
time = System.currentTimeMillis() - time;
- System.out.println( "Time: " + time + "ms" );
- System.out.println( "OK" );
+ System.out.println( "Time :\t" + time + "ms" );
System.exit( 0 );
}
private final static void printHelp() {
System.out.println( "Usage" );
System.out.println();
- System.out
- .println( PRG_NAME
- + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
+ System.out.println( PRG_NAME
+ + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
System.out.println();
System.out.println( " Options" );
System.out.println( " -" + GT_FIRST + "=<first> : first gene tree to analyze (0-based index)" );
.println( " -" + RETURN_SPECIES_TREE + "=<outfile> : to write the (stripped) species tree to file" );
System.out.println( " -" + RETURN_BEST_GENE_TREE
+ "=<outfile> : to write (one) minimal duplication gene tree to file" );
+ System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
+ + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n"
+ + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" );
System.out.println( " -" + USE_SDIR
+ " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
System.out.println( " disallowed, as are most options)" );
System.out.println( " in the species tree." );
System.out.println();
System.out.println( " Examples" );
- System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" );
- System.out.println();
- System.out.println( " More information: http://code.google.com/p/forester/wiki/RIO" );
+ System.out.println( " rio gene_trees.nh species.xml outtable.tsv log.txt" );
+ System.out
+ .println( " rio -t -f=10 -l=100 -r=none -g=out_gene_tree.xml -s=stripped_species.xml gene_trees.xml species.xml outtable.tsv log.txt" );
System.out.println();
System.exit( -1 );
}
final String prg_name,
final String prg_v,
final String prg_date,
- final String f ) throws IOException {
+ final String f )
+ throws IOException {
final EasyWriter out = ForesterUtil.createEasyWriter( logfile );
out.println( prg_name );
out.println( "version : " + prg_v );
out.println( "date : " + prg_date );
out.println( "based on: " + f );
out.println( "----------------------------------" );
- out.println( "Gene trees : " + gene_trees_file );
- out.println( "Species tree : " + species_tree_file );
- out.println( "All vs all orthology table : " + outtable );
+ out.println( "Gene trees : " + gene_trees_file.getCanonicalPath() );
+ out.println( "Species tree : " + species_tree_file.getCanonicalPath() );
+ out.println( "All vs all orthology table : " + outtable.getCanonicalPath() );
out.flush();
out.println( rio.getLog().toString() );
out.close();
- System.out.println( "Wrote log to \"" + logfile + "\"" );
+ System.out.println( "Wrote log to :\t" + logfile.getCanonicalPath() );
}
private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m )
throws IOException {
final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile );
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" );
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
df.setDecimalSeparatorAlwaysShown( false );
+ df.setRoundingMode( RoundingMode.HALF_UP );
for( int i = 0; i < m.size(); ++i ) {
w.print( "\t" );
w.print( m.getLabel( i ) );
w.println();
}
w.close();
- System.out.println( "Wrote table to \"" + table_outfile + "\"" );
+ System.out.println( "Wrote table to :\t" + table_outfile.getCanonicalPath() );
}
private static void writeTree( final Phylogeny p, final File f, final String comment ) throws IOException {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( f, p, 0 );
- System.out.println( comment + " \"" + f + "\"" );
+ System.out.println( comment + f.getCanonicalPath() );
}
}