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 java.util.TreeMap;
import java.util.TreeSet;
-import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
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.phyloxml.PhyloXmlUtil;
-import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.BinaryDomainCombination;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.surfacing.BasicGenomeWideCombinableDomains;
import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
-import org.forester.surfacing.DomainCountsDifferenceUtil;
import org.forester.surfacing.DomainLengthsTable;
import org.forester.surfacing.DomainParsimonyCalculator;
import org.forester.surfacing.DomainSimilarity;
final static private String PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION = "dc_regain_stats";
final static private String DA_ANALYSIS_OPTION = "DA_analyis";
final static private String USE_LAST_IN_FITCH_OPTION = "last";
- final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
+ public final static String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
final static private String OUTPUT_FILE_OPTION = "o";
final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
final static private boolean IGNORE_DUFS_DEFAULT = true;
final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
final static private double MAX_E_VALUE_DEFAULT = -1;
- final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+ public final static int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
- private static final String SEQ_EXTRACT_SUFFIX = ".prot";
- private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
- private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
- private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
- private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
- private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
- private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
- private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
- private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
+ public static final String SEQ_EXTRACT_SUFFIX = ".prot";
+ public static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
+ public static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
+ public static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
+ public static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
+ public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
+ public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
+ public static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
+ public static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e";
- private static final boolean VERBOSE = false;
+ public static final boolean VERBOSE = false;
private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
private static final boolean CALC_SIMILARITY_SCORES = false;
- private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
- final String[][] input_file_properties,
- final String automated_pairwise_comparison_suffix,
- final File outdir ) {
- for( int i = 0; i < input_file_properties.length; ++i ) {
- for( int j = 0; j < i; ++j ) {
- final String species_i = input_file_properties[ i ][ 1 ];
- final String species_j = input_file_properties[ j ][ 1 ];
- String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
- + species_j + automated_pairwise_comparison_suffix;
- switch ( domain_similarity_print_option ) {
- case HTML:
- if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
- pairwise_similarities_output_file_str += ".html";
- }
- break;
- }
- final String error = ForesterUtil
- .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
- + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- }
- }
- }
- }
-
- private static StringBuilder createParametersAsString( final boolean ignore_dufs,
- final double e_value_max,
- final int max_allowed_overlap,
- final boolean no_engulfing_overlaps,
- final File cutoff_scores_file,
- final BinaryDomainCombination.DomainCombinationType dc_type ) {
- final StringBuilder parameters_sb = new StringBuilder();
- parameters_sb.append( "E-value: " + e_value_max );
- if ( cutoff_scores_file != null ) {
- parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
- }
- else {
- parameters_sb.append( ", Cutoff-scores-file: not-set" );
- }
- if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
- parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
- }
- else {
- parameters_sb.append( ", Max-overlap: not-set" );
- }
- if ( no_engulfing_overlaps ) {
- parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
- }
- else {
- parameters_sb.append( ", Engulfing-overlaps: allowed" );
- }
- if ( ignore_dufs ) {
- parameters_sb.append( ", Ignore-dufs: true" );
- }
- else {
- parameters_sb.append( ", Ignore-dufs: false" );
- }
- parameters_sb.append( ", DC type (if applicable): " + dc_type );
- return parameters_sb;
- }
-
- /**
- * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
- *
- *
- * @param output_file
- * @param all_bin_domain_combinations_changed
- * @param sum_of_all_domains_encountered
- * @param all_bin_domain_combinations_encountered
- * @param is_gains_analysis
- * @param protein_length_stats_by_dc
- * @throws IOException
- */
- private static void executeFitchGainsAnalysis( final File output_file,
- final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
- final int sum_of_all_domains_encountered,
- final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
- final boolean is_gains_analysis ) throws IOException {
- SurfacingUtil.checkForOutputFileWriteability( output_file );
- final Writer out = ForesterUtil.createBufferedWriter( output_file );
- final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
- .listToSortedCountsMap( all_bin_domain_combinations_changed );
- final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
- final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
- int above_one = 0;
- int one = 0;
- for( final Object bdc_object : bdc_to_counts.keySet() ) {
- final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
- final int count = bdc_to_counts.get( bdc_object );
- if ( count < 1 ) {
- ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
- }
- out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
- if ( count > 1 ) {
- all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
- all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
- above_one++;
- }
- else if ( count == 1 ) {
- all_domains_in_combination_changed_only_once.add( bdc.getId0() );
- all_domains_in_combination_changed_only_once.add( bdc.getId1() );
- one++;
- }
- }
- final int all = all_bin_domain_combinations_encountered.size();
- int never_lost = -1;
- if ( !is_gains_analysis ) {
- all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
- never_lost = all_bin_domain_combinations_encountered.size();
- for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
- out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
- }
- }
- if ( is_gains_analysis ) {
- out.write( "Sum of all distinct domain combinations appearing once : " + one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations apppearing only once : "
- + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations apppearing more than once: "
- + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
- }
- else {
- out.write( "Sum of all distinct domain combinations never lost : " + never_lost
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations lost once : " + one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations lost only once : "
- + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations lost more than once: "
- + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
- }
- out.write( "All binary combinations : " + all
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "All domains : "
- + sum_of_all_domains_encountered );
- out.close();
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
- + "\"" );
- }
-
- private static void executePlusMinusAnalysis( final File output_file,
- final List<String> plus_minus_analysis_high_copy_base,
- final List<String> plus_minus_analysis_high_copy_target,
- final List<String> plus_minus_analysis_low_copy,
- final List<GenomeWideCombinableDomains> gwcd_list,
- final SortedMap<Species, List<Protein>> protein_lists_per_species,
- final Map<String, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final List<Object> plus_minus_analysis_numbers ) {
- final Set<String> all_spec = new HashSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- all_spec.add( gwcd.getSpecies().getSpeciesId() );
- }
- final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
- final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
- final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
- final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
- final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
- final File proteins_file_base = new File( output_file + "" );
- final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
- final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
- try {
- DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
- protein_lists_per_species,
- plus_minus_analysis_high_copy_base,
- plus_minus_analysis_high_copy_target,
- plus_minus_analysis_low_copy,
- min_diff,
- factor,
- plain_out_dom,
- html_out_dom,
- html_out_dc,
- domain_id_to_go_ids_map,
- go_id_to_term_map,
- all_domains_go_ids_out_dom,
- passing_domains_go_ids_out_dom,
- proteins_file_base );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
- + html_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
- + plain_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
- + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
- + passing_domains_go_ids_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
- + all_domains_go_ids_out_dom + "\"" );
- }
-
- private static Phylogeny[] getIntrees( final File[] intree_files,
- final int number_of_genomes,
- final String[][] input_file_properties ) {
- final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
- int i = 0;
- for( final File intree_file : intree_files ) {
- Phylogeny intree = null;
- final String error = ForesterUtil.isReadableFile( intree_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
- + error );
- }
- try {
- final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
- .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" );
- }
- else if ( p_array.length > 1 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
- + "] contains more than one phylogeny in phyloXML format" );
- }
- intree = p_array[ 0 ];
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
- + "]: " + error );
- }
- if ( ( intree == null ) || intree.isEmpty() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
- }
- if ( !intree.isRooted() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
- }
- if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "number of external nodes [" + intree.getNumberOfExternalNodes()
- + "] of input tree [" + intree_file
- + "] is smaller than the number of genomes the be analyzed ["
- + number_of_genomes + "]" );
- }
- final StringBuilder parent_names = new StringBuilder();
- final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
- if ( nodes_lacking_name > 0 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
- + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
- }
- preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
- if ( !intree.isCompletelyBinary() ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
- + "] is not completely binary" );
- }
- intrees[ i++ ] = intree;
- }
- return intrees;
- }
-
- private static void log( final String msg, final Writer w ) {
- try {
- w.write( msg );
- w.write( ForesterUtil.LINE_SEPARATOR );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
- }
-
public static void main( final String args[] ) {
final long start_time = new Date().getTime();
// final StringBuffer log = new StringBuffer();
if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
ignore_species_specific_domains = true;
}
+
+
+
+ if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no input species tree file given: "
+ + surfacing.INPUT_SPECIES_TREE_OPTION + "=<file>" );
+ }
+
+
+
+
File output_file = null;
if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
- processPlusMinusAnalysisOption( cla,
+ SurfacingUtil.processPlusMinusAnalysisOption( cla,
plus_minus_analysis_high_copy_base_species,
plus_minus_analysis_high_copy_target_species,
plus_minus_analysis_high_low_copy_species,
ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
+ surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
}
+
+
+
DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
+ surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
}
}
- final String[][] input_file_properties = processInputGenomesFile( input_genomes_file );
+ final String[][] input_file_properties = SurfacingUtil.processInputGenomesFile( input_genomes_file );
final int number_of_genomes = input_file_properties.length;
if ( number_of_genomes < 2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
+ surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ "=<suffix> to turn on pairwise analyses with less than three input files" );
}
- checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
+ SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
input_file_properties,
automated_pairwise_comparison_suffix,
out_dir );
intree_files = new File[ 1 ];
intree_files[ 0 ] = new File( intrees_str );
}
- intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
+ intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, number_of_genomes, input_file_properties );
+
}
+ final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ]);
long random_number_seed_for_fitch_parsimony = 0l;
boolean radomize_fitch_parsimony = false;
if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
|| ( negative_domains_filter_file != null ) ) {
filter = new TreeSet<String>();
if ( positive_filter_file != null ) {
- processFilter( positive_filter_file, filter );
+ SurfacingUtil.processFilter( positive_filter_file, filter );
}
else if ( negative_filter_file != null ) {
- processFilter( negative_filter_file, filter );
+ SurfacingUtil.processFilter( negative_filter_file, filter );
}
else if ( negative_domains_filter_file != null ) {
- processFilter( negative_domains_filter_file, filter );
+ SurfacingUtil.processFilter( negative_domains_filter_file, filter );
}
}
Map<String, Set<String>>[] domain_id_to_secondary_features_maps = null;
for( int i = 0; i < number_of_genomes; ++i ) {
System.out.println();
System.out.println( ( i + 1 ) + "/" + number_of_genomes );
- log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
+ SurfacingUtil.log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
System.out.println( "Processing : " + input_file_properties[ i ][ 1 ]
+ " [" + input_file_properties[ i ][ 0 ] + "]" );
- log( "Genome : " + input_file_properties[ i ][ 1 ] + " ["
+ SurfacingUtil.log( "Genome : " + input_file_properties[ i ][ 1 ] + " ["
+ input_file_properties[ i ][ 0 ] + "]", log_writer );
HmmscanPerDomainTableParser parser = null;
INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
distinct_domain_architecuture_counts );
}
System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
- log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
+ SurfacingUtil.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 );
+ SurfacingUtil.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 )
+ SurfacingUtil.log( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage )
+ "%", log_writer );
System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
- log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
+ SurfacingUtil.log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
System.out.println( "Domains stored : " + parser.getDomainsStored() );
- log( "Domains stored : " + parser.getDomainsStored(), log_writer );
+ SurfacingUtil.log( "Domains stored : " + parser.getDomainsStored(), log_writer );
System.out.println( "Distinct domains stored : "
+ parser.getDomainsStoredSet().size() );
- log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), log_writer );
+ SurfacingUtil.log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), log_writer );
System.out.println( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
- log( "Domains ignored due to individual score cutoffs: "
+ SurfacingUtil.log( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
log_writer );
System.out.println( "Domains ignored due to E-value : "
+ parser.getDomainsIgnoredDueToEval() );
- log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
+ SurfacingUtil.log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
System.out.println( "Domains ignored due to DUF designation : "
+ parser.getDomainsIgnoredDueToDuf() );
- log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
+ SurfacingUtil.log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
if ( ignore_virus_like_ids ) {
System.out.println( "Domains ignored due virus like ids : "
+ parser.getDomainsIgnoredDueToVirusLikeIds() );
- log( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
+ SurfacingUtil.log( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
log_writer );
}
System.out.println( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter() );
- log( "Domains ignored due negative domain filter : "
+ SurfacingUtil.log( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter(),
log_writer );
System.out.println( "Domains ignored due to overlap : "
+ parser.getDomainsIgnoredDueToOverlap() );
- log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
+ SurfacingUtil.log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
log_writer );
if ( negative_filter_file != null ) {
System.out.println( "Proteins ignored due to negative filter : "
+ parser.getProteinsIgnoredDueToFilter() );
- log( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter(),
+ SurfacingUtil.log( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
if ( positive_filter_file != null ) {
System.out.println( "Proteins ignored due to positive filter : "
+ parser.getProteinsIgnoredDueToFilter() );
- log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
+ SurfacingUtil.log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
if ( da_analysis ) {
System.out.println( "Distinct domain architectures stored : " + distinct_das );
- log( "Distinct domain architectures stored : " + distinct_das, log_writer );
+ SurfacingUtil.log( "Distinct domain architectures stored : " + distinct_das, log_writer );
}
System.out.println( "Time for processing : " + parser.getTime() + "ms" );
- log( "", log_writer );
+ SurfacingUtil.log( "", log_writer );
try {
int count = 0;
for( final Protein protein : protein_list ) {
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 );
+ SurfacingUtil.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
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() )
+ SurfacingUtil.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() ) + "%-"
+ SurfacingUtil.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 ) {
my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
}
split_writers = new HashMap<Character, Writer>();
- createSplitWriters( out_dir, my_outfile, split_writers );
+ SurfacingUtil.createSplitWriters( out_dir, my_outfile, split_writers );
}
else if ( !my_outfile.endsWith( ".html" ) ) {
my_outfile += ".html";
scoring,
true,
tax_code_to_id_map,
- intrees[ 0 ] );
+ intree_0_orig );
simple_tab_writer.close();
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
write_pwc_files,
tax_code_to_id_map,
CALC_SIMILARITY_SCORES,
- intrees[ 0 ] );
+ intree_0_orig );
String matrix_output_file = new String( output_file.toString() );
if ( matrix_output_file.indexOf( '.' ) > 1 ) {
matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
}
if ( write_to_nexus ) {
- writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ SurfacingUtil.writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
}
if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
- final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs,
e_value_max,
max_allowed_overlap,
no_engulfing_overlaps,
} // for( final Phylogeny intree : intrees ) {
}
if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
- executePlusMinusAnalysis( output_file,
+ SurfacingUtil.executePlusMinusAnalysis( output_file,
plus_minus_analysis_high_copy_base_species,
plus_minus_analysis_high_copy_target_species,
plus_minus_analysis_high_low_copy_species,
plus_minus_analysis_numbers );
}
if ( output_protein_lists_for_all_domains ) {
- writeProteinListsForAllSpecies( out_dir,
+ SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
protein_lists_per_species,
gwcd_list,
output_list_of_all_proteins_per_domain_e_value_max );
gwcd_list = null;
if ( all_bin_domain_combinations_gained_fitch != null ) {
try {
- executeFitchGainsAnalysis( new File( output_file
+ SurfacingUtil.executeFitchGainsAnalysis( new File( output_file
+ surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
all_bin_domain_combinations_gained_fitch,
all_domains_encountered.size(),
}
if ( all_bin_domain_combinations_lost_fitch != null ) {
try {
- executeFitchGainsAnalysis( new File( output_file
+ SurfacingUtil.executeFitchGainsAnalysis( new File( output_file
+ surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
all_bin_domain_combinations_lost_fitch,
all_domains_encountered.size(),
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 ];
- for( int i = 0; i < input_file_properties.length; ++i ) {
- if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
- + "] is not unique in input tree " + intree.getName() );
- }
- genomes[ i ] = input_file_properties[ i ][ 1 ];
- }
- //
- final PhylogenyNodeIterator it = intree.iteratorPostorder();
- while ( it.hasNext() ) {
- 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 with no name, scientific name, common name, or taxonomy code present" );
- }
- }
- }
- //
- final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
- if ( igns.size() > 0 ) {
- System.out.println( "Not using the following " + igns.size() + " nodes:" );
- for( int i = 0; i < igns.size(); ++i ) {
- System.out.println( " " + i + ": " + igns.get( i ) );
- }
- System.out.println( "--" );
- }
- for( final String[] input_file_propertie : input_file_properties ) {
- try {
- intree.getNode( input_file_propertie[ 1 ] );
- }
- catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
- + "] not present/not unique in input tree" );
- }
- }
- }
-
private static void printHelp() {
System.out.println();
System.out.println( "Usage:" );
+ "-ds_output=detailed_html -scoring=domains -sort=alpha " );
System.out.println();
}
-
- private static void processFilter( final File filter_file, final SortedSet<String> filter ) {
- SortedSet<String> filter_str = null;
- try {
- filter_str = ForesterUtil.file2set( filter_file );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
- }
- if ( filter_str != null ) {
- for( final String string : filter_str ) {
- filter.add( string );
- }
- }
- if ( VERBOSE ) {
- System.out.println( "Filter:" );
- for( final String domainId : filter ) {
- System.out.println( domainId );
- }
- }
- }
-
- private static String[][] processInputGenomesFile( final File input_genomes ) {
- String[][] input_file_properties = null;
- try {
- input_file_properties = ForesterUtil.file22dArray( input_genomes );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
- + e.getLocalizedMessage() );
- }
- final Set<String> specs = new HashSet<String>();
- final Set<String> paths = new HashSet<String>();
- for( int i = 0; i < input_file_properties.length; ++i ) {
- if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
- + input_file_properties[ i ][ 1 ] );
- }
- if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
- + " is not unique" );
- }
- specs.add( input_file_properties[ i ][ 1 ] );
- if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
- + " is not unique" );
- }
- paths.add( input_file_properties[ i ][ 0 ] );
- final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- }
- }
- return input_file_properties;
- }
-
- private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
- final List<String> high_copy_base,
- final List<String> high_copy_target,
- final List<String> low_copy,
- final List<Object> numbers ) {
- if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
- + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
- }
- final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( plus_minus_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
- }
- processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
- }
- }
-
- // First numbers is minimal difference, second is factor.
- private static void processPlusMinusFile( final File plus_minus_file,
- final List<String> high_copy_base,
- final List<String> high_copy_target,
- final List<String> low_copy,
- final List<Object> numbers ) {
- Set<String> species_set = null;
- int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
- double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
- try {
- species_set = ForesterUtil.file2set( plus_minus_file );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
- }
- if ( species_set != null ) {
- for( final String species : species_set ) {
- final String species_trimmed = species.substring( 1 );
- if ( species.startsWith( "+" ) ) {
- if ( low_copy.contains( species_trimmed ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
- + species_trimmed + "\"" );
- }
- high_copy_base.add( species_trimmed );
- }
- else if ( species.startsWith( "*" ) ) {
- if ( low_copy.contains( species_trimmed ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
- + species_trimmed + "\"" );
- }
- high_copy_target.add( species_trimmed );
- }
- else if ( species.startsWith( "-" ) ) {
- if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
- + species_trimmed + "\"" );
- }
- low_copy.add( species_trimmed );
- }
- else if ( species.startsWith( "$D" ) ) {
- try {
- min_diff = Integer.parseInt( species.substring( 3 ) );
- }
- catch ( final NumberFormatException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "could not parse integer value for minimal difference from: \""
- + species.substring( 3 ) + "\"" );
- }
- }
- else if ( species.startsWith( "$F" ) ) {
- try {
- factor = Double.parseDouble( species.substring( 3 ) );
- }
- catch ( final NumberFormatException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
- + species.substring( 3 ) + "\"" );
- }
- }
- else if ( species.startsWith( "#" ) ) {
- // Comment, ignore.
- }
- else {
- ForesterUtil
- .fatalError( surfacing.PRG_NAME,
- "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
- + species + "\"" );
- }
- numbers.add( new Integer( min_diff + "" ) );
- numbers.add( new Double( factor + "" ) );
- }
- }
- else {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
- }
- }
-
- private static void writePresentToNexus( final File output_file,
- final File positive_filter_file,
- final SortedSet<String> filter,
- final List<GenomeWideCombinableDomains> gwcd_list ) {
- try {
- SurfacingUtil
- .writeMatrixToFile( DomainParsimonyCalculator
- .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
- : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
- SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
- .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
- + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
- }
-
- private static void writeProteinListsForAllSpecies( final File output_dir,
- final SortedMap<Species, List<Protein>> protein_lists_per_species,
- final List<GenomeWideCombinableDomains> gwcd_list,
- final double domain_e_cutoff ) {
- final SortedSet<String> all_domains = new TreeSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- all_domains.addAll( gwcd.getAllDomainIds() );
- }
- for( final String domain : all_domains ) {
- final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
- SurfacingUtil.checkForOutputFileWriteability( out );
- try {
- final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
- SurfacingUtil.extractProteinNames( protein_lists_per_species,
- domain,
- proteins_file_writer,
- "\t",
- LIMIT_SPEC_FOR_PROT_EX,
- domain_e_cutoff );
- proteins_file_writer.close();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
- }
- }
}
package org.forester.surfacing;
-import java.awt.Color;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import org.forester.go.GoTerm;
import org.forester.go.PfamToGoMapping;
import org.forester.io.parsers.nexus.NexusConstants;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+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.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public final class SurfacingUtil {
+ final static class DomainComparator implements Comparator<Domain> {
+
+ final private boolean _ascending;
+
+ public DomainComparator( final boolean ascending ) {
+ _ascending = ascending;
+ }
+
+ @Override
+ public final int compare( final Domain d0, final Domain d1 ) {
+ if ( d0.getFrom() < d1.getFrom() ) {
+ return _ascending ? -1 : 1;
+ }
+ else if ( d0.getFrom() > d1.getFrom() ) {
+ return _ascending ? 1 : -1;
+ }
+ return 0;
+ }
+ }
private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" );
private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
};
public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
- private SurfacingUtil() {
- // Hidden constructor.
- }
-
public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
w.write( SurfacingConstants.NL );
}
+ private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
+ if ( map.containsKey( s ) ) {
+ map.put( s, map.get( s ) + 1 );
+ }
+ else {
+ map.put( s, 1 );
+ }
+ }
+
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final DomainSimilarity similarity : similarities ) {
return stats;
}
- public static void checkForOutputFileWriteability( final File outfile ) {
- final String error = ForesterUtil.isWritableFile( outfile );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- }
- }
-
- public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
- final BinaryDomainCombination.DomainCombinationType dc_type,
- final List<BinaryDomainCombination> all_binary_domains_combination_gained,
- final boolean get_gains ) {
- final SortedSet<String> sorted_ids = new TreeSet<String>();
- for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
- sorted_ids.add( matrix.getIdentifier( i ) );
- }
- for( final String id : sorted_ids ) {
- for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
- if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
- || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
- if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
- all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
- .createInstance( matrix.getCharacter( c ) ) );
- }
- else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
- all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
- .createInstance( matrix.getCharacter( c ) ) );
+ private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
+ final String outfilename_for_counts,
+ final String outfilename_for_dc,
+ final String outfilename_for_dc_for_go_mapping,
+ final String outfilename_for_dc_for_go_mapping_unique,
+ final String outfilename_for_rank_counts,
+ final String outfilename_for_ancestor_species_counts,
+ final String outfilename_for_protein_stats,
+ final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
+ final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
+ final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
+ try {
+ //
+ // if ( protein_length_stats_by_dc != null ) {
+ // for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
+ // System.out.print( entry.getKey().toString() );
+ // System.out.print( ": " );
+ // double[] a = entry.getValue().getDataAsDoubleArray();
+ // for( int i = 0; i < a.length; i++ ) {
+ // System.out.print( a[ i ] + " " );
+ // }
+ // System.out.println();
+ // }
+ // }
+ // if ( domain_number_stats_by_dc != null ) {
+ // for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
+ // System.out.print( entry.getKey().toString() );
+ // System.out.print( ": " );
+ // double[] a = entry.getValue().getDataAsDoubleArray();
+ // for( int i = 0; i < a.length; i++ ) {
+ // System.out.print( a[ i ] + " " );
+ // }
+ // System.out.println();
+ // }
+ // }
+ //
+ final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
+ final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
+ final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
+ final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
+ final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
+ for( final String dc : gained_dc ) {
+ if ( dc_gain_counts.containsKey( dc ) ) {
+ dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
}
else {
- all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
- .getCharacter( c ) ) );
+ dc_gain_counts.put( dc, 1 );
}
}
}
- }
- }
-
- public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
- final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
- for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
- if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
- domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
- }
- domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
- }
- return domain_id_to_go_ids_map;
- }
-
- public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
- throws IOException {
- final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
- final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
- for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
- final String domain_id = primary_table.getValue( 0, r );
- if ( !map.containsKey( domain_id ) ) {
- map.put( domain_id, new HashSet<String>() );
- }
- map.get( domain_id ).add( primary_table.getValue( 1, r ) );
- }
- return map;
- }
-
- public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
- checkForOutputFileWriteability( nj_tree_outfile );
- final NeighborJoining nj = NeighborJoining.createInstance();
- final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
- phylogeny.setName( nj_tree_outfile.getName() );
- writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
- return phylogeny;
- }
-
- public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
- final Map<String, Integer> m = new HashMap<String, Integer>();
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- final Taxonomy t = n.getNodeData().getTaxonomy();
- final String c = t.getTaxonomyCode();
- if ( !ForesterUtil.isEmpty( c ) ) {
- if ( n.getNodeData().getTaxonomy() == null ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
+ final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
+ final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
+ final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
+ final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
+ final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
+ final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
+ final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
+ final Set<String> dcs = dc_gain_counts.keySet();
+ final SortedSet<String> more_than_once = new TreeSet<String>();
+ DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
+ DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
+ DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
+ final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
+ long gained_multiple_times_domain_length_sum = 0;
+ long gained_once_domain_length_sum = 0;
+ long gained_multiple_times_domain_length_count = 0;
+ long gained_once_domain_length_count = 0;
+ for( final String dc : dcs ) {
+ final int count = dc_gain_counts.get( dc );
+ if ( histogram.containsKey( count ) ) {
+ histogram.put( count, histogram.get( count ) + 1 );
+ domain_lists.get( count ).append( ", " + dc );
+ domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
+ domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
+ }
+ else {
+ histogram.put( count, 1 );
+ domain_lists.put( count, new StringBuilder( dc ) );
+ final PriorityQueue<String> q = new PriorityQueue<String>();
+ q.addAll( splitDomainCombination( dc ) );
+ domain_lists_go.put( count, q );
+ final SortedSet<String> set = new TreeSet<String>();
+ set.addAll( splitDomainCombination( dc ) );
+ domain_lists_go_unique.put( count, set );
+ }
+ if ( protein_length_stats_by_dc != null ) {
+ if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
+ dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
}
- final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
- if ( ForesterUtil.isEmpty( id ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
+ dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
+ .arithmeticMean() );
+ }
+ if ( domain_number_stats_by_dc != null ) {
+ if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
+ dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
}
- if ( m.containsKey( c ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
+ dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
+ .arithmeticMean() );
+ }
+ if ( domain_length_stats_by_domain != null ) {
+ if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
+ dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
}
- final int iid = Integer.valueOf( id );
- if ( m.containsValue( iid ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
+ final String[] ds = dc.split( "=" );
+ dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
+ .get( ds[ 0 ] ).arithmeticMean() );
+ dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
+ .get( ds[ 1 ] ).arithmeticMean() );
+ }
+ if ( count > 1 ) {
+ more_than_once.add( dc );
+ if ( protein_length_stats_by_dc != null ) {
+ final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
+ for( final double element : s.getData() ) {
+ gained_multiple_times_lengths_stats.addValue( element );
+ }
+ }
+ if ( domain_number_stats_by_dc != null ) {
+ final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
+ for( final double element : s.getData() ) {
+ gained_multiple_times_domain_count_stats.addValue( element );
+ }
+ }
+ if ( domain_length_stats_by_domain != null ) {
+ final String[] ds = dc.split( "=" );
+ final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
+ final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
+ for( final double element : s0.getData() ) {
+ gained_multiple_times_domain_length_sum += element;
+ ++gained_multiple_times_domain_length_count;
+ }
+ for( final double element : s1.getData() ) {
+ gained_multiple_times_domain_length_sum += element;
+ ++gained_multiple_times_domain_length_count;
+ }
}
- m.put( c, iid );
}
- }
- else {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
- }
- }
- return m;
- }
-
- public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
- final Detailedness detailedness ) {
- for( final DomainSimilarity domain_similarity : domain_similarities ) {
- if ( domain_similarity instanceof PrintableDomainSimilarity ) {
- final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
- printable_domain_similarity.setDetailedness( detailedness );
- }
- }
- }
-
- public static void doit( final List<Protein> proteins,
- final List<String> query_domain_ids_nc_order,
- final Writer out,
- final String separator,
- final String limit_to_species,
- final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
- for( final Protein protein : proteins ) {
- if ( ForesterUtil.isEmpty( limit_to_species )
- || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
- if ( protein.contains( query_domain_ids_nc_order, true ) ) {
- out.write( protein.getSpecies().getSpeciesId() );
- out.write( separator );
- out.write( protein.getProteinId().getId() );
- out.write( separator );
- out.write( "[" );
- final Set<String> visited_domain_ids = new HashSet<String>();
- boolean first = true;
- for( final Domain domain : protein.getProteinDomains() ) {
- if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
- visited_domain_ids.add( domain.getDomainId() );
- if ( first ) {
- first = false;
- }
- else {
- out.write( " " );
- }
- out.write( domain.getDomainId() );
- out.write( " {" );
- out.write( "" + domain.getTotalCount() );
- out.write( "}" );
+ else {
+ if ( protein_length_stats_by_dc != null ) {
+ final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
+ for( final double element : s.getData() ) {
+ gained_once_lengths_stats.addValue( element );
}
}
- out.write( "]" );
- out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
- .equals( SurfacingConstants.NONE ) ) ) {
- out.write( protein.getDescription() );
+ if ( domain_number_stats_by_dc != null ) {
+ final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
+ for( final double element : s.getData() ) {
+ gained_once_domain_count_stats.addValue( element );
+ }
}
- out.write( separator );
- if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
- .equals( SurfacingConstants.NONE ) ) ) {
- out.write( protein.getAccession() );
+ if ( domain_length_stats_by_domain != null ) {
+ final String[] ds = dc.split( "=" );
+ final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
+ final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
+ for( final double element : s0.getData() ) {
+ gained_once_domain_length_sum += element;
+ ++gained_once_domain_length_count;
+ }
+ for( final double element : s1.getData() ) {
+ gained_once_domain_length_sum += element;
+ ++gained_once_domain_length_count;
+ }
}
- out.write( SurfacingConstants.NL );
}
}
- }
- out.flush();
- }
-
- public static void domainsPerProteinsStatistics( final String genome,
- final List<Protein> protein_list,
- final DescriptiveStatistics all_genomes_domains_per_potein_stats,
- final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
- final SortedSet<String> domains_which_are_always_single,
- final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
- final SortedSet<String> domains_which_never_single,
- final Writer writer ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final Protein protein : protein_list ) {
- final int domains = protein.getNumberOfProteinDomains();
- //System.out.println( domains );
- stats.addValue( domains );
- all_genomes_domains_per_potein_stats.addValue( domains );
- if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
- all_genomes_domains_per_potein_histo.put( domains, 1 );
- }
- else {
- all_genomes_domains_per_potein_histo.put( domains,
- 1 + all_genomes_domains_per_potein_histo.get( domains ) );
+ final Set<Integer> histogram_keys = histogram.keySet();
+ for( final Integer histogram_key : histogram_keys ) {
+ final int count = histogram.get( histogram_key );
+ final StringBuilder dc = domain_lists.get( histogram_key );
+ out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
+ out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+ final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
+ Arrays.sort( sorted );
+ for( final Object domain : sorted ) {
+ out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
+ }
+ out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+ for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
+ out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
+ }
}
- if ( domains == 1 ) {
- final String domain = protein.getProteinDomain( 0 ).getDomainId();
- if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
- if ( domains_which_never_single.contains( domain ) ) {
- domains_which_never_single.remove( domain );
- domains_which_are_sometimes_single_sometimes_not.add( domain );
- }
- else {
- domains_which_are_always_single.add( domain );
+ out_counts.close();
+ out_dc.close();
+ out_dc_for_go_mapping.close();
+ out_dc_for_go_mapping_unique.close();
+ final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
+ final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
+ for( final String dc : more_than_once ) {
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
+ nodes.add( n );
}
}
- }
- else if ( domains > 1 ) {
- for( final Domain d : protein.getProteinDomains() ) {
- final String domain = d.getDomainId();
- // System.out.println( domain );
- if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
- if ( domains_which_are_always_single.contains( domain ) ) {
- domains_which_are_always_single.remove( domain );
- domains_which_are_sometimes_single_sometimes_not.add( domain );
+ for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
+ for( int j = i + 1; j < nodes.size(); ++j ) {
+ final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
+ String rank = "unknown";
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
+ rank = lca.getNodeData().getTaxonomy().getRank();
+ }
+ addToCountMap( lca_rank_counts, rank );
+ String lca_species;
+ if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getScientificName();
+ }
+ else if ( lca.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
+ lca_species = lca.getNodeData().getTaxonomy().getCommonName();
}
else {
- domains_which_never_single.add( domain );
+ lca_species = lca.getName();
}
+ addToCountMap( lca_ancestor_species_counts, lca_species );
}
}
}
- }
- try {
- writer.write( genome );
- writer.write( "\t" );
- if ( stats.getN() >= 1 ) {
- writer.write( stats.arithmeticMean() + "" );
- writer.write( "\t" );
- if ( stats.getN() >= 2 ) {
- writer.write( stats.sampleStandardDeviation() + "" );
- }
- else {
- writer.write( "" );
+ final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
+ final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
+ ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
+ ForesterUtil.map2writer( out_for_ancestor_species_counts,
+ lca_ancestor_species_counts,
+ "\t",
+ ForesterUtil.LINE_SEPARATOR );
+ out_for_rank_counts.close();
+ out_for_ancestor_species_counts.close();
+ if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
+ && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
+ final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
+ w.write( "Domain Lengths: " );
+ w.write( "\n" );
+ if ( domain_length_stats_by_domain != null ) {
+ for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
+ .entrySet() ) {
+ w.write( entry.getKey().toString() );
+ w.write( "\t" + entry.getValue().arithmeticMean() );
+ w.write( "\t" + entry.getValue().median() );
+ w.write( "\n" );
+ }
}
- writer.write( "\t" );
- writer.write( stats.median() + "" );
- writer.write( "\t" );
- writer.write( stats.getN() + "" );
- writer.write( "\t" );
- writer.write( stats.getMin() + "" );
- writer.write( "\t" );
- writer.write( stats.getMax() + "" );
- }
- else {
- writer.write( "\t" );
- writer.write( "\t" );
- writer.write( "\t" );
- writer.write( "0" );
- writer.write( "\t" );
- writer.write( "\t" );
- }
- writer.write( "\n" );
- }
- catch ( final IOException e ) {
- e.printStackTrace();
- }
- }
-
- public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
- final int number_of_genomes,
- final DomainLengthsTable domain_lengths_table,
- final File outfile ) throws IOException {
- final DecimalFormat df = new DecimalFormat( "#.00" );
- checkForOutputFileWriteability( outfile );
- final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
- out.write( "MEAN BASED STATISTICS PER SPECIES" );
- out.write( ForesterUtil.LINE_SEPARATOR );
- out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
- out.write( ForesterUtil.LINE_SEPARATOR );
- out.write( ForesterUtil.LINE_SEPARATOR );
- final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
- out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
- out.write( ForesterUtil.LINE_SEPARATOR );
- for( final DomainLengths domain_lengths : domain_lengths_list ) {
- final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
- if ( species_list.size() > 0 ) {
- out.write( domain_lengths.getDomainId() + "\t" );
- for( final Species species : species_list ) {
- out.write( species + "\t" );
+ w.flush();
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Protein Lengths: " );
+ w.write( "\n" );
+ if ( protein_length_stats_by_dc != null ) {
+ for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
+ .entrySet() ) {
+ w.write( entry.getKey().toString() );
+ w.write( "\t" + entry.getValue().arithmeticMean() );
+ w.write( "\t" + entry.getValue().median() );
+ w.write( "\n" );
+ }
}
- out.write( ForesterUtil.LINE_SEPARATOR );
- }
- }
- out.write( ForesterUtil.LINE_SEPARATOR );
+ w.flush();
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Number of domains: " );
+ w.write( "\n" );
+ if ( domain_number_stats_by_dc != null ) {
+ for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
+ .entrySet() ) {
+ w.write( entry.getKey().toString() );
+ w.write( "\t" + entry.getValue().arithmeticMean() );
+ w.write( "\t" + entry.getValue().median() );
+ w.write( "\n" );
+ }
+ }
+ w.flush();
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained once, domain lengths:" );
+ w.write( "\n" );
+ w.write( "N: " + gained_once_domain_length_count );
+ w.write( "\n" );
+ w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained multiple times, domain lengths:" );
+ w.write( "\n" );
+ w.write( "N: " + gained_multiple_times_domain_length_count );
+ w.write( "\n" );
+ w.write( "Avg: "
+ + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained once, protein lengths:" );
+ w.write( "\n" );
+ w.write( gained_once_lengths_stats.toString() );
+ gained_once_lengths_stats = null;
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained once, domain counts:" );
+ w.write( "\n" );
+ w.write( gained_once_domain_count_stats.toString() );
+ gained_once_domain_count_stats = null;
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained multiple times, protein lengths:" );
+ w.write( "\n" );
+ w.write( gained_multiple_times_lengths_stats.toString() );
+ gained_multiple_times_lengths_stats = null;
+ w.write( "\n" );
+ w.write( "\n" );
+ w.write( "Gained multiple times, domain counts:" );
+ w.write( "\n" );
+ w.write( gained_multiple_times_domain_count_stats.toString() );
+ w.flush();
+ w.close();
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
+ + outfilename_for_counts + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
+ + outfilename_for_dc + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
+ + outfilename_for_dc_for_go_mapping + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
+ + outfilename_for_dc_for_go_mapping_unique + "]" );
+ }
+
+ public static void checkForOutputFileWriteability( final File outfile ) {
+ final String error = ForesterUtil.isWritableFile( outfile );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+
+ public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final String[][] input_file_properties,
+ final String automated_pairwise_comparison_suffix,
+ final File outdir ) {
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ final String species_i = input_file_properties[ i ][ 1 ];
+ final String species_j = input_file_properties[ j ][ 1 ];
+ String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
+ + "_" + species_j + automated_pairwise_comparison_suffix;
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+ pairwise_similarities_output_file_str += ".html";
+ }
+ break;
+ }
+ final String error = ForesterUtil
+ .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+ + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+ }
+ }
+
+ private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
+ final boolean get_gains ) {
+ final SortedSet<String> domains = new TreeSet<String>();
+ for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
+ final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
+ if ( get_gains ) {
+ domains.addAll( chars.getGainedCharacters() );
+ }
+ else {
+ domains.addAll( chars.getLostCharacters() );
+ }
+ }
+ return domains;
+ }
+
+ public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+ final BinaryDomainCombination.DomainCombinationType dc_type,
+ final List<BinaryDomainCombination> all_binary_domains_combination_gained,
+ final boolean get_gains ) {
+ final SortedSet<String> sorted_ids = new TreeSet<String>();
+ for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+ sorted_ids.add( matrix.getIdentifier( i ) );
+ }
+ for( final String id : sorted_ids ) {
+ for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+ if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
+ || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
+ if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
+ all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
+ .createInstance( matrix.getCharacter( c ) ) );
+ }
+ else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
+ all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
+ .createInstance( matrix.getCharacter( c ) ) );
+ }
+ else {
+ all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
+ .getCharacter( c ) ) );
+ }
+ }
+ }
+ }
+ }
+
+ private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
+ final boolean domain_combinations,
+ final CharacterStateMatrix.GainLossStates state,
+ final String outfile ) {
+ File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
+ + ForesterUtil.FILE_SEPARATOR + base_dir );
+ if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+ }
+ if ( domain_combinations ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + "DC" );
+ }
+ else {
+ per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
+ }
+ if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+ }
+ if ( state == GainLossStates.GAIN ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + "GAINS" );
+ }
+ else if ( state == GainLossStates.LOSS ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
+ }
+ else {
+ per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
+ }
+ if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+ per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+ }
+ return per_node_go_mapped_domain_gain_loss_files_base_dir;
+ }
+
+ public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
+ final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
+ for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
+ if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
+ domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
+ }
+ domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
+ }
+ return domain_id_to_go_ids_map;
+ }
+
+ public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
+ throws IOException {
+ final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
+ final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
+ for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
+ final String domain_id = primary_table.getValue( 0, r );
+ if ( !map.containsKey( domain_id ) ) {
+ map.put( domain_id, new HashSet<String>() );
+ }
+ map.get( domain_id ).add( primary_table.getValue( 1, r ) );
+ }
+ return map;
+ }
+
+ public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
+ checkForOutputFileWriteability( nj_tree_outfile );
+ final NeighborJoining nj = NeighborJoining.createInstance();
+ final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
+ phylogeny.setName( nj_tree_outfile.getName() );
+ writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
+ return phylogeny;
+ }
+
+ public static StringBuilder createParametersAsString( final boolean ignore_dufs,
+ final double e_value_max,
+ final int max_allowed_overlap,
+ final boolean no_engulfing_overlaps,
+ final File cutoff_scores_file,
+ final BinaryDomainCombination.DomainCombinationType dc_type ) {
+ final StringBuilder parameters_sb = new StringBuilder();
+ parameters_sb.append( "E-value: " + e_value_max );
+ if ( cutoff_scores_file != null ) {
+ parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+ }
+ else {
+ parameters_sb.append( ", Cutoff-scores-file: not-set" );
+ }
+ if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+ }
+ else {
+ parameters_sb.append( ", Max-overlap: not-set" );
+ }
+ if ( no_engulfing_overlaps ) {
+ parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+ }
+ else {
+ parameters_sb.append( ", Engulfing-overlaps: allowed" );
+ }
+ if ( ignore_dufs ) {
+ parameters_sb.append( ", Ignore-dufs: true" );
+ }
+ else {
+ parameters_sb.append( ", Ignore-dufs: false" );
+ }
+ parameters_sb.append( ", DC type (if applicable): " + dc_type );
+ return parameters_sb;
+ }
+
+ private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
+ final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
+ final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
+ for( final String domain_id : cds.keySet() ) {
+ final CombinableDomains cd = cds.get( domain_id );
+ binary_combinations.addAll( cd.toBinaryDomainCombinations() );
+ }
+ return binary_combinations;
+ }
+
+ public 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" ) ) );
+ }
+
+ public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
+ final Map<String, Integer> m = new HashMap<String, Integer>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ final Taxonomy t = n.getNodeData().getTaxonomy();
+ final String c = t.getTaxonomyCode();
+ if ( !ForesterUtil.isEmpty( c ) ) {
+ if ( n.getNodeData().getTaxonomy() == null ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
+ }
+ final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
+ if ( ForesterUtil.isEmpty( id ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
+ }
+ if ( m.containsKey( c ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
+ }
+ final int iid = Integer.valueOf( id );
+ if ( m.containsValue( iid ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
+ }
+ m.put( c, iid );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
+ }
+ }
+ return m;
+ }
+
+ public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
+ final Detailedness detailedness ) {
+ for( final DomainSimilarity domain_similarity : domain_similarities ) {
+ if ( domain_similarity instanceof PrintableDomainSimilarity ) {
+ final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
+ printable_domain_similarity.setDetailedness( detailedness );
+ }
+ }
+ }
+
+ public static void doit( final List<Protein> proteins,
+ final List<String> query_domain_ids_nc_order,
+ final Writer out,
+ final String separator,
+ final String limit_to_species,
+ final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
+ for( final Protein protein : proteins ) {
+ if ( ForesterUtil.isEmpty( limit_to_species )
+ || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
+ if ( protein.contains( query_domain_ids_nc_order, true ) ) {
+ out.write( protein.getSpecies().getSpeciesId() );
+ out.write( separator );
+ out.write( protein.getProteinId().getId() );
+ out.write( separator );
+ out.write( "[" );
+ final Set<String> visited_domain_ids = new HashSet<String>();
+ boolean first = true;
+ for( final Domain domain : protein.getProteinDomains() ) {
+ if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
+ visited_domain_ids.add( domain.getDomainId() );
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out.write( " " );
+ }
+ out.write( domain.getDomainId() );
+ out.write( " {" );
+ out.write( "" + domain.getTotalCount() );
+ out.write( "}" );
+ }
+ }
+ out.write( "]" );
+ out.write( separator );
+ if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
+ .equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getDescription() );
+ }
+ out.write( separator );
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
+ .equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getAccession() );
+ }
+ out.write( SurfacingConstants.NL );
+ }
+ }
+ }
+ out.flush();
+ }
+
+ public static void domainsPerProteinsStatistics( final String genome,
+ final List<Protein> protein_list,
+ final DescriptiveStatistics all_genomes_domains_per_potein_stats,
+ final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+ final SortedSet<String> domains_which_are_always_single,
+ final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
+ final SortedSet<String> domains_which_never_single,
+ final Writer writer ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final Protein protein : protein_list ) {
+ final int domains = protein.getNumberOfProteinDomains();
+ //System.out.println( domains );
+ stats.addValue( domains );
+ all_genomes_domains_per_potein_stats.addValue( domains );
+ if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
+ all_genomes_domains_per_potein_histo.put( domains, 1 );
+ }
+ else {
+ all_genomes_domains_per_potein_histo.put( domains,
+ 1 + all_genomes_domains_per_potein_histo.get( domains ) );
+ }
+ if ( domains == 1 ) {
+ final String domain = protein.getProteinDomain( 0 ).getDomainId();
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_never_single.contains( domain ) ) {
+ domains_which_never_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_are_always_single.add( domain );
+ }
+ }
+ }
+ else if ( domains > 1 ) {
+ for( final Domain d : protein.getProteinDomains() ) {
+ final String domain = d.getDomainId();
+ // System.out.println( domain );
+ if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+ if ( domains_which_are_always_single.contains( domain ) ) {
+ domains_which_are_always_single.remove( domain );
+ domains_which_are_sometimes_single_sometimes_not.add( domain );
+ }
+ else {
+ domains_which_never_single.add( domain );
+ }
+ }
+ }
+ }
+ }
+ try {
+ writer.write( genome );
+ writer.write( "\t" );
+ if ( stats.getN() >= 1 ) {
+ writer.write( stats.arithmeticMean() + "" );
+ writer.write( "\t" );
+ if ( stats.getN() >= 2 ) {
+ writer.write( stats.sampleStandardDeviation() + "" );
+ }
+ else {
+ writer.write( "" );
+ }
+ writer.write( "\t" );
+ writer.write( stats.median() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getN() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMin() + "" );
+ writer.write( "\t" );
+ writer.write( stats.getMax() + "" );
+ }
+ else {
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ writer.write( "0" );
+ writer.write( "\t" );
+ writer.write( "\t" );
+ }
+ writer.write( "\n" );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+
+ public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
+ final int number_of_genomes,
+ final DomainLengthsTable domain_lengths_table,
+ final File outfile ) throws IOException {
+ final DecimalFormat df = new DecimalFormat( "#.00" );
+ checkForOutputFileWriteability( outfile );
+ final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+ out.write( "MEAN BASED STATISTICS PER SPECIES" );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
+ out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ for( final DomainLengths domain_lengths : domain_lengths_list ) {
+ final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
+ if ( species_list.size() > 0 ) {
+ out.write( domain_lengths.getDomainId() + "\t" );
+ for( final Species species : species_list ) {
+ out.write( species + "\t" );
+ }
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ out.write( ForesterUtil.LINE_SEPARATOR );
out.write( ForesterUtil.LINE_SEPARATOR );
out.write( "OUTLIER SPECIES (Z 1.0)" );
out.write( ForesterUtil.LINE_SEPARATOR );
}
/**
+ * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
+ *
+ *
+ * @param output_file
+ * @param all_bin_domain_combinations_changed
+ * @param sum_of_all_domains_encountered
+ * @param all_bin_domain_combinations_encountered
+ * @param is_gains_analysis
+ * @param protein_length_stats_by_dc
+ * @throws IOException
+ */
+ public static void executeFitchGainsAnalysis( final File output_file,
+ final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+ final int sum_of_all_domains_encountered,
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+ final boolean is_gains_analysis ) throws IOException {
+ checkForOutputFileWriteability( output_file );
+ final Writer out = ForesterUtil.createBufferedWriter( output_file );
+ final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+ .listToSortedCountsMap( all_bin_domain_combinations_changed );
+ final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
+ final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
+ int above_one = 0;
+ int one = 0;
+ for( final Object bdc_object : bdc_to_counts.keySet() ) {
+ final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+ final int count = bdc_to_counts.get( bdc_object );
+ if ( count < 1 ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " );
+ }
+ out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ if ( count > 1 ) {
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+ above_one++;
+ }
+ else if ( count == 1 ) {
+ all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+ one++;
+ }
+ }
+ final int all = all_bin_domain_combinations_encountered.size();
+ int never_lost = -1;
+ if ( !is_gains_analysis ) {
+ all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+ never_lost = all_bin_domain_combinations_encountered.size();
+ for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+ out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ if ( is_gains_analysis ) {
+ out.write( "Sum of all distinct domain combinations appearing once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ out.write( "All binary combinations : " + all
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "All domains : "
+ + sum_of_all_domains_encountered );
+ out.close();
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
+ + "\"" );
+ }
+
+ /**
*
* @param all_binary_domains_combination_lost_fitch
* @param use_last_in_fitch_parsimony
+ "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
}
+ public static void executePlusMinusAnalysis( final File output_file,
+ final List<String> plus_minus_analysis_high_copy_base,
+ final List<String> plus_minus_analysis_high_copy_target,
+ final List<String> plus_minus_analysis_low_copy,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final List<Object> plus_minus_analysis_numbers ) {
+ final Set<String> all_spec = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_spec.add( gwcd.getSpecies().getSpeciesId() );
+ }
+ final File html_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX_HTML );
+ final File plain_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX );
+ final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML );
+ final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
+ final File passing_domains_go_ids_out_dom = new File( output_file
+ + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+ final File proteins_file_base = new File( output_file + "" );
+ final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
+ final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
+ try {
+ DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+ protein_lists_per_species,
+ plus_minus_analysis_high_copy_base,
+ plus_minus_analysis_high_copy_target,
+ plus_minus_analysis_low_copy,
+ min_diff,
+ factor,
+ plain_out_dom,
+ html_out_dom,
+ html_out_dc,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ all_domains_go_ids_out_dom,
+ passing_domains_go_ids_out_dom,
+ proteins_file_base );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + plain_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
+ + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
+ + passing_domains_go_ids_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
+ + all_domains_go_ids_out_dom + "\"" );
+ }
+
public static void extractProteinNames( final List<Protein> proteins,
final List<String> query_domain_ids_nc_order,
final Writer out,
final String separator,
final String limit_to_species,
final double domain_e_cutoff ) throws IOException {
- System.out.println( "Per domain E-value: " + domain_e_cutoff );
+ //System.out.println( "Per domain E-value: " + domain_e_cutoff );
for( final Species species : protein_lists_per_species.keySet() ) {
- System.out.println( species + ":" );
+ //System.out.println( species + ":" );
for( final Protein protein : protein_lists_per_species.get( species ) ) {
if ( ForesterUtil.isEmpty( limit_to_species )
|| protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
out.write( domain.getFrom() + "-" + domain.getTo() );
if ( prev_to >= 0 ) {
final int l = domain.getFrom() - prev_to;
- System.out.println( l );
+ // System.out.println( l );
}
prev_to = domain.getTo();
}
++c;
}
}
- return c;
+ return c;
+ }
+
+ public static void log( final String msg, final Writer w ) {
+ try {
+ w.write( msg );
+ w.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
+ final int number_of_genomes,
+ final String[][] input_file_properties ) {
+ final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+ int i = 0;
+ for( final File intree_file : intree_files ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
+ + error );
+ }
+ try {
+ final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+ .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" );
+ }
+ else if ( p_array.length > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = p_array[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
+ + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "number of external nodes [" + intree.getNumberOfExternalNodes()
+ + "] of input tree [" + intree_file
+ + "] is smaller than the number of genomes the be analyzed ["
+ + number_of_genomes + "]" );
+ }
+ final StringBuilder parent_names = new StringBuilder();
+ final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
+ if ( nodes_lacking_name > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
+ + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
+ }
+ preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+ if ( !intree.isCompletelyBinary() ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
+ + "] is not completely binary" );
+ }
+ intrees[ i++ ] = intree;
+ }
+ return intrees;
+ }
+
+ public static Phylogeny obtainFirstIntree( final File intree_file ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: " + error );
+ }
+ try {
+ final Phylogeny[] phys = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
+ if ( phys.length < 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( phys.length > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = phys[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file + "]: "
+ + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ return intree;
}
public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
p.setRooted( true );
}
- /*
- * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
- *
- *
- */
- static public StringBuffer proteinToDomainCombinations( final Protein protein,
- final String protein_id,
- final String separator ) {
- final StringBuffer sb = new StringBuffer();
- if ( protein.getSpecies() == null ) {
- throw new IllegalArgumentException( "species must not be null" );
- }
- if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
- throw new IllegalArgumentException( "species id must not be empty" );
+ public static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+ final String[][] input_file_properties ) {
+ final String[] genomes = new String[ input_file_properties.length ];
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] is not unique in input tree " + intree.getName() );
+ }
+ genomes[ i ] = input_file_properties[ i ][ 1 ];
}
- final List<Domain> domains = protein.getProteinDomains();
- if ( domains.size() > 1 ) {
- final Map<String, Integer> counts = new HashMap<String, Integer>();
- for( final Domain domain : domains ) {
- final String id = domain.getDomainId();
- if ( counts.containsKey( id ) ) {
- counts.put( id, counts.get( id ) + 1 );
+ //
+ final PhylogenyNodeIterator it = intree.iteratorPostorder();
+ while ( it.hasNext() ) {
+ 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 {
- counts.put( id, 1 );
+ else if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getScientificName() );
}
- }
- final Set<String> dcs = new HashSet<String>();
- for( int i = 1; i < domains.size(); ++i ) {
- for( int j = 0; j < i; ++j ) {
- Domain domain_n = domains.get( i );
- Domain domain_c = domains.get( j );
- if ( domain_n.getFrom() > domain_c.getFrom() ) {
- domain_n = domains.get( j );
- domain_c = domains.get( i );
- }
- final String dc = domain_n.getDomainId() + domain_c.getDomainId();
- if ( !dcs.contains( dc ) ) {
- dcs.add( dc );
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( domain_n.getDomainId() );
- sb.append( separator );
- sb.append( domain_c.getDomainId() );
- sb.append( separator );
- sb.append( domain_n.getPerDomainEvalue() );
- sb.append( separator );
- sb.append( domain_c.getPerDomainEvalue() );
- sb.append( separator );
- sb.append( counts.get( domain_n.getDomainId() ) );
- sb.append( separator );
- sb.append( counts.get( domain_c.getDomainId() ) );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
+ else if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "node with no name, scientific name, common name, or taxonomy code present" );
}
}
}
- else if ( domains.size() == 1 ) {
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( domains.get( 0 ).getDomainId() );
- sb.append( separator );
- sb.append( separator );
- sb.append( domains.get( 0 ).getPerDomainEvalue() );
- sb.append( separator );
- sb.append( separator );
- sb.append( 1 );
- sb.append( separator );
- sb.append( ForesterUtil.LINE_SEPARATOR );
+ //
+ final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+ if ( igns.size() > 0 ) {
+ System.out.println( "Not using the following " + igns.size() + " nodes:" );
+ for( int i = 0; i < igns.size(); ++i ) {
+ System.out.println( " " + i + ": " + igns.get( i ) );
+ }
+ System.out.println( "--" );
}
- else {
- sb.append( protein.getSpecies() );
- sb.append( separator );
- sb.append( protein_id );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( separator );
- sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final String[] input_file_propertie : input_file_properties ) {
+ try {
+ intree.getNode( input_file_propertie[ 1 ] );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
+ + "] not present/not unique in input tree" );
+ }
}
- return sb;
}
- public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
- final List<Domain> domains = new ArrayList<Domain>();
- for( final Domain d : protein.getProteinDomains() ) {
- domains.add( d );
- }
- Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
- return domains;
+ public 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( surfacing.PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
+ log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer );
}
- public static int storeDomainArchitectures( final String genome,
- final SortedMap<String, Set<String>> domain_architecutures,
- final List<Protein> protein_list,
- final Map<String, Integer> distinct_domain_architecuture_counts ) {
- final Set<String> da = new HashSet<String>();
- domain_architecutures.put( genome, da );
- for( final Protein protein : protein_list ) {
- final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
- if ( !da.contains( da_str ) ) {
- if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
- distinct_domain_architecuture_counts.put( da_str, 1 );
- }
- else {
- distinct_domain_architecuture_counts.put( da_str,
- distinct_domain_architecuture_counts.get( da_str ) + 1 );
- }
- da.add( da_str );
- }
+ private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
+ throws IOException {
+ w.write( "<hr>" );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tt><pre>" );
+ w.write( SurfacingConstants.NL );
+ if ( histo != null ) {
+ w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
+ w.write( SurfacingConstants.NL );
}
- return da.size();
+ w.write( "</pre></tt>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ if ( stats.getN() > 1 ) {
+ w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
+ }
+ else {
+ w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
}
- public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
- final boolean get_gains,
- final String outdir,
- final String suffix_for_filename ) throws IOException {
- CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
- if ( !get_gains ) {
- state = CharacterStateMatrix.GainLossStates.LOSS;
+ public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
+ SortedSet<String> filter_str = null;
+ try {
+ filter_str = ForesterUtil.file2set( filter_file );
}
- final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
- false,
- state,
- outdir );
- for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- if ( !node.isExternal() ) {
- final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
- if ( domains.size() > 0 ) {
- final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
- + node.getName() + suffix_for_filename );
- for( final String domain : domains ) {
- writer.write( domain );
- writer.write( ForesterUtil.LINE_SEPARATOR );
- }
- writer.close();
- }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( filter_str != null ) {
+ for( final String string : filter_str ) {
+ filter.add( string );
+ }
+ }
+ if ( surfacing.VERBOSE ) {
+ System.out.println( "Filter:" );
+ for( final String domainId : filter ) {
+ System.out.println( domainId );
}
}
}
- public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
- final File output_dir,
- final GenomeWideCombinableDomains gwcd,
- final int i,
- final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
- File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
- + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
- if ( output_dir != null ) {
- dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
- }
- checkForOutputFileWriteability( dc_outfile_dot );
- final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
+ public static String[][] processInputGenomesFile( final File input_genomes ) {
+ String[][] input_file_properties = null;
try {
- final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
- for( final BinaryDomainCombination bdc : binary_combinations ) {
- out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
- .toString() );
- out_dot.write( SurfacingConstants.NL );
- }
- out_dot.close();
+ input_file_properties = ForesterUtil.file22dArray( input_genomes );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
+ + e.getLocalizedMessage() );
+ }
+ final Set<String> specs = new HashSet<String>();
+ final Set<String> paths = new HashSet<String>();
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
+ + input_file_properties[ i ][ 1 ] );
+ }
+ if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
+ + " is not unique" );
+ }
+ specs.add( input_file_properties[ i ][ 1 ] );
+ if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
+ + " is not unique" );
+ }
+ paths.add( input_file_properties[ i ][ 0 ] );
+ final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
- + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+ return input_file_properties;
}
- public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
- final CharacterStateMatrix.GainLossStates state,
- final String filename,
- final String indentifier_characters_separator,
- final String character_separator,
- final Map<String, String> descriptions ) {
- final File outfile = new File( filename );
- checkForOutputFileWriteability( outfile );
- final SortedSet<String> sorted_ids = new TreeSet<String>();
- for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
- sorted_ids.add( matrix.getIdentifier( i ) );
+ public static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
+ + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
+ }
+ final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
+ }
+ processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
}
+ }
+
+ // First numbers is minimal difference, second is factor.
+ public static void processPlusMinusFile( final File plus_minus_file,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ Set<String> species_set = null;
+ int min_diff = surfacing.PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+ double factor = surfacing.PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
try {
- final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
- for( final String id : sorted_ids ) {
- out.write( indentifier_characters_separator );
- out.write( "#" + id );
- out.write( indentifier_characters_separator );
- for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
- // Not nice:
- // using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
- out.write( matrix.getCharacter( c ) );
- if ( ( descriptions != null ) && !descriptions.isEmpty()
- && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
- out.write( "\t" );
- out.write( descriptions.get( matrix.getCharacter( c ) ) );
- }
- out.write( character_separator );
- }
- }
- }
- out.flush();
- out.close();
+ species_set = ForesterUtil.file2set( plus_minus_file );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
- }
-
- public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
- final CharacterStateMatrix.GainLossStates state,
- final String filename,
- final String indentifier_characters_separator,
- final String character_separator,
- final BinaryDomainCombination.OutputFormat bc_output_format ) {
- final File outfile = new File( filename );
- checkForOutputFileWriteability( outfile );
- final SortedSet<String> sorted_ids = new TreeSet<String>();
- for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
- sorted_ids.add( matrix.getIdentifier( i ) );
- }
- try {
- final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
- for( final String id : sorted_ids ) {
- out.write( indentifier_characters_separator );
- out.write( "#" + id );
- out.write( indentifier_characters_separator );
- for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
- // Not nice:
- // using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
- BinaryDomainCombination bdc = null;
- try {
- bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
- }
- out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
- out.write( character_separator );
+ if ( species_set != null ) {
+ for( final String species : species_set ) {
+ final String species_trimmed = species.substring( 1 );
+ if ( species.startsWith( "+" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_base.add( species_trimmed );
+ }
+ else if ( species.startsWith( "*" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_target.add( species_trimmed );
+ }
+ else if ( species.startsWith( "-" ) ) {
+ if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
}
+ low_copy.add( species_trimmed );
+ }
+ else if ( species.startsWith( "$D" ) ) {
+ try {
+ min_diff = Integer.parseInt( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "could not parse integer value for minimal difference from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "$F" ) ) {
+ try {
+ factor = Double.parseDouble( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "#" ) ) {
+ // Comment, ignore.
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+ + species + "\"" );
}
+ numbers.add( new Integer( min_diff + "" ) );
+ numbers.add( new Double( factor + "" ) );
}
- out.flush();
- out.close();
}
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
- public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final GoNameSpace go_namespace_limit,
- final boolean domain_combinations,
- final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
- final CharacterStateMatrix.GainLossStates state,
- final String filename,
- final String indentifier_characters_separator,
- final String character_separator,
- final String title_for_html,
- final String prefix_for_html,
- final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
- final SortedSet<String> all_pfams_encountered,
- final SortedSet<String> pfams_gained_or_lost,
- final String suffix_for_per_node_events_file,
- final Map<String, Integer> tax_code_to_id_map ) {
- if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
- }
- else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
- }
- else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
+ /*
+ * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
+ *
+ *
+ */
+ static public StringBuffer proteinToDomainCombinations( final Protein protein,
+ final String protein_id,
+ final String separator ) {
+ final StringBuffer sb = new StringBuffer();
+ if ( protein.getSpecies() == null ) {
+ throw new IllegalArgumentException( "species must not be null" );
}
- final File outfile = new File( filename );
- checkForOutputFileWriteability( outfile );
- final SortedSet<String> sorted_ids = new TreeSet<String>();
- for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
- sorted_ids.add( matrix.getIdentifier( i ) );
+ if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
+ throw new IllegalArgumentException( "species id must not be empty" );
}
- try {
- final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
- domain_combinations,
- state,
- filename );
- Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
- File per_node_go_mapped_domain_gain_loss_outfile = null;
- int per_node_counter = 0;
- out.write( "<html>" );
- out.write( SurfacingConstants.NL );
- addHtmlHead( out, title_for_html );
- out.write( SurfacingConstants.NL );
- out.write( "<body>" );
- out.write( SurfacingConstants.NL );
- out.write( "<h1>" );
- out.write( SurfacingConstants.NL );
- out.write( title_for_html );
- out.write( SurfacingConstants.NL );
- out.write( "</h1>" );
- out.write( SurfacingConstants.NL );
- out.write( "<table>" );
- out.write( SurfacingConstants.NL );
- for( final String id : sorted_ids ) {
- final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
- if ( matcher.matches() ) {
- continue;
- }
- out.write( "<tr>" );
- out.write( "<td>" );
- out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
- out.write( "</td>" );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- }
- out.write( "</table>" );
- out.write( SurfacingConstants.NL );
- for( final String id : sorted_ids ) {
- final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
- if ( matcher.matches() ) {
- continue;
- }
- out.write( SurfacingConstants.NL );
- out.write( "<h2>" );
- out.write( "<a name=\"" + id + "\">" + id + "</a>" );
- writeTaxonomyLinks( out, id, tax_code_to_id_map );
- out.write( "</h2>" );
- out.write( SurfacingConstants.NL );
- out.write( "<table>" );
- out.write( SurfacingConstants.NL );
- out.write( "<tr>" );
- out.write( "<td><b>" );
- out.write( "Pfam domain(s)" );
- out.write( "</b></td><td><b>" );
- out.write( "GO term acc" );
- out.write( "</b></td><td><b>" );
- out.write( "GO term" );
- out.write( "</b></td><td><b>" );
- out.write( "GO namespace" );
- out.write( "</b></td>" );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- per_node_counter = 0;
- if ( matrix.getNumberOfCharacters() > 0 ) {
- per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
- SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
- per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
- .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
+ final List<Domain> domains = protein.getProteinDomains();
+ if ( domains.size() > 1 ) {
+ final Map<String, Integer> counts = new HashMap<String, Integer>();
+ for( final Domain domain : domains ) {
+ final String id = domain.getDomainId();
+ if ( counts.containsKey( id ) ) {
+ counts.put( id, counts.get( id ) + 1 );
}
else {
- per_node_go_mapped_domain_gain_loss_outfile = null;
- per_node_go_mapped_domain_gain_loss_outfile_writer = null;
+ counts.put( id, 1 );
}
- for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
- // Not nice:
- // using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
- final String character = matrix.getCharacter( c );
- String domain_0 = "";
- String domain_1 = "";
- if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
- final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
- if ( s.length != 2 ) {
- throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
- + character + "]" );
- }
- domain_0 = s[ 0 ];
- domain_1 = s[ 1 ];
- }
- else {
- domain_0 = character;
- }
- writeDomainData( domain_id_to_go_ids_map,
- go_id_to_term_map,
- go_namespace_limit,
- out,
- domain_0,
- domain_1,
- prefix_for_html,
- character_separator,
- domain_id_to_secondary_features_maps,
- null );
- all_pfams_encountered.add( domain_0 );
- if ( pfams_gained_or_lost != null ) {
- pfams_gained_or_lost.add( domain_0 );
- }
- if ( !ForesterUtil.isEmpty( domain_1 ) ) {
- all_pfams_encountered.add( domain_1 );
- if ( pfams_gained_or_lost != null ) {
- pfams_gained_or_lost.add( domain_1 );
- }
- }
- if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
- writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
- domain_0,
- domain_1 );
- per_node_counter++;
- }
+ }
+ final Set<String> dcs = new HashSet<String>();
+ for( int i = 1; i < domains.size(); ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ Domain domain_n = domains.get( i );
+ Domain domain_c = domains.get( j );
+ if ( domain_n.getFrom() > domain_c.getFrom() ) {
+ domain_n = domains.get( j );
+ domain_c = domains.get( i );
}
- }
- if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
- per_node_go_mapped_domain_gain_loss_outfile_writer.close();
- if ( per_node_counter < 1 ) {
- per_node_go_mapped_domain_gain_loss_outfile.delete();
+ final String dc = domain_n.getDomainId() + domain_c.getDomainId();
+ if ( !dcs.contains( dc ) ) {
+ dcs.add( dc );
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( domain_n.getDomainId() );
+ sb.append( separator );
+ sb.append( domain_c.getDomainId() );
+ sb.append( separator );
+ sb.append( domain_n.getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( domain_c.getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( counts.get( domain_n.getDomainId() ) );
+ sb.append( separator );
+ sb.append( counts.get( domain_c.getDomainId() ) );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
}
- per_node_counter = 0;
}
- out.write( "</table>" );
- out.write( SurfacingConstants.NL );
- out.write( "<hr>" );
- out.write( SurfacingConstants.NL );
- } // for( final String id : sorted_ids ) {
- out.write( "</body>" );
- out.write( SurfacingConstants.NL );
- out.write( "</html>" );
- out.write( SurfacingConstants.NL );
- out.flush();
- out.close();
+ }
}
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ else if ( domains.size() == 1 ) {
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( domains.get( 0 ).getDomainId() );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( domains.get( 0 ).getPerDomainEvalue() );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( 1 );
+ sb.append( separator );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
+ else {
+ sb.append( protein.getSpecies() );
+ sb.append( separator );
+ sb.append( protein_id );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( separator );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ return sb;
}
- public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
- final File output_dir,
- final Writer per_genome_domain_promiscuity_statistics_writer,
- final GenomeWideCombinableDomains gwcd,
- final int i,
- final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
- File dc_outfile = new File( input_file_properties[ i ][ 1 ]
- + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
- if ( output_dir != null ) {
- dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
- }
- checkForOutputFileWriteability( dc_outfile );
- try {
- final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
- out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
- out.close();
+ public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
+ final List<Domain> domains = new ArrayList<Domain>();
+ for( final Domain d : protein.getProteinDomains() ) {
+ domains.add( d );
}
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
+ return domains;
+ }
+
+ private static List<String> splitDomainCombination( final String dc ) {
+ final String[] s = dc.split( "=" );
+ if ( s.length != 2 ) {
+ ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
+ + dc );
+ System.exit( -1 );
}
- final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
- try {
- per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
- per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
- if ( stats.getN() < 2 ) {
- per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
- }
- else {
- per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
- .sampleStandardDeviation() ) + "\t" );
- }
- per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
- per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
- per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
- per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
- final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
- for( final String mpd : mpds ) {
- per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
+ final List<String> l = new ArrayList<String>( 2 );
+ l.add( s[ 0 ] );
+ l.add( s[ 1 ] );
+ return l;
+ }
+
+ public static int storeDomainArchitectures( final String genome,
+ final SortedMap<String, Set<String>> domain_architecutures,
+ final List<Protein> protein_list,
+ final Map<String, Integer> distinct_domain_architecuture_counts ) {
+ final Set<String> da = new HashSet<String>();
+ domain_architecutures.put( genome, da );
+ for( final Protein protein : protein_list ) {
+ final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
+ if ( !da.contains( da_str ) ) {
+ if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
+ distinct_domain_architecuture_counts.put( da_str, 1 );
+ }
+ else {
+ distinct_domain_architecuture_counts.put( da_str,
+ distinct_domain_architecuture_counts.get( da_str ) + 1 );
+ }
+ da.add( da_str );
}
- per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
- }
- if ( input_file_properties[ i ].length == 3 ) {
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
- + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
- }
- else {
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
- + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
- + dc_outfile + "\"" );
}
+ return da.size();
}
- public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
- final StringBuilder html_title,
- final Writer simple_tab_writer,
- final Writer single_writer,
- Map<Character, Writer> split_writers,
- final SortedSet<DomainSimilarity> similarities,
- final boolean treat_as_binary,
- final List<Species> species_order,
- final PrintableDomainSimilarity.PRINT_OPTION print_option,
- final DomainSimilarity.DomainSimilarityScoring scoring,
- final boolean verbose,
- final Map<String, Integer> tax_code_to_id_map,
- Phylogeny phy ) throws IOException {
- if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
- split_writers = new HashMap<Character, Writer>();
- split_writers.put( '_', single_writer );
+ public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
+ final boolean get_gains,
+ final String outdir,
+ final String suffix_for_filename ) throws IOException {
+ CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
+ if ( !get_gains ) {
+ state = CharacterStateMatrix.GainLossStates.LOSS;
}
- switch ( print_option ) {
- case SIMPLE_TAB_DELIMITED:
- break;
- case HTML:
- for( final Character key : split_writers.keySet() ) {
- final Writer w = split_writers.get( key );
- w.write( "<html>" );
- w.write( SurfacingConstants.NL );
- if ( key != '_' ) {
- addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
- }
- else {
- addHtmlHead( w, "DC analysis (" + html_title + ")" );
+ final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
+ false,
+ state,
+ outdir );
+ for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ if ( !node.isExternal() ) {
+ final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
+ if ( domains.size() > 0 ) {
+ final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
+ + node.getName() + suffix_for_filename );
+ for( final String domain : domains ) {
+ writer.write( domain );
+ writer.write( ForesterUtil.LINE_SEPARATOR );
}
- w.write( SurfacingConstants.NL );
- w.write( "<body>" );
- w.write( SurfacingConstants.NL );
- w.write( html_desc.toString() );
- w.write( SurfacingConstants.NL );
- w.write( "<hr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td><b>Domains:</b></td></tr>" );
- w.write( SurfacingConstants.NL );
+ writer.close();
}
- break;
- }
- //
- for( final DomainSimilarity similarity : similarities ) {
- if ( ( species_order != null ) && !species_order.isEmpty() ) {
- ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
- }
- if ( single_writer != null ) {
- single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
- single_writer.write( SurfacingConstants.NL );
}
- else {
- Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
- .charAt( 0 ) );
- if ( local_writer == null ) {
- local_writer = split_writers.get( '0' );
+ }
+ }
+
+ private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final String outfile_name,
+ final SortedSet<String> all_pfams_encountered ) {
+ final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
+ final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
+ + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
+ final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
+ int biological_process_counter = 0;
+ int cellular_component_counter = 0;
+ int molecular_function_counter = 0;
+ int pfams_with_mappings_counter = 0;
+ int pfams_without_mappings_counter = 0;
+ int pfams_without_mappings_to_bp_or_mf_counter = 0;
+ int pfams_with_mappings_to_bp_or_mf_counter = 0;
+ try {
+ final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
+ final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
+ final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
+ summary_writer.write( "# Pfam to GO mapping summary" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Actual summary is at the end of this file." );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Encountered Pfams without a GO mapping:" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ for( final String pfam : all_pfams_encountered ) {
+ all_pfams_encountered_writer.write( pfam );
+ all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
+ final String domain_id = new String( pfam );
+ if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
+ ++pfams_with_mappings_counter;
+ all_pfams_encountered_with_go_annotation_writer.write( pfam );
+ all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
+ final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
+ boolean maps_to_bp = false;
+ boolean maps_to_cc = false;
+ boolean maps_to_mf = false;
+ for( final GoId go_id : go_ids ) {
+ final GoTerm go_term = go_id_to_term_map.get( go_id );
+ if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
+ maps_to_bp = true;
+ }
+ else if ( go_term.getGoNameSpace().isCellularComponent() ) {
+ maps_to_cc = true;
+ }
+ else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
+ maps_to_mf = true;
+ }
+ }
+ if ( maps_to_bp ) {
+ ++biological_process_counter;
+ }
+ if ( maps_to_cc ) {
+ ++cellular_component_counter;
+ }
+ if ( maps_to_mf ) {
+ ++molecular_function_counter;
+ }
+ if ( maps_to_bp || maps_to_mf ) {
+ ++pfams_with_mappings_to_bp_or_mf_counter;
+ }
+ else {
+ ++pfams_without_mappings_to_bp_or_mf_counter;
+ }
}
- local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
- + similarity.getDomainId() + "</a></b></td></tr>" );
- local_writer.write( SurfacingConstants.NL );
- }
- }
- for( final Writer w : split_writers.values() ) {
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<hr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
- }
- //
- for( final DomainSimilarity similarity : similarities ) {
- if ( ( species_order != null ) && !species_order.isEmpty() ) {
- ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
- }
- if ( simple_tab_writer != null ) {
- simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
- tax_code_to_id_map,
- null ).toString() );
- }
- if ( single_writer != null ) {
- single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
- single_writer.write( SurfacingConstants.NL );
- }
- else {
- Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
- .charAt( 0 ) );
- if ( local_writer == null ) {
- local_writer = split_writers.get( '0' );
+ else {
+ ++pfams_without_mappings_to_bp_or_mf_counter;
+ ++pfams_without_mappings_counter;
+ summary_writer.write( pfam );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
}
- local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
- local_writer.write( SurfacingConstants.NL );
}
+ all_pfams_encountered_writer.close();
+ all_pfams_encountered_with_go_annotation_writer.close();
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
+ + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+ + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
+ + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
+ + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
+ + encountered_pfams_summary_file + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
+ + all_pfams_encountered.size() );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
+ + pfams_without_mappings_counter + " ["
+ + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ + pfams_without_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : "
+ + pfams_with_mappings_counter + " ["
+ + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ + pfams_with_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
+ + biological_process_counter + " ["
+ + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
+ + molecular_function_counter + " ["
+ + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
+ + cellular_component_counter + " ["
+ + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
+ + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams without mapping to proc. or func. : "
+ + pfams_without_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
+ + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams with a mapping to proc. or func. : "
+ + pfams_with_mappings_to_bp_or_mf_counter + " ["
+ + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
+ + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
+ + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
+ + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
+ summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+ summary_writer.close();
}
- switch ( print_option ) {
- case HTML:
- for( final Writer w : split_writers.values() ) {
- w.write( SurfacingConstants.NL );
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "</font>" );
- w.write( SurfacingConstants.NL );
- w.write( "</body>" );
- w.write( SurfacingConstants.NL );
- w.write( "</html>" );
- w.write( SurfacingConstants.NL );
- }
- break;
- }
- for( final Writer w : split_writers.values() ) {
- w.close();
+ catch ( final IOException e ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
}
- private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
- throws IOException {
- w.write( "<hr>" );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tt><pre>" );
- w.write( SurfacingConstants.NL );
- if ( histo != null ) {
- w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
- w.write( SurfacingConstants.NL );
+ public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
+ final File output_dir,
+ final GenomeWideCombinableDomains gwcd,
+ final int i,
+ final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
+ File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
+ + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
+ if ( output_dir != null ) {
+ dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
}
- w.write( "</pre></tt>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- if ( stats.getN() > 1 ) {
- w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
+ checkForOutputFileWriteability( dc_outfile_dot );
+ final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
+ try {
+ final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
+ for( final BinaryDomainCombination bdc : binary_combinations ) {
+ out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
+ .toString() );
+ out_dot.write( SurfacingConstants.NL );
+ }
+ out_dot.close();
}
- else {
- w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- w.write( SurfacingConstants.NL );
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+ + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
}
- public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
- final String filename,
- final Format format ) {
+ public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+ final CharacterStateMatrix.GainLossStates state,
+ final String filename,
+ final String indentifier_characters_separator,
+ final String character_separator,
+ final Map<String, String> descriptions ) {
final File outfile = new File( filename );
checkForOutputFileWriteability( outfile );
+ final SortedSet<String> sorted_ids = new TreeSet<String>();
+ for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+ sorted_ids.add( matrix.getIdentifier( i ) );
+ }
try {
final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
- matrix.toWriter( out, format );
+ for( final String id : sorted_ids ) {
+ out.write( indentifier_characters_separator );
+ out.write( "#" + id );
+ out.write( indentifier_characters_separator );
+ for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+ // Not nice:
+ // using null to indicate either UNCHANGED_PRESENT or GAIN.
+ if ( ( matrix.getState( id, c ) == state )
+ || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
+ .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
+ out.write( matrix.getCharacter( c ) );
+ if ( ( descriptions != null ) && !descriptions.isEmpty()
+ && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
+ out.write( "\t" );
+ out.write( descriptions.get( matrix.getCharacter( c ) ) );
+ }
+ out.write( character_separator );
+ }
+ }
+ }
out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
- public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
- checkForOutputFileWriteability( matrix_outfile );
+ public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+ final CharacterStateMatrix.GainLossStates state,
+ final String filename,
+ final String indentifier_characters_separator,
+ final String character_separator,
+ final BinaryDomainCombination.OutputFormat bc_output_format ) {
+ final File outfile = new File( filename );
+ checkForOutputFileWriteability( outfile );
+ final SortedSet<String> sorted_ids = new TreeSet<String>();
+ for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+ sorted_ids.add( matrix.getIdentifier( i ) );
+ }
try {
- final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
- for( final DistanceMatrix distance_matrix : matrices ) {
- out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
- out.write( ForesterUtil.LINE_SEPARATOR );
- out.flush();
+ final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+ for( final String id : sorted_ids ) {
+ out.write( indentifier_characters_separator );
+ out.write( "#" + id );
+ out.write( indentifier_characters_separator );
+ for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+ // Not nice:
+ // using null to indicate either UNCHANGED_PRESENT or GAIN.
+ if ( ( matrix.getState( id, c ) == state )
+ || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
+ .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
+ BinaryDomainCombination bdc = null;
+ try {
+ bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
+ out.write( character_separator );
+ }
+ }
}
+ out.flush();
out.close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
- public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
- final PhylogenyWriter writer = new PhylogenyWriter();
- try {
- writer.toPhyloXML( new File( filename ), phylogeny, 1 );
- }
- catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
- + e );
+ public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final GoNameSpace go_namespace_limit,
+ final boolean domain_combinations,
+ final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+ final CharacterStateMatrix.GainLossStates state,
+ final String filename,
+ final String indentifier_characters_separator,
+ final String character_separator,
+ final String title_for_html,
+ final String prefix_for_html,
+ final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
+ final SortedSet<String> all_pfams_encountered,
+ final SortedSet<String> pfams_gained_or_lost,
+ final String suffix_for_per_node_events_file,
+ final Map<String, Integer> tax_code_to_id_map ) {
+ if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
+ throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
}
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
- }
-
- public static void writeTaxonomyLinks( final Writer writer,
- final String species,
- final Map<String, Integer> tax_code_to_id_map ) throws IOException {
- if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
- writer.write( " [" );
- if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
- writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
- + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
- }
- else {
- writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
- + "\" target=\"taxonomy_window\">eol</a>" );
- writer.write( "|" );
- writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
- + "\" target=\"taxonomy_window\">scholar</a>" );
- writer.write( "|" );
- writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
- + "\" target=\"taxonomy_window\">google</a>" );
- }
- writer.write( "]" );
+ else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
+ throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
}
- }
-
- private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
- if ( map.containsKey( s ) ) {
- map.put( s, map.get( s ) + 1 );
+ else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
+ throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
}
- else {
- map.put( s, 1 );
+ final File outfile = new File( filename );
+ checkForOutputFileWriteability( outfile );
+ final SortedSet<String> sorted_ids = new TreeSet<String>();
+ for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+ sorted_ids.add( matrix.getIdentifier( i ) );
}
- }
-
- private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
- final String outfilename_for_counts,
- final String outfilename_for_dc,
- final String outfilename_for_dc_for_go_mapping,
- final String outfilename_for_dc_for_go_mapping_unique,
- final String outfilename_for_rank_counts,
- final String outfilename_for_ancestor_species_counts,
- final String outfilename_for_protein_stats,
- final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
- final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
- final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
try {
- //
- // if ( protein_length_stats_by_dc != null ) {
- // for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
- // System.out.print( entry.getKey().toString() );
- // System.out.print( ": " );
- // double[] a = entry.getValue().getDataAsDoubleArray();
- // for( int i = 0; i < a.length; i++ ) {
- // System.out.print( a[ i ] + " " );
- // }
- // System.out.println();
- // }
- // }
- // if ( domain_number_stats_by_dc != null ) {
- // for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
- // System.out.print( entry.getKey().toString() );
- // System.out.print( ": " );
- // double[] a = entry.getValue().getDataAsDoubleArray();
- // for( int i = 0; i < a.length; i++ ) {
- // System.out.print( a[ i ] + " " );
- // }
- // System.out.println();
- // }
- // }
- //
- final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
- final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
- final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
- final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
- final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
- for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
- for( final String dc : gained_dc ) {
- if ( dc_gain_counts.containsKey( dc ) ) {
- dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
- }
- else {
- dc_gain_counts.put( dc, 1 );
- }
- }
- }
- final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
- final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
- final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
- final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
- final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
- final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
- final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
- final Set<String> dcs = dc_gain_counts.keySet();
- final SortedSet<String> more_than_once = new TreeSet<String>();
- DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
- DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
- DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
- final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
- long gained_multiple_times_domain_length_sum = 0;
- long gained_once_domain_length_sum = 0;
- long gained_multiple_times_domain_length_count = 0;
- long gained_once_domain_length_count = 0;
- for( final String dc : dcs ) {
- final int count = dc_gain_counts.get( dc );
- if ( histogram.containsKey( count ) ) {
- histogram.put( count, histogram.get( count ) + 1 );
- domain_lists.get( count ).append( ", " + dc );
- domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
- domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
- }
- else {
- histogram.put( count, 1 );
- domain_lists.put( count, new StringBuilder( dc ) );
- final PriorityQueue<String> q = new PriorityQueue<String>();
- q.addAll( splitDomainCombination( dc ) );
- domain_lists_go.put( count, q );
- final SortedSet<String> set = new TreeSet<String>();
- set.addAll( splitDomainCombination( dc ) );
- domain_lists_go_unique.put( count, set );
- }
- if ( protein_length_stats_by_dc != null ) {
- if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
- dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
- }
- dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
- .arithmeticMean() );
- }
- if ( domain_number_stats_by_dc != null ) {
- if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
- dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
- }
- dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
- .arithmeticMean() );
- }
- if ( domain_length_stats_by_domain != null ) {
- if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
- dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
- }
- final String[] ds = dc.split( "=" );
- dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
- .get( ds[ 0 ] ).arithmeticMean() );
- dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
- .get( ds[ 1 ] ).arithmeticMean() );
- }
- if ( count > 1 ) {
- more_than_once.add( dc );
- if ( protein_length_stats_by_dc != null ) {
- final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
- for( final double element : s.getData() ) {
- gained_multiple_times_lengths_stats.addValue( element );
- }
- }
- if ( domain_number_stats_by_dc != null ) {
- final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
- for( final double element : s.getData() ) {
- gained_multiple_times_domain_count_stats.addValue( element );
- }
- }
- if ( domain_length_stats_by_domain != null ) {
- final String[] ds = dc.split( "=" );
- final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
- final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
- for( final double element : s0.getData() ) {
- gained_multiple_times_domain_length_sum += element;
- ++gained_multiple_times_domain_length_count;
- }
- for( final double element : s1.getData() ) {
- gained_multiple_times_domain_length_sum += element;
- ++gained_multiple_times_domain_length_count;
- }
- }
- }
- else {
- if ( protein_length_stats_by_dc != null ) {
- final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
- for( final double element : s.getData() ) {
- gained_once_lengths_stats.addValue( element );
- }
- }
- if ( domain_number_stats_by_dc != null ) {
- final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
- for( final double element : s.getData() ) {
- gained_once_domain_count_stats.addValue( element );
- }
- }
- if ( domain_length_stats_by_domain != null ) {
- final String[] ds = dc.split( "=" );
- final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
- final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
- for( final double element : s0.getData() ) {
- gained_once_domain_length_sum += element;
- ++gained_once_domain_length_count;
- }
- for( final double element : s1.getData() ) {
- gained_once_domain_length_sum += element;
- ++gained_once_domain_length_count;
- }
- }
+ final Writer out = new BufferedWriter( new FileWriter( outfile ) );
+ final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
+ domain_combinations,
+ state,
+ filename );
+ Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
+ File per_node_go_mapped_domain_gain_loss_outfile = null;
+ int per_node_counter = 0;
+ out.write( "<html>" );
+ out.write( SurfacingConstants.NL );
+ addHtmlHead( out, title_for_html );
+ out.write( SurfacingConstants.NL );
+ out.write( "<body>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "<h1>" );
+ out.write( SurfacingConstants.NL );
+ out.write( title_for_html );
+ out.write( SurfacingConstants.NL );
+ out.write( "</h1>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "<table>" );
+ out.write( SurfacingConstants.NL );
+ for( final String id : sorted_ids ) {
+ final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
+ if ( matcher.matches() ) {
+ continue;
}
+ out.write( "<tr>" );
+ out.write( "<td>" );
+ out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
+ out.write( "</td>" );
+ out.write( "</tr>" );
+ out.write( SurfacingConstants.NL );
}
- final Set<Integer> histogram_keys = histogram.keySet();
- for( final Integer histogram_key : histogram_keys ) {
- final int count = histogram.get( histogram_key );
- final StringBuilder dc = domain_lists.get( histogram_key );
- out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
- out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
- out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
- final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
- Arrays.sort( sorted );
- for( final Object domain : sorted ) {
- out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
+ out.write( "</table>" );
+ out.write( SurfacingConstants.NL );
+ for( final String id : sorted_ids ) {
+ final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
+ if ( matcher.matches() ) {
+ continue;
}
- out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
- for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
- out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
+ out.write( SurfacingConstants.NL );
+ out.write( "<h2>" );
+ out.write( "<a name=\"" + id + "\">" + id + "</a>" );
+ writeTaxonomyLinks( out, id, tax_code_to_id_map );
+ out.write( "</h2>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "<table>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "<tr>" );
+ out.write( "<td><b>" );
+ out.write( "Pfam domain(s)" );
+ out.write( "</b></td><td><b>" );
+ out.write( "GO term acc" );
+ out.write( "</b></td><td><b>" );
+ out.write( "GO term" );
+ out.write( "</b></td><td><b>" );
+ out.write( "GO namespace" );
+ out.write( "</b></td>" );
+ out.write( "</tr>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "</tr>" );
+ out.write( SurfacingConstants.NL );
+ per_node_counter = 0;
+ if ( matrix.getNumberOfCharacters() > 0 ) {
+ per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+ + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
+ SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
+ per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
+ .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
}
- }
- out_counts.close();
- out_dc.close();
- out_dc_for_go_mapping.close();
- out_dc_for_go_mapping_unique.close();
- final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
- final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
- for( final String dc : more_than_once ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
- nodes.add( n );
- }
+ else {
+ per_node_go_mapped_domain_gain_loss_outfile = null;
+ per_node_go_mapped_domain_gain_loss_outfile_writer = null;
}
- for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
- for( int j = i + 1; j < nodes.size(); ++j ) {
- final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
- String rank = "unknown";
- if ( lca.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
- rank = lca.getNodeData().getTaxonomy().getRank();
+ for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+ // Not nice:
+ // using null to indicate either UNCHANGED_PRESENT or GAIN.
+ if ( ( matrix.getState( id, c ) == state )
+ || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
+ .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
+ final String character = matrix.getCharacter( c );
+ String domain_0 = "";
+ String domain_1 = "";
+ if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
+ final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
+ if ( s.length != 2 ) {
+ throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
+ + character + "]" );
+ }
+ domain_0 = s[ 0 ];
+ domain_1 = s[ 1 ];
}
- addToCountMap( lca_rank_counts, rank );
- String lca_species;
- if ( lca.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
- lca_species = lca.getNodeData().getTaxonomy().getScientificName();
+ else {
+ domain_0 = character;
}
- else if ( lca.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
- lca_species = lca.getNodeData().getTaxonomy().getCommonName();
+ writeDomainData( domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ out,
+ domain_0,
+ domain_1,
+ prefix_for_html,
+ character_separator,
+ domain_id_to_secondary_features_maps,
+ null );
+ all_pfams_encountered.add( domain_0 );
+ if ( pfams_gained_or_lost != null ) {
+ pfams_gained_or_lost.add( domain_0 );
}
- else {
- lca_species = lca.getName();
+ if ( !ForesterUtil.isEmpty( domain_1 ) ) {
+ all_pfams_encountered.add( domain_1 );
+ if ( pfams_gained_or_lost != null ) {
+ pfams_gained_or_lost.add( domain_1 );
+ }
+ }
+ if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
+ writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
+ domain_0,
+ domain_1 );
+ per_node_counter++;
}
- addToCountMap( lca_ancestor_species_counts, lca_species );
- }
- }
- }
- final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
- final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
- ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
- ForesterUtil.map2writer( out_for_ancestor_species_counts,
- lca_ancestor_species_counts,
- "\t",
- ForesterUtil.LINE_SEPARATOR );
- out_for_rank_counts.close();
- out_for_ancestor_species_counts.close();
- if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
- && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
- final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
- w.write( "Domain Lengths: " );
- w.write( "\n" );
- if ( domain_length_stats_by_domain != null ) {
- for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
- .entrySet() ) {
- w.write( entry.getKey().toString() );
- w.write( "\t" + entry.getValue().arithmeticMean() );
- w.write( "\t" + entry.getValue().median() );
- w.write( "\n" );
- }
- }
- w.flush();
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Protein Lengths: " );
- w.write( "\n" );
- if ( protein_length_stats_by_dc != null ) {
- for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
- .entrySet() ) {
- w.write( entry.getKey().toString() );
- w.write( "\t" + entry.getValue().arithmeticMean() );
- w.write( "\t" + entry.getValue().median() );
- w.write( "\n" );
}
}
- w.flush();
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Number of domains: " );
- w.write( "\n" );
- if ( domain_number_stats_by_dc != null ) {
- for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
- .entrySet() ) {
- w.write( entry.getKey().toString() );
- w.write( "\t" + entry.getValue().arithmeticMean() );
- w.write( "\t" + entry.getValue().median() );
- w.write( "\n" );
+ if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
+ per_node_go_mapped_domain_gain_loss_outfile_writer.close();
+ if ( per_node_counter < 1 ) {
+ per_node_go_mapped_domain_gain_loss_outfile.delete();
}
+ per_node_counter = 0;
}
- w.flush();
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained once, domain lengths:" );
- w.write( "\n" );
- w.write( "N: " + gained_once_domain_length_count );
- w.write( "\n" );
- w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained multiple times, domain lengths:" );
- w.write( "\n" );
- w.write( "N: " + gained_multiple_times_domain_length_count );
- w.write( "\n" );
- w.write( "Avg: "
- + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
- w.write( "\n" );
- w.write( "\n" );
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained once, protein lengths:" );
- w.write( "\n" );
- w.write( gained_once_lengths_stats.toString() );
- gained_once_lengths_stats = null;
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained once, domain counts:" );
- w.write( "\n" );
- w.write( gained_once_domain_count_stats.toString() );
- gained_once_domain_count_stats = null;
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained multiple times, protein lengths:" );
- w.write( "\n" );
- w.write( gained_multiple_times_lengths_stats.toString() );
- gained_multiple_times_lengths_stats = null;
- w.write( "\n" );
- w.write( "\n" );
- w.write( "Gained multiple times, domain counts:" );
- w.write( "\n" );
- w.write( gained_multiple_times_domain_count_stats.toString() );
- w.flush();
- w.close();
- }
+ out.write( "</table>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "<hr>" );
+ out.write( SurfacingConstants.NL );
+ } // for( final String id : sorted_ids ) {
+ out.write( "</body>" );
+ out.write( SurfacingConstants.NL );
+ out.write( "</html>" );
+ out.write( SurfacingConstants.NL );
+ out.flush();
+ out.close();
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
- }
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
- + outfilename_for_counts + "]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
- + outfilename_for_dc + "]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
- + outfilename_for_dc_for_go_mapping + "]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
- + outfilename_for_dc_for_go_mapping_unique + "]" );
- }
-
- private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
- final boolean get_gains ) {
- final SortedSet<String> domains = new TreeSet<String>();
- for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
- final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
- if ( get_gains ) {
- domains.addAll( chars.getGainedCharacters() );
- }
- else {
- domains.addAll( chars.getLostCharacters() );
- }
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- return domains;
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
}
- private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
- final boolean domain_combinations,
- final CharacterStateMatrix.GainLossStates state,
- final String outfile ) {
- File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
- + ForesterUtil.FILE_SEPARATOR + base_dir );
- if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
- }
- if ( domain_combinations ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + "DC" );
- }
- else {
- per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
- }
- if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
- }
- if ( state == GainLossStates.GAIN ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + "GAINS" );
- }
- else if ( state == GainLossStates.LOSS ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
- }
- else {
- per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
- }
- if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
- per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+ public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
+ final File output_dir,
+ final Writer per_genome_domain_promiscuity_statistics_writer,
+ final GenomeWideCombinableDomains gwcd,
+ final int i,
+ final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
+ File dc_outfile = new File( input_file_properties[ i ][ 1 ]
+ + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ if ( output_dir != null ) {
+ dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
}
- return per_node_go_mapped_domain_gain_loss_files_base_dir;
- }
-
- private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
- final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
- final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
- for( final String domain_id : cds.keySet() ) {
- final CombinableDomains cd = cds.get( domain_id );
- binary_combinations.addAll( cd.toBinaryDomainCombinations() );
+ checkForOutputFileWriteability( dc_outfile );
+ try {
+ final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
+ out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
+ out.close();
}
- return binary_combinations;
- }
-
- private static List<String> splitDomainCombination( final String dc ) {
- final String[] s = dc.split( "=" );
- if ( s.length != 2 ) {
- ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
- + dc );
- System.exit( -1 );
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- final List<String> l = new ArrayList<String>( 2 );
- l.add( s[ 0 ] );
- l.add( s[ 1 ] );
- return l;
- }
-
- private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final String outfile_name,
- final SortedSet<String> all_pfams_encountered ) {
- final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
- final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
- + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
- final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
- int biological_process_counter = 0;
- int cellular_component_counter = 0;
- int molecular_function_counter = 0;
- int pfams_with_mappings_counter = 0;
- int pfams_without_mappings_counter = 0;
- int pfams_without_mappings_to_bp_or_mf_counter = 0;
- int pfams_with_mappings_to_bp_or_mf_counter = 0;
+ final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
try {
- final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
- final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
- final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
- summary_writer.write( "# Pfam to GO mapping summary" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Actual summary is at the end of this file." );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Encountered Pfams without a GO mapping:" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- for( final String pfam : all_pfams_encountered ) {
- all_pfams_encountered_writer.write( pfam );
- all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
- final String domain_id = new String( pfam );
- if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
- ++pfams_with_mappings_counter;
- all_pfams_encountered_with_go_annotation_writer.write( pfam );
- all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
- final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
- boolean maps_to_bp = false;
- boolean maps_to_cc = false;
- boolean maps_to_mf = false;
- for( final GoId go_id : go_ids ) {
- final GoTerm go_term = go_id_to_term_map.get( go_id );
- if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
- maps_to_bp = true;
- }
- else if ( go_term.getGoNameSpace().isCellularComponent() ) {
- maps_to_cc = true;
- }
- else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
- maps_to_mf = true;
- }
- }
- if ( maps_to_bp ) {
- ++biological_process_counter;
- }
- if ( maps_to_cc ) {
- ++cellular_component_counter;
- }
- if ( maps_to_mf ) {
- ++molecular_function_counter;
- }
- if ( maps_to_bp || maps_to_mf ) {
- ++pfams_with_mappings_to_bp_or_mf_counter;
- }
- else {
- ++pfams_without_mappings_to_bp_or_mf_counter;
- }
- }
- else {
- ++pfams_without_mappings_to_bp_or_mf_counter;
- ++pfams_without_mappings_counter;
- summary_writer.write( pfam );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- }
+ per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
+ if ( stats.getN() < 2 ) {
+ per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
}
- all_pfams_encountered_writer.close();
- all_pfams_encountered_with_go_annotation_writer.close();
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
- + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
- + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
- + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
- + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
- + encountered_pfams_summary_file + "\"" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
- + all_pfams_encountered.size() );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
- + pfams_without_mappings_counter + " ["
- + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
- + pfams_without_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : "
- + pfams_with_mappings_counter + " ["
- + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
- + pfams_with_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
- + biological_process_counter + " ["
- + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
- + molecular_function_counter + " ["
- + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
- + cellular_component_counter + " ["
- + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
- + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams without mapping to proc. or func. : "
- + pfams_without_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
- + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams with a mapping to proc. or func. : "
- + pfams_with_mappings_to_bp_or_mf_counter + " ["
- + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
- + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
- + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
- + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
- summary_writer.write( ForesterUtil.LINE_SEPARATOR );
- summary_writer.close();
+ else {
+ per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
+ .sampleStandardDeviation() ) + "\t" );
+ }
+ per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
+ final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
+ for( final String mpd : mpds ) {
+ per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
+ }
+ per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( input_file_properties[ i ].length == 3 ) {
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+ + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
+ }
+ else {
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+ + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+ + dc_outfile + "\"" );
}
}
out.write( "</td>" );
}
+ public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
+ final StringBuilder html_title,
+ final Writer simple_tab_writer,
+ final Writer single_writer,
+ Map<Character, Writer> split_writers,
+ final SortedSet<DomainSimilarity> similarities,
+ final boolean treat_as_binary,
+ final List<Species> species_order,
+ final PrintableDomainSimilarity.PRINT_OPTION print_option,
+ final DomainSimilarity.DomainSimilarityScoring scoring,
+ final boolean verbose,
+ final Map<String, Integer> tax_code_to_id_map,
+ Phylogeny phy ) throws IOException {
+ if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
+ split_writers = new HashMap<Character, Writer>();
+ split_writers.put( '_', single_writer );
+ }
+ switch ( print_option ) {
+ case SIMPLE_TAB_DELIMITED:
+ break;
+ case HTML:
+ for( final Character key : split_writers.keySet() ) {
+ final Writer w = split_writers.get( key );
+ w.write( "<html>" );
+ w.write( SurfacingConstants.NL );
+ if ( key != '_' ) {
+ addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
+ }
+ else {
+ addHtmlHead( w, "DC analysis (" + html_title + ")" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "<body>" );
+ w.write( SurfacingConstants.NL );
+ w.write( html_desc.toString() );
+ w.write( SurfacingConstants.NL );
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td><b>Domains:</b></td></tr>" );
+ w.write( SurfacingConstants.NL );
+ }
+ break;
+ }
+ //
+ for( final DomainSimilarity similarity : similarities ) {
+ if ( ( species_order != null ) && !species_order.isEmpty() ) {
+ ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+ }
+ if ( single_writer != null ) {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ single_writer.write( SurfacingConstants.NL );
+ }
+ else {
+ Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+ .charAt( 0 ) );
+ if ( local_writer == null ) {
+ local_writer = split_writers.get( '0' );
+ }
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ local_writer.write( SurfacingConstants.NL );
+ }
+ }
+ for( final Writer w : split_writers.values() ) {
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ }
+ //
+ for( final DomainSimilarity similarity : similarities ) {
+ if ( ( species_order != null ) && !species_order.isEmpty() ) {
+ ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+ }
+ if ( simple_tab_writer != null ) {
+ simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
+ tax_code_to_id_map,
+ null ).toString() );
+ }
+ if ( single_writer != null ) {
+ single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
+ single_writer.write( SurfacingConstants.NL );
+ }
+ else {
+ Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+ .charAt( 0 ) );
+ if ( local_writer == null ) {
+ local_writer = split_writers.get( '0' );
+ }
+ local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
+ local_writer.write( SurfacingConstants.NL );
+ }
+ }
+ switch ( print_option ) {
+ case HTML:
+ for( final Writer w : split_writers.values() ) {
+ w.write( SurfacingConstants.NL );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</font>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</body>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "</html>" );
+ w.write( SurfacingConstants.NL );
+ }
+ break;
+ }
+ for( final Writer w : split_writers.values() ) {
+ w.close();
+ }
+ }
+
private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
final String domain_0,
final String domain_1 ) throws IOException {
}
}
+ public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
+ final String filename,
+ final Format format ) {
+ final File outfile = new File( filename );
+ checkForOutputFileWriteability( outfile );
+ try {
+ final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+ matrix.toWriter( out, format );
+ out.flush();
+ out.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
+ }
+
+ public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
+ checkForOutputFileWriteability( matrix_outfile );
+ try {
+ final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
+ for( final DistanceMatrix distance_matrix : matrices ) {
+ out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ out.flush();
+ }
+ out.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
+ }
+
private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
try {
final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
}
}
+ public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ try {
+ writer.toPhyloXML( new File( filename ), phylogeny, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
+ + e );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
+ }
+
+ public static void writePresentToNexus( final File output_file,
+ final File positive_filter_file,
+ final SortedSet<String> filter,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ try {
+ writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
+ positive_filter_file == null ? null
+ : filter ),
+ output_file + surfacing.DOMAINS_PRESENT_NEXUS,
+ Format.NEXUS_BINARY );
+ writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
+ output_file + surfacing.BDC_PRESENT_NEXUS,
+ Format.NEXUS_BINARY );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ public static void writeProteinListsForAllSpecies( final File output_dir,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final double domain_e_cutoff ) {
+ final SortedSet<String> all_domains = new TreeSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_domains.addAll( gwcd.getAllDomainIds() );
+ }
+ for( final String domain : all_domains ) {
+ final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
+ checkForOutputFileWriteability( out );
+ try {
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+ extractProteinNames( protein_lists_per_species,
+ domain,
+ proteins_file_writer,
+ "\t",
+ surfacing.LIMIT_SPEC_FOR_PROT_EX,
+ domain_e_cutoff );
+ proteins_file_writer.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+ }
+ }
+
+ public static void writeTaxonomyLinks( final Writer writer,
+ final String species,
+ final Map<String, Integer> tax_code_to_id_map ) throws IOException {
+ if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
+ writer.write( " [" );
+ if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
+ writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
+ + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
+ }
+ else {
+ writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
+ + "\" target=\"taxonomy_window\">eol</a>" );
+ writer.write( "|" );
+ writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
+ + "\" target=\"taxonomy_window\">scholar</a>" );
+ writer.write( "|" );
+ writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
+ + "\" target=\"taxonomy_window\">google</a>" );
+ }
+ writer.write( "]" );
+ }
+ }
+
private static void writeToNexus( final String outfile_name,
final CharacterStateMatrix<BinaryStates> matrix,
final Phylogeny phylogeny ) {
phylogeny );
}
- final static class DomainComparator implements Comparator<Domain> {
-
- final private boolean _ascending;
-
- public DomainComparator( final boolean ascending ) {
- _ascending = ascending;
- }
-
- @Override
- public final int compare( final Domain d0, final Domain d1 ) {
- if ( d0.getFrom() < d1.getFrom() ) {
- return _ascending ? -1 : 1;
- }
- else if ( d0.getFrom() > d1.getFrom() ) {
- return _ascending ? 1 : -1;
- }
- return 0;
- }
- }
-
- final static Color getColorForTaxCode( final String tax ) {
- if ( tax.equals( "Deuterostomia" ) ) {
- return ForesterUtil.DEUTEROSTOMIA_COLOR;
- }
- else if ( tax.equals( "Protostomia" ) ) {
- return ForesterUtil.PROTOSTOMIA_COLOR;
- }
- else if ( tax.equals( "Metazoa" ) ) {
- return ForesterUtil.METAZOA_COLOR;
- }
- else if ( tax.equals( "Holozoa" ) ) {
- return ForesterUtil.HOLOZOA_COLOR;
- }
- else if ( tax.equals( "Fungi" ) ) {
- return ForesterUtil.FUNGI_COLOR;
- }
- else if ( tax.equals( "Holomycota" ) ) {
- return ForesterUtil.HOLOMYCOTA_COLOR;
- }
- else if ( tax.equals( "Amoebozoa" ) ) {
- return ForesterUtil.AMOEBOZOA_COLOR;
- }
- else if ( tax.equals( "Viridiplantae" ) ) {
- return ForesterUtil.VIRIDPLANTAE_COLOR;
- }
- else if ( tax.equals( "Rhodophytaa" ) ) {
- return ForesterUtil.RHODOPHYTA_COLOR;
- }
- else if ( tax.startsWith( "Hacrobia" ) ) {
- return ForesterUtil.HACROBIA_COLOR;
- }
- else if ( tax.equals( "Stramenopiles" ) ) {
- return ForesterUtil.STRAMENOPILES_COLOR;
- }
- else if ( tax.equals( "Alveolata" ) ) {
- return ForesterUtil.ALVEOLATA_COLOR;
- }
- else if ( tax.equals( "Rhizaria" ) ) {
- return ForesterUtil.RHIZARIA_COLOR;
- }
- else if ( tax.equals( "Excavata" ) ) {
- return ForesterUtil.EXCAVATA_COLOR;
- }
- else if ( tax.equals( "Archaea" ) ) {
- return ForesterUtil.ARCHAEA_COLOR;
- }
- else if ( tax.equals( "Bacteria" ) ) {
- return ForesterUtil.BACTERIA_COLOR;
- }
- return null;
+ private SurfacingUtil() {
+ // Hidden constructor.
}
}
git://source.jalview.org / jalview.git / commitdiff