import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import org.forester.datastructures.IntMatrix;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.RIO;
import org.forester.util.CommandLineArguments;
+import org.forester.util.EasyWriter;
import org.forester.util.ForesterUtil;
public class rio {
final static private String PRG_NAME = "rio";
final static private String PRG_VERSION = "3.00 beta 1";
- final static private String PRG_DATE = "2010.01.15";
+ final static private String PRG_DATE = "2012.11.27";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org/forester/";
final static private String HELP_OPTION_1 = "help";
}
if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
printHelp();
- System.exit( 0 );
}
- if ( ( args.length < 3 ) || ( args.length > 10 ) ) {
+ if ( ( args.length < 2 ) || ( args.length > 10 ) ) {
System.out.println();
System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
System.out.println();
printHelp();
- System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( QUERY_OPTION );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
}
- final File multiple_trees_file = cla.getFile( 0 );
+ final File gene_trees_file = cla.getFile( 0 );
final File species_tree_file = cla.getFile( 1 );
- final File outfile = cla.getFile( 2 );
- ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, multiple_trees_file );
+ File outfile = null;
+ if ( cla.getNumberOfNames() > 2 ) {
+ outfile = cla.getFile( 2 );
+ }
+ ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file );
ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file );
if ( outfile.exists() ) {
ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
}
- String seq_name = null;
+ String query = null;
if ( cla.isOptionSet( QUERY_OPTION ) ) {
- seq_name = cla.getOptionValue( QUERY_OPTION );
+ query = cla.getOptionValue( QUERY_OPTION );
}
File table_outfile = null;
if ( cla.isOptionSet( TABLE_OUTPUT_OPTION ) ) {
table_outfile = new File( cla.getOptionValue( TABLE_OUTPUT_OPTION ) );
if ( table_outfile.exists() ) {
- ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
+ ForesterUtil.fatalError( PRG_NAME, "[" + table_outfile + "] already exists" );
}
}
boolean output_ultraparalogs = false;
if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
output_ultraparalogs = true;
}
- double t_orthologs = 0.0;
- double threshold_ultra_paralogs = 0.0;
+ double cutoff_for_orthologs = 50;
+ double cutoff_for_ultra_paralogs = 50;
int sort = 2;
try {
if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) {
- t_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION );
+ cutoff_for_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION );
}
if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) {
- threshold_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION );
+ cutoff_for_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION );
+ if ( !output_ultraparalogs ) {
+ printHelp();
+ }
}
if ( cla.isOptionSet( SORT_OPTION ) ) {
sort = cla.getOptionValueAsInt( SORT_OPTION );
catch ( final Exception e ) {
ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() );
}
- if ( sort < 0 ) {
- sort = 0;
+ if ( ( cutoff_for_orthologs < 0 ) || ( cutoff_for_ultra_paralogs < 0 ) || ( sort < 0 ) || ( sort > 2 ) ) {
+ printHelp();
+ }
+ if ( ( ( query == null ) && ( outfile != null ) ) || ( ( query != null ) && ( outfile == null ) ) ) {
+ printHelp();
}
- else if ( sort > 2 ) {
- sort = 2;
+ if ( output_ultraparalogs && ( outfile == null ) ) {
+ printHelp();
}
long time = 0;
- System.out.println( "\n" );
- System.out.println( "Gene trees: " + multiple_trees_file );
- System.out.println( "Species tree: " + species_tree_file );
- System.out.println( "Query: " + seq_name );
- System.out.println( "Outfile: " + outfile );
- System.out.println( "Outfile: " + table_outfile );
- System.out.println( "Sort: " + sort );
- System.out.println( "Threshold orthologs: " + t_orthologs );
- if ( output_ultraparalogs ) {
- System.out.println( "Threshold ultra paralogs: " + threshold_ultra_paralogs );
+ System.out.println( "Gene trees : " + gene_trees_file );
+ System.out.println( "Species tree : " + species_tree_file );
+ if ( query != null ) {
+ System.out.println( "Query : " + query );
+ System.out.println( "Outfile : " + outfile );
+ System.out.println( "Sort : " + sort );
+ System.out.println( "Cutoff for orthologs : " + cutoff_for_orthologs );
+ if ( output_ultraparalogs ) {
+ System.out.println( "Cutoff for ultra paralogs : " + cutoff_for_ultra_paralogs );
+ }
+ }
+ if ( table_outfile != null ) {
+ System.out.println( "Table output : " + table_outfile );
}
+ System.out.println();
time = System.currentTimeMillis();
Phylogeny species_tree = null;
try {
System.exit( -1 );
}
if ( !species_tree.isRooted() ) {
- ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" );
+ ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not rooted" );
System.exit( -1 );
}
if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" );
+ ForesterUtil.printErrorMessage( PRG_NAME, "species tree is not completely binary" );
System.exit( -1 );
}
- final RIO rio_instance = new RIO();
- final StringBuffer output = new StringBuffer();
- PrintWriter out = null;
try {
- rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name );
- output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs ) );
- if ( output_ultraparalogs ) {
- output.append( "\n\nUltra paralogs:\n" );
- output.append( rio_instance.inferredUltraParalogsToString( seq_name, threshold_ultra_paralogs ) );
+ RIO rio;
+ if ( ForesterUtil.isEmpty( query ) ) {
+ rio = new RIO( gene_trees_file, species_tree );
+ }
+ else {
+ rio = new RIO( gene_trees_file, species_tree, query );
+ }
+ if ( outfile != null ) {
+ final StringBuilder output = new StringBuilder();
+ output.append( rio.inferredOrthologsToString( query, sort, cutoff_for_orthologs ) );
+ if ( output_ultraparalogs ) {
+ output.append( "\n\nUltra paralogs:\n" );
+ output.append( rio.inferredUltraParalogsToString( query, cutoff_for_ultra_paralogs ) );
+ }
+ output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
+ output.append( "\nExt nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() );
+ output.append( "\nSamples : " + rio.getNumberOfSamples() + "\n" );
+ final PrintWriter out = new PrintWriter( new FileWriter( outfile ), true );
+ out.println( output );
+ out.close();
+ }
+ if ( table_outfile != null ) {
+ tableOutput( table_outfile, rio );
}
- output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
- output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() );
- output.append( "\nSamples : " + rio_instance.getNumberOfSamples() + "\n" );
- out = new PrintWriter( new FileWriter( outfile ), true );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() );
e.printStackTrace();
System.exit( -1 );
}
- out.println( output );
- out.close();
- ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
+ if ( outfile != null ) {
+ ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
+ }
time = System.currentTimeMillis() - time;
ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
- ForesterUtil.programMessage( PRG_NAME, "OK." );
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
System.exit( 0 );
}
+ private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException {
+ final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees() );
+ writeTable( table_outfile, rio, m );
+ }
+
+ private static void writeTable( final File table_outfile, final RIO rio, final IntMatrix m ) throws IOException {
+ final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile );
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" );
+ df.setDecimalSeparatorAlwaysShown( false );
+ w.print( "\t" );
+ for( int i = 0; i < m.size(); ++i ) {
+ w.print( "\t" );
+ w.print( m.getLabel( i ) );
+ }
+ w.println();
+ for( int x = 0; x < m.size(); ++x ) {
+ w.print( m.getLabel( x ) );
+ w.print( "\t" );
+ for( int y = 0; y < m.size(); ++y ) {
+ w.print( "\t" );
+ if ( x == y ) {
+ if ( m.get( x, y ) != rio.getNumberOfSamples() ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "diagonal value is off" );
+ }
+ w.print( "-" );
+ }
+ else {
+ w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getNumberOfSamples() ) );
+ }
+ }
+ w.println();
+ }
+ w.close();
+ ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" );
+ }
+
private final static void printHelp() {
- System.out.println( "Usage:" );
+ System.out.println( "usage:" );
System.out.println();
System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
System.out.println();
- System.out.println( "options:" );
+ System.out.println( " options:" );
+ System.out.println();
+ System.out.println( " -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" );
+ System.out.println( " -" + TABLE_OUTPUT_OPTION + " : file-name for output table" );
+ System.out.println( " -" + QUERY_OPTION + " : name for query (sequence/node)" );
+ System.out.println( " -" + SORT_OPTION + " : sort (default: 2)" );
+ System.out.println( " -" + OUTPUT_ULTRA_P_OPTION
+ + " : to output ultra-paralogs (species specific expansions/paralogs)" );
+ System.out.println( " -" + CUTOFF_ULTRA_P_OPTION + " : cutoff for ultra-paralog output (default: 50)" );
System.out.println();
- // System.out.println( " -" + STRICT_OPTION
- // + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
- // System.out.println( " -" + NORMALIZE_OPTION
- // + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
- // System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
- // System.out.println( " -" + LAST_OPTION
- // + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
- // System.out.println();
- // System.out.println( "M= (String) Multiple gene tree file (mandatory)" );
- // System.out.println( "N= (String) Query sequence name (mandatory)" );
- // System.out.println( "S= (String) Species tree file (mandatory)" );
- // System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" );
- // System.out.println( "P= (int) Sort priority" );
- // System.out.println( "L= (double) Threshold orthologs for output" );
- // System.out.println( " Sort priority (\"P=\"):" );
+ System.out.println( " sort:" );
System.out.println( RIO.getOrderHelp().toString() );
System.out.println();
System.out
- .println( " Example: \"rio -q=D_NEMVE -s=1 -t=out -u Bcl-2_e1_20_mafft_05_40_fme.mlt species.xml out\"" );
+ .println( " example: \"rio gene_trees.nh species.xml outfile -q=D_HUMAN -t=outtable -u -cu=60 -co=60\"" );
System.out.println();
+ System.exit( -1 );
}
}
git://source.jalview.org / jalview.git / blobdiff