- public final static String PRG_NAME = "surfacing";
- public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
- public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
- public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
- public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
- public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
- public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
- public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
- public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
- public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String OUTPUT_DIR_OPTION = "out_dir";
- final static private String SCORING_OPTION = "scoring";
- private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
- final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
- final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
- final static private String SCORING_COMBINATION_BASED = "combinations";
- final static private String DETAILEDNESS_OPTION = "detail";
- private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
- final static private String SPECIES_MATRIX_OPTION = "smatrix";
- final static private String DETAILEDNESS_BASIC = "basic";
- final static private String DETAILEDNESS_LIST_IDS = "list_ids";
- final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
- final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
- private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
- final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
- final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
- final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
- final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
- final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
- final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
- final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
- final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
- final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
- final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
- final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
- private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
- final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
- final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
- final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
- final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
- final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
- final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
- final static private String MAX_E_VALUE_OPTION = "e";
- final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
- final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
- final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
- final static private 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 String GO_OBO_FILE_USE_OPTION = "obo";
- final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
- final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
- final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
- final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
- final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
- final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
- final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
- final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
- final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
- private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML;
- final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
- final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
- final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
- final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
- final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
- final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
- final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
- final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
- final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String JACKNIFE_OPTION = "jack";
- final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
- final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
- private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
- final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
- final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
- //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
- final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh";
- final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh";
- final static private String FILTER_POSITIVE_OPTION = "pos_filter";
- final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
- final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
- final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
- final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
- final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
- final static private String PRG_VERSION = "2.240";
- final static private String PRG_DATE = "2012.05.04";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
- final static private boolean IGNORE_DUFS_DEFAULT = true;
- 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;
- 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";
- private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
- private 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";
- private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true;
- public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
- public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
- public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
- public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
- public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
- public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
- public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
- public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
- public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
- public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
- private static final String LOG_FILE_SUFFIX = "_log.txt";
- private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
- private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
- private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt";
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt";
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
- public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default).
- public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch"
- + ForesterConstants.PHYLO_XML_SUFFIX;
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt";
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt";
- public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
- 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 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<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
- final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
- 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<DomainId, 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 List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
- final NeighborJoining nj = NeighborJoining.createInstance();
- final List<Phylogeny> phylogenies = nj.execute( distances_list );
- final PhylogenyWriter w = new PhylogenyWriter();
- try {
- w.toNewHampshire( phylogenies, true, true, outfile, ";" );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
- }
- return phylogenies;
- }
-
- 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 final static String PRG_NAME = "surfacing";
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
+ public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
+ public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
+ public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
+ public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
+ public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String OUTPUT_DIR_OPTION = "out_dir";
+ final static private String SCORING_OPTION = "scoring";
+ private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
+ final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
+ final static private String SCORING_COMBINATION_BASED = "combinations";
+ final static private String DETAILEDNESS_OPTION = "detail";
+ private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ final static private String SPECIES_MATRIX_OPTION = "smatrix";
+ final static private String DETAILEDNESS_BASIC = "basic";
+ final static private String DETAILEDNESS_LIST_IDS = "list_ids";
+ final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
+ final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
+ private static final DomainSimilarity.DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
+ final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
+ final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
+ final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
+ final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
+ final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
+ final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
+ final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
+ private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
+ final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
+ final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
+ final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
+ final static private String MAX_FS_E_VALUE_OPTION = "fs_e";
+ final static private String MAX_I_E_VALUE_OPTION = "ie";
+ final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
+ final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
+ final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ 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";
+ 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 String GO_OBO_FILE_USE_OPTION = "obo";
+ final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
+ final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
+ private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = DomainSimilarity.PRINT_OPTION.HTML;
+ final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
+ final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
+ final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
+ final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
+ final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
+ final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
+ final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
+ final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
+ final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String FILTER_POSITIVE_OPTION = "pos_filter";
+ final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
+ final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
+ final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
+ final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
+ final static private String SEQ_EXTRACT_OPTION = "prot_extract";
+ final static private String PRG_VERSION = "2.404";
+ final static private String PRG_DATE = "140709";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
+ 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;
+ 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";
+ 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";
+ 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";
+ private static final String PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION = "dla";
+ public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
+ public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
+ public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
+ public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
+ public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
+ public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
+ public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
+ public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
+ public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
+ public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
+ private static final String LOG_FILE_SUFFIX = "_log.txt";
+ private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
+ private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
+ private static final String WRITE_TO_NEXUS_OPTION = "nexus";
+ private static final String PERFORM_DC_FITCH = "dc_pars";
+ private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change?
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
+ public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default).
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt";
+ public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
+ 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;
+ @SuppressWarnings("unchecked")