import java.io.Writer;
import java.util.ArrayList;
import java.util.Date;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
import org.forester.surfacing.Species;
import org.forester.surfacing.SurfacingUtil;
+import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.CommandLineArguments;
public class surfacing {
+ private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000;
public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out";
public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot";
public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
- final static private String PRG_VERSION = "2.100";
- final static private String PRG_DATE = "2011.06.17";
+ final static private String PRG_VERSION = "2.210";
+ final static private String PRG_DATE = "2011.12.08";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
}
try {
final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
- .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+ .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
if ( p_array.length < 1 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ "] does not contain any phylogeny in phyloXML format" );
}
} // if ( perform_pwc ) {
System.out.println();
- html_desc.append( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
BufferedWriter[] query_domains_writer_ary = null;
List<DomainId>[] query_domain_ids_array = null;
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
}
+ final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics();
+ final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics();
+ final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
+ final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
+ final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
+ final SortedSet<String> domains_which_never_single = new TreeSet<String>();
+ BufferedWriter domains_per_potein_stats_writer = null;
+ try {
+ domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
+ + output_file + "__domains_per_potein_stats.txt" ) );
+ domains_per_potein_stats_writer.write( "Genome" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "Mean" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "SD" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "Median" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "N" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "Min" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( "Max" );
+ domains_per_potein_stats_writer.write( "\n" );
+ }
+ catch ( final IOException e3 ) {
+ e3.printStackTrace();
+ }
+ // Main loop:
for( int i = 0; i < number_of_genomes; ++i ) {
System.out.println();
System.out.println( ( i + 1 ) + "/" + number_of_genomes );
input_file_properties[ i ][ 1 ],
filter,
filter_type,
- ind_score_cutoff );
+ ind_score_cutoff,
+ true );
}
else {
parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
input_file_properties[ i ][ 1 ],
- ind_score_cutoff );
+ ind_score_cutoff,
+ true );
}
if ( e_value_max >= 0.0 ) {
parser.setEValueMaximum( e_value_max );
System.out.println( "Domains ignored due to virus like id: " );
ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
}
+ final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
+ protein_coverage_stats.addValue( coverage );
System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
System.out.println( "Number of proteins stored : " + protein_list.size() );
log( "Number of proteins stored : " + protein_list.size(), log_writer );
+ System.out.println( "Coverage : "
+ + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
+ log( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage )
+ + "%", log_writer );
System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
System.out.println( "Domains stored : " + parser.getDomainsStored() );
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
}
+ SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ],
+ protein_list,
+ all_genomes_domains_per_potein_stats,
+ all_genomes_domains_per_potein_histo,
+ domains_which_are_always_single,
+ domains_which_are_sometimes_single_sometimes_not,
+ domains_which_never_single,
+ domains_per_potein_stats_writer );
gwcd_list.add( BasicGenomeWideCombinableDomains
.createInstance( protein_list,
ignore_combination_with_same,
}
System.gc();
} // for( int i = 0; i < number_of_genomes; ++i ) {
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ + per_genome_domain_promiscuity_statistics_file );
+ //
try {
- per_genome_domain_promiscuity_statistics_writer.flush();
- per_genome_domain_promiscuity_statistics_writer.close();
- dc_data_writer.flush();
- dc_data_writer.close();
- log_writer.flush();
- log_writer.close();
+ domains_per_potein_stats_writer.write( "ALL" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" );
+ domains_per_potein_stats_writer.write( "\t" );
+ domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
+ domains_per_potein_stats_writer.write( "\n" );
+ domains_per_potein_stats_writer.close();
+ printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
+ ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
+ ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
+ ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
+ ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + "__domains_always_combined.txt" ), domains_which_never_single, "\n" );
+ ForesterUtil.programMessage( PRG_NAME,
+ "Average of proteins with a least one domain assigned: "
+ + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
+ + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" );
+ ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " + 100
+ * protein_coverage_stats.getMin() + "%-" + 100 * protein_coverage_stats.getMax() + "%" );
+ log( "Average of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.arithmeticMean() )
+ + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
+ log( "Range of prot with a least one dom assigned : " + 100 * protein_coverage_stats.getMin() + "%-"
+ + 100 * protein_coverage_stats.getMax() + "%", log_writer );
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
}
- ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
- + per_genome_domain_promiscuity_statistics_file );
if ( query_domains_writer_ary != null ) {
for( int j = 0; j < query_domain_ids_array.length; j++ ) {
try {
}
}
}
+ try {
+ per_genome_domain_promiscuity_statistics_writer.close();
+ dc_data_writer.close();
+ log_writer.close();
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
+ }
if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
try {
SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
DescriptiveStatistics pw_stats = null;
try {
String my_outfile = output_file.toString();
- if ( !my_outfile.endsWith( ".html" ) ) {
+ Map<Character, Writer> split_writers = null;
+ Writer writer = null;
+ if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
+ if ( my_outfile.endsWith( ".html" ) ) {
+ my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
+ }
+ split_writers = new HashMap<Character, Writer>();
+ createSplitWriters( out_dir, my_outfile, split_writers );
+ }
+ else if ( !my_outfile.endsWith( ".html" ) ) {
my_outfile += ".html";
+ writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
}
- final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir
- + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
List<Species> species_order = null;
if ( species_matrix ) {
species_order = new ArrayList<Species>();
.writeDomainSimilaritiesToFile( html_desc,
new StringBuilder( number_of_genomes + " genomes" ),
writer,
+ split_writers,
similarities,
number_of_genomes == 2,
species_order,
System.out.println();
}
+ private static void createSplitWriters( final File out_dir,
+ final String my_outfile,
+ final Map<Character, Writer> split_writers ) throws IOException {
+ split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_A.html" ) ) );
+ split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_B.html" ) ) );
+ split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_C.html" ) ) );
+ split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_D.html" ) ) );
+ split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_E.html" ) ) );
+ split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_F.html" ) ) );
+ split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_G.html" ) ) );
+ split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_H.html" ) ) );
+ split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_I.html" ) ) );
+ split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_J.html" ) ) );
+ split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_K.html" ) ) );
+ split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_L.html" ) ) );
+ split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_M.html" ) ) );
+ split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_N.html" ) ) );
+ split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_O.html" ) ) );
+ split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_P.html" ) ) );
+ split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Q.html" ) ) );
+ split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_R.html" ) ) );
+ split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_S.html" ) ) );
+ split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_T.html" ) ) );
+ split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_U.html" ) ) );
+ split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_V.html" ) ) );
+ split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_W.html" ) ) );
+ split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_X.html" ) ) );
+ split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Y.html" ) ) );
+ split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_Z.html" ) ) );
+ split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+ + "_domains_0.html" ) ) );
+ }
+
+ private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+ final Writer log_writer ) {
+ int sum = 0;
+ for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
+ sum += entry.getValue();
+ }
+ final double percentage = 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) / sum;
+ ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
+ log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer );
+ }
+
private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
final String[][] input_file_properties ) {
final String[] genomes = new String[ input_file_properties.length ];
final PhylogenyNode n = it.next();
if ( ForesterUtil.isEmpty( n.getName() ) ) {
if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ else if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
n.setName( n.getNodeData().getTaxonomy().getScientificName() );
}
+ else if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getCommonName() );
+ }
else {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "node without both name and scientific taxonomy name found" );
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "node with no name, scientific name, common name, or taxonomy code present" );
}
}
}
git://source.jalview.org / jalview.git / blobdiff