X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=2b5c7c4de89636f694bb760dbfd42224190fed21;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=aafd989e07eb749fb468e22dfcc8ecd2d8de535d;hpb=ebd968cbfe6c82c7fa085a974397de9606fce677;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index aafd989..2b5c7c4 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; @@ -34,19 +34,14 @@ import java.io.Writer; import java.util.ArrayList; import java.util.Date; import java.util.HashMap; -import java.util.HashSet; import java.util.List; import java.util.Map; -import java.util.Map.Entry; import java.util.Set; import java.util.SortedMap; import java.util.SortedSet; import java.util.TreeMap; import java.util.TreeSet; -import org.forester.evoinference.distance.NeighborJoining; -import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format; -import org.forester.evoinference.matrix.distance.DistanceMatrix; import org.forester.go.GoId; import org.forester.go.GoNameSpace; import org.forester.go.GoTerm; @@ -56,26 +51,21 @@ import org.forester.go.PfamToGoMapping; import org.forester.go.PfamToGoParser; import org.forester.io.parsers.HmmscanPerDomainTableParser; import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF; -import org.forester.io.parsers.util.ParserUtils; -import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.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.species.BasicSpecies; +import org.forester.species.Species; import org.forester.surfacing.BasicDomainSimilarityCalculator; import org.forester.surfacing.BasicGenomeWideCombinableDomains; -import org.forester.surfacing.BasicSpecies; -import org.forester.surfacing.BinaryDomainCombination; import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator; import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator; -import org.forester.surfacing.DomainCountsDifferenceUtil; -import org.forester.surfacing.DomainId; import org.forester.surfacing.DomainLengthsTable; import org.forester.surfacing.DomainParsimonyCalculator; import org.forester.surfacing.DomainSimilarity; import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring; -import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField; +import org.forester.surfacing.DomainSimilarity.PRINT_OPTION; import org.forester.surfacing.DomainSimilarityCalculator; import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; import org.forester.surfacing.GenomeWideCombinableDomains; @@ -83,11 +73,7 @@ import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDo import org.forester.surfacing.MappingResults; import org.forester.surfacing.PairwiseDomainSimilarityCalculator; import org.forester.surfacing.PairwiseGenomeComparator; -import org.forester.surfacing.PrintableDomainSimilarity; -import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; -import org.forester.surfacing.Protein; import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator; -import org.forester.surfacing.Species; import org.forester.surfacing.SurfacingUtil; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.BasicTable; @@ -99,464 +85,191 @@ import org.forester.util.ForesterUtil; public class surfacing { - public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; - public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; - public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; + private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; + public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; + public final static String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION = "dcc"; + public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; + public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; // gain/loss: - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; // gain/loss counts: - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; // tables: - public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; - public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; - public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; - public final static String BDC_PRESENT_NEXUS = "_dc.nex"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; + public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; + public final static String BDC_PRESENT_NEXUS = "_dc.nex"; // --- - 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 = "2.210"; - final static private String PRG_DATE = "2011.12.08"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; - final static private boolean IGNORE_DUFS_DEFAULT = true; - 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"; - - 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 - * @throws IOException - */ - private static void executeFitchGainsAnalysis( final File output_file, - final List all_bin_domain_combinations_changed, - final int sum_of_all_domains_encountered, - final SortedSet 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 bdc_to_counts = ForesterUtil - .listToSortedCountsMap( all_bin_domain_combinations_changed ); - final SortedSet all_domains_in_combination_changed_more_than_once = new TreeSet(); - final SortedSet all_domains_in_combination_changed_only_once = new TreeSet(); - 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 plus_minus_analysis_high_copy_base, - final List plus_minus_analysis_high_copy_target, - final List plus_minus_analysis_low_copy, - final List gwcd_list, - final SortedMap> protein_lists_per_species, - final Map> domain_id_to_go_ids_map, - final Map go_id_to_term_map, - final List plus_minus_analysis_numbers ) { - final Set all_spec = new HashSet(); - 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 inferSpeciesTrees( final File outfile, final List distances_list ) { - final NeighborJoining nj = NeighborJoining.createInstance(); - final List 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; public static void main( final String args[] ) { final long start_time = new Date().getTime(); @@ -591,7 +304,8 @@ public class surfacing { } final List allowed_options = new ArrayList(); allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION ); - allowed_options.add( surfacing.MAX_E_VALUE_OPTION ); + allowed_options.add( surfacing.MAX_FS_E_VALUE_OPTION ); + allowed_options.add( surfacing.MAX_I_E_VALUE_OPTION ); allowed_options.add( surfacing.DETAILEDNESS_OPTION ); allowed_options.add( surfacing.OUTPUT_FILE_OPTION ); allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ); @@ -611,38 +325,75 @@ public class surfacing { allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ); allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ); - allowed_options.add( JACKNIFE_OPTION ); - allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION ); - allowed_options.add( JACKNIFE_RATIO_OPTION ); allowed_options.add( INPUT_SPECIES_TREE_OPTION ); - //allowed_options.add( INFER_SPECIES_TREES_OPTION ); allowed_options.add( FILTER_POSITIVE_OPTION ); allowed_options.add( FILTER_NEGATIVE_OPTION ); - allowed_options.add( INPUT_FILES_FROM_FILE_OPTION ); + allowed_options.add( INPUT_GENOMES_FILE_OPTION ); allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ); allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION ); allowed_options.add( IGNORE_VIRAL_IDS ); allowed_options.add( SEQ_EXTRACT_OPTION ); + allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE ); allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION ); allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ); + allowed_options.add( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ); allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ); allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ); + allowed_options.add( WRITE_TO_NEXUS_OPTION ); + allowed_options.add( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ); + allowed_options.add( DA_ANALYSIS_OPTION ); + allowed_options.add( USE_LAST_IN_FITCH_OPTION ); + allowed_options.add( PERFORM_DC_FITCH ); + allowed_options.add( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION ); boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT; boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT; - double e_value_max = surfacing.MAX_E_VALUE_DEFAULT; + double fs_e_value_max = surfacing.MAX_E_VALUE_DEFAULT; + double ie_value_max = surfacing.MAX_E_VALUE_DEFAULT; int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT; final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options ); } + boolean use_last_in_fitch_parsimony = false; + if ( cla.isOptionSet( USE_LAST_IN_FITCH_OPTION ) ) { + use_last_in_fitch_parsimony = true; + } + boolean write_to_nexus = false; + if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) { + write_to_nexus = true; + } + boolean perform_dc_fich = false; + if ( cla.isOptionSet( PERFORM_DC_FITCH ) ) { + perform_dc_fich = true; + } + boolean perform_dc_regain_proteins_stats = false; + if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) { + perform_dc_regain_proteins_stats = true; + } + boolean da_analysis = false; + if ( cla.isOptionSet( DA_ANALYSIS_OPTION ) ) { + da_analysis = true; + } boolean output_binary_domain_combinationsfor_graph_analysis = false; if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) { output_binary_domain_combinationsfor_graph_analysis = true; } - if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) { + boolean output_binary_domain_combinationsfor_counts = false; + if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) { + output_binary_domain_combinationsfor_counts = true; + } + if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) { + try { + fs_e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_FS_E_VALUE_OPTION ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" ); + } + } + if ( cla.isOptionSet( surfacing.MAX_I_E_VALUE_OPTION ) ) { try { - e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION ); + ie_value_max = cla.getOptionValueAsDouble( surfacing.MAX_I_E_VALUE_OPTION ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" ); @@ -670,6 +421,10 @@ public class surfacing { if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) { ignore_combination_with_same = true; } + boolean domain_length_analysis = false; + if ( cla.isOptionSet( surfacing.PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION ) ) { + domain_length_analysis = true; + } boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT; if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) { ignore_domains_without_combs_in_all_spec = true; @@ -678,6 +433,10 @@ public class surfacing { 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 output_file = null; if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) { @@ -702,7 +461,7 @@ public class surfacing { + error ); } try { - final BasicTable scores_table = BasicTableParser.parse( cutoff_scores_file, " " ); + final BasicTable scores_table = BasicTableParser.parse( cutoff_scores_file, ' ' ); individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 ); } catch ( final IOException e ) { @@ -746,8 +505,8 @@ public class surfacing { && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); + .fatalError( surfacing.PRG_NAME, + "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { @@ -782,42 +541,34 @@ public class surfacing { final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file - + "\": " + msg ); + + "\": " + msg ); } } final List plus_minus_analysis_high_copy_base_species = new ArrayList(); final List plus_minus_analysis_high_copy_target_species = new ArrayList(); final List plus_minus_analysis_high_low_copy_species = new ArrayList(); final List plus_minus_analysis_numbers = new ArrayList(); - processPlusMinusAnalysisOption( cla, - 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 ); - File input_files_file = null; - String[] input_file_names_from_file = null; - if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -" - + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=" ); - } - input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( input_files_file ); + SurfacingUtil.processPlusMinusAnalysisOption( cla, + 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 ); + File input_genomes_file = null; + if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) { + if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -" + + surfacing.INPUT_GENOMES_FILE_OPTION + "=" ); + } + input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) ); + final String msg = ForesterUtil.isReadableFile( input_genomes_file ); if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg ); - } - try { - input_file_names_from_file = ForesterUtil.file2array( input_files_file ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg ); } } - if ( ( cla.getNumberOfNames() < 1 ) - && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, - "No hmmpfam output file indicated is input: use comand line directly or " - + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=" ); + else { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: " + + surfacing.INPUT_GENOMES_FILE_OPTION + "=" ); } DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT; if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) { @@ -841,9 +592,9 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str - + "\" for scoring method for domain combinations similarity calculation: \"-" - + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" ); + + "\" for scoring method for domain combinations similarity calculation: \"-" + + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" + + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" ); } } boolean sort_by_species_count_first = false; @@ -855,8 +606,18 @@ public class surfacing { species_matrix = true; } boolean output_protein_lists_for_all_domains = false; + double output_list_of_all_proteins_per_domain_e_value_max = -1; if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) { output_protein_lists_for_all_domains = true; + if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) { + try { + output_list_of_all_proteins_per_domain_e_value_max = cla + .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" ); + } + } } Detailedness detailedness = DETAILEDNESS_DEFAULT; if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) { @@ -899,10 +660,10 @@ public class surfacing { if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "no domain ids given for sequences with given domains to be extracted : -" - + surfacing.SEQ_EXTRACT_OPTION - + "=" ); + .fatalError( surfacing.PRG_NAME, + "no domain ids given for sequences with given domains to be extracted : -" + + surfacing.SEQ_EXTRACT_OPTION + + "=" ); } query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION ); } @@ -958,17 +719,17 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str - + "\" for domain combinations similarities sorting: \"-" - + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD - + ">\"" ); + + "\" for domain combinations similarities sorting: \"-" + + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD + + ">\"" ); } } - PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT; + DomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -" @@ -978,15 +739,13 @@ public class surfacing { } final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase(); if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) { - domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML; + domain_similarity_print_option = DomainSimilarity.PRINT_OPTION.HTML; } else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) { - // domain_similarity_print_option = - // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML; ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" ); } else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) { - domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED; + domain_similarity_print_option = DomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED; } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -" @@ -1019,19 +778,13 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort - + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" - + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); + + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); } } - String[][] input_file_properties = null; - if ( input_file_names_from_file != null ) { - input_file_properties = surfacing.processInputFileNames( input_file_names_from_file ); - } - else { - input_file_properties = surfacing.processInputFileNames( cla.getNames() ); - } + 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" ); @@ -1041,74 +794,68 @@ public class surfacing { + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION + "= to turn on pairwise analyses with less than three input files" ); } - checkWriteabilityForPairwiseComparisons( domain_similarity_print_option, - input_file_properties, - automated_pairwise_comparison_suffix, - out_dir ); + SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option, + input_file_properties, + automated_pairwise_comparison_suffix, + out_dir ); for( int i = 0; i < number_of_genomes; i++ ) { - File dcc_outfile = new File( input_file_properties[ i ][ 0 ] + File dcc_outfile = new File( input_file_properties[ i ][ 1 ] + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ); if ( out_dir != null ) { dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile ); } SurfacingUtil.checkForOutputFileWriteability( dcc_outfile ); } - File pfam_to_go_file = null; - Map> domain_id_to_go_ids_map = null; - int domain_id_to_go_ids_count = 0; + File pfam_to_go_file = new File( "pfam2go.txt" ); if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -" + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=" ); } pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ); - final String error = ForesterUtil.isReadableFile( pfam_to_go_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error ); - } - try { - final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file ); - final List pfam_to_go_mappings = parser.parse(); - domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings ); - if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) { - ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, - "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); - } - domain_id_to_go_ids_count = parser.getMappingCount(); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e ); + } + final String error1 = ForesterUtil.isReadableFile( pfam_to_go_file ); + if ( !ForesterUtil.isEmpty( error1 ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error1 ); + } + Map> domain_id_to_go_ids_map = null; + int domain_id_to_go_ids_count = 0; + try { + final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file ); + final List pfam_to_go_mappings = parser.parse(); + domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings ); + if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) { + ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, + "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); } + domain_id_to_go_ids_count = parser.getMappingCount(); } - File go_obo_file = null; - List go_terms = null; + catch ( final IOException e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e ); + } + File go_obo_file = new File( "go.obo" ); if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -" + surfacing.GO_OBO_FILE_USE_OPTION + "=" ); } - if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-" - + surfacing.GO_OBO_FILE_USE_OPTION + "=) without Pfam to GO mapping file (" - + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=)" ); - } go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) ); - final String error = ForesterUtil.isReadableFile( go_obo_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error ); - } - try { - final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM ); - go_terms = parser.parse(); - if ( parser.getGoTermCount() != go_terms.size() ) { - ForesterUtil - .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" ); - } - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e ); + } + final String error2 = ForesterUtil.isReadableFile( go_obo_file ); + if ( !ForesterUtil.isEmpty( error2 ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error2 ); + } + List go_terms = null; + try { + final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM ); + go_terms = parser.parse(); + if ( parser.getGoTermCount() != go_terms.size() ) { + ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" ); } } + catch ( final IOException e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e ); + } Map go_id_to_term_map = null; if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) ) && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) { @@ -1142,77 +889,19 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str - + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); + + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); } } if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE ) && ( number_of_genomes > 2 ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; } - boolean jacknifed_distances = false; - int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT; - double jacknife_ratio = JACKNIFE_RATIO_DEFAULT; - long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT; - if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) { - if ( ( number_of_genomes < 3 ) || !perform_pwc ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-" - + surfacing.JACKNIFE_OPTION + "[=]) without pairwise analyses (" - + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "=)" ); - } - jacknifed_distances = true; - if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) { - try { - jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" ); - } - if ( jacknife_resamplings < 2 ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" ); - } - } - if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION ) - && cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) { - try { - jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" ); - } - if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: " - + jacknife_ratio ); - } - } - if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) - && cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) { - try { - random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" ); - } - } - } - // boolean infer_species_trees = false; - // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) { - // if ( ( output_file == null ) || ( number_of_genomes < 3 ) - // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) { - // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-" - // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses (" - // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - // + "=)" ); - // } - // infer_species_trees = true; - // } File[] intree_files = null; Phylogeny[] intrees = null; if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) { - // TODO FIXME if jacknife.... maybe not if ( number_of_genomes < 3 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-" + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses (" @@ -1236,8 +925,9 @@ public class surfacing { 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 ) ) { @@ -1254,25 +944,25 @@ public class surfacing { } radomize_fitch_parsimony = true; } - SortedSet filter = null; + SortedSet filter = null; if ( ( positive_filter_file != null ) || ( negative_filter_file != null ) || ( negative_domains_filter_file != null ) ) { - filter = new TreeSet(); + filter = new TreeSet(); 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>[] domain_id_to_secondary_features_maps = null; + Map>[] domain_id_to_secondary_features_maps = null; File[] secondary_features_map_files = null; final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); - if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { + + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); + if ( domain_length_analysis ) { SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); } if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { @@ -1325,30 +1015,26 @@ public class surfacing { + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); } System.out.println( "Output directory : " + out_dir ); - if ( input_file_names_from_file != null ) { - System.out.println( "Input files names from : " + input_files_file + " [" - + input_file_names_from_file.length + " input files]" ); - html_desc.append( "Input files names from:" + input_files_file + " [" - + input_file_names_from_file.length + " input files]" + nl ); - } + System.out.println( "Input genomes from : " + input_genomes_file ); + html_desc.append( "Input genomes from:" + input_genomes_file + "" + nl ); if ( positive_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Positive protein filter:" + positive_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative protein filter:" + negative_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_domains_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative domain filter:" + negative_domains_filter_file + " [" + filter_size + " domain ids]" + nl ); } @@ -1367,15 +1053,24 @@ public class surfacing { } System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus ); html_desc.append( "Plus-minus analysis:" + plus1 + "&& " + plus0 + "&& " + minus - + "" + nl ); + + "" + nl ); } if ( cutoff_scores_file != null ) { System.out.println( "Cutoff scores file : " + cutoff_scores_file ); html_desc.append( "Cutoff scores file:" + cutoff_scores_file + "" + nl ); } - if ( e_value_max >= 0.0 ) { - System.out.println( "E-value maximum (inclusive) : " + e_value_max ); - html_desc.append( "E-value maximum (inclusive):" + e_value_max + "" + nl ); + if ( ie_value_max >= 0.0 ) { + System.out.println( "iE-value maximum (incl) : " + ie_value_max ); + html_desc.append( "iE-value maximum (inclusive):" + ie_value_max + "" + nl ); + } + if ( fs_e_value_max >= 0.0 ) { + System.out.println( "FS E-value maximum (incl) : " + fs_e_value_max ); + html_desc.append( "FS E-value maximum (inclusive):" + fs_e_value_max + "" + nl ); + } + if ( output_protein_lists_for_all_domains ) { + System.out.println( "Domain E-value max : " + output_list_of_all_proteins_per_domain_e_value_max ); + html_desc.append( "Protein lists: E-value maximum per domain (inclusive):" + + output_list_of_all_proteins_per_domain_e_value_max + "" + nl ); } System.out.println( "Ignore DUFs : " + ignore_dufs ); if ( ignore_virus_like_ids ) { @@ -1391,20 +1086,19 @@ public class surfacing { if ( no_engulfing_overlaps ) { System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps ); html_desc.append( "Ignore (lower confidence) engulfed domains:" + no_engulfing_overlaps - + "" + nl ); + + "" + nl ); } System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec ); html_desc - .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_domains_without_combs_in_all_spec + "" + nl ); + .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_domains_without_combs_in_all_spec + "" + nl ); System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains ); html_desc - .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_species_specific_domains + "" + nl ); + .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_species_specific_domains + "" + nl ); System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); html_desc.append( "Ignore combination with self for domain combination similarity analyses:" + ignore_combination_with_same + "" + nl ); - ; System.out.println( "Consider directedness : " + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) ); html_desc.append( "Consider directedness of binary domain combinations:" @@ -1416,26 +1110,47 @@ public class surfacing { + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "" + nl ); } + System.out.println( "Fitch parsimony of DCs : " + perform_dc_fich ); + html_desc.append( "Fitch parsimony of DCs:" + perform_dc_fich + "" + nl ); + if ( perform_dc_fich ) { + System.out.println( "Use last in Fitch parsimony : " + use_last_in_fitch_parsimony ); + html_desc.append( "Use last in Fitch parsimony:" + use_last_in_fitch_parsimony + + "" + nl ); + } + System.out.println( "Write to Nexus files : " + write_to_nexus ); + html_desc.append( "Write to Nexus files:" + write_to_nexus + "" + nl ); + if ( perform_dc_fich ) { + System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats ); + html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats + + "" + nl ); + } + System.out.println( "DA analysis : " + da_analysis ); + html_desc.append( "DA analysis :" + da_analysis + "" + nl ); System.out.print( "Domain counts sort order : " ); + html_desc.append( "Domain counts sort order:" ); switch ( dc_sort_order ) { case ALPHABETICAL_KEY_ID: System.out.println( "alphabetical" ); + html_desc.append( "alphabetical" + "" + nl ); break; case KEY_DOMAIN_COUNT: System.out.println( "domain count" ); + html_desc.append( "domain count" + "" + nl ); break; case KEY_DOMAIN_PROTEINS_COUNT: System.out.println( "domain proteins count" ); + html_desc.append( "domain proteins count" + "" + nl ); break; case COMBINATIONS_COUNT: System.out.println( "domain combinations count" ); + html_desc.append( "domain combinations count" + "" + nl ); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" ); } if ( domain_id_to_go_ids_map != null ) { System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count - + " mappings]" ); + + " mappings]" ); html_desc.append( "Pfam to GO mappings from:" + pfam_to_go_file + " [" + domain_id_to_go_ids_count + " mappings]" + "" + nl ); } @@ -1451,7 +1166,7 @@ public class surfacing { if ( perform_pwc ) { System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix ); html_desc.append( "Suffix for PWC files" + automated_pairwise_comparison_suffix - + "" + nl ); + + "" + nl ); } if ( out_dir != null ) { System.out.println( "Output directory : " + out_dir ); @@ -1588,27 +1303,14 @@ public class surfacing { break; default: ForesterUtil - .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); + .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); } System.out.println(); html_desc.append( "" + nl ); - if ( jacknifed_distances ) { - html_desc.append( "Jacknife:" + jacknife_resamplings + " resamplings" + nl ); - html_desc.append( "Jacknife ratio:" + ForesterUtil.round( jacknife_ratio, 2 ) - + "" + nl ); - html_desc.append( "Jacknife random number seed:" + random_seed + "" + nl ); - System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" ); - System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) ); - System.out.println( " Random number seed : " + random_seed ); - } - // if ( infer_species_trees ) { - // html_desc.append( "Infer species trees:true" + nl ); - // System.out.println( " Infer species trees : true" ); - // } if ( ( intrees != null ) && ( intrees.length > 0 ) ) { for( final File intree_file : intree_files ) { html_desc.append( "Intree for gain/loss parsimony analysis:" + intree_file - + "" + nl ); + + "" + nl ); System.out.println( " Intree for gain/loss pars.: " + intree_file ); } } @@ -1626,8 +1328,8 @@ public class surfacing { if ( VERBOSE ) { System.out.println(); System.out.println( "Domain ids to secondary features map:" ); - for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) { - System.out.print( domain_id.getId() ); + for( final String domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) { + System.out.print( domain_id ); System.out.print( " => " ); for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) { System.out.print( sec ); @@ -1640,10 +1342,11 @@ public class surfacing { } } // if ( perform_pwc ) { System.out.println(); - html_desc.append( "Command line:\n" + cla.getCommandLineArgsAsString() + "\n" + nl ); + html_desc.append( "Command line:" + nl + nl + cla.getCommandLineArgsAsString() + nl + nl + + "" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = null; - List[] query_domain_ids_array = null; + List[] query_domain_ids_array = null; if ( query_domain_ids != null ) { final String[] query_domain_ids_str_array = query_domain_ids.split( "#" ); query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ]; @@ -1651,9 +1354,9 @@ public class surfacing { for( int i = 0; i < query_domain_ids_str_array.length; i++ ) { String query_domain_ids_str = query_domain_ids_str_array[ i ]; final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" ); - final List query = new ArrayList(); + final List query = new ArrayList(); for( final String element : query_domain_ids_str_ary ) { - query.add( new DomainId( element ) ); + query.add( element ); } query_domain_ids_array[ i ] = query; query_domain_ids_str = query_domain_ids_str.replace( '~', '_' ); @@ -1678,8 +1381,8 @@ public class surfacing { if ( need_protein_lists_per_species ) { protein_lists_per_species = new TreeMap>(); } - final List gwcd_list = new ArrayList( number_of_genomes ); - final SortedSet all_domains_encountered = new TreeSet(); + List gwcd_list = new ArrayList( number_of_genomes ); + final SortedSet all_domains_encountered = new TreeSet(); final SortedSet all_bin_domain_combinations_encountered = new TreeSet(); List all_bin_domain_combinations_gained_fitch = null; List all_bin_domain_combinations_lost_fitch = null; @@ -1687,9 +1390,8 @@ public class surfacing { all_bin_domain_combinations_gained_fitch = new ArrayList(); all_bin_domain_combinations_lost_fitch = new ArrayList(); } - final DomainLengthsTable domain_lengths_table = new DomainLengthsTable(); final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + D_PROMISCUITY_FILE_SUFFIX ); + + output_file + D_PROMISCUITY_FILE_SUFFIX ); BufferedWriter per_genome_domain_promiscuity_statistics_writer = null; try { per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) ); @@ -1723,8 +1425,8 @@ public class surfacing { catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } - final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics(); - final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics(); + DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics(); + DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics(); final SortedMap all_genomes_domains_per_potein_histo = new TreeMap(); final SortedSet domains_which_are_always_single = new TreeSet(); final SortedSet domains_which_are_sometimes_single_sometimes_not = new TreeSet(); @@ -1732,7 +1434,7 @@ public class surfacing { BufferedWriter domains_per_potein_stats_writer = null; try { domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + "__domains_per_potein_stats.txt" ) ); + + output_file + "_domains_per_potein_stats.txt" ) ); domains_per_potein_stats_writer.write( "Genome" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( "Mean" ); @@ -1751,13 +1453,28 @@ public class surfacing { catch ( final IOException e3 ) { e3.printStackTrace(); } + Map protein_length_stats_by_dc = null; + Map domain_number_stats_by_dc = null; + final Map domain_length_stats_by_domain = new HashMap(); + if ( perform_dc_regain_proteins_stats ) { + protein_length_stats_by_dc = new HashMap(); + domain_number_stats_by_dc = new HashMap(); + } + DomainLengthsTable domain_lengths_table = null; + if ( domain_length_analysis ) { + domain_lengths_table = new DomainLengthsTable(); + } // Main loop: + final SortedMap> distinct_domain_architecutures_per_genome = new TreeMap>(); + final SortedMap distinct_domain_architecuture_counts = new TreeMap(); 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 ); - System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] ); - log( "Genome : " + input_file_properties[ i ][ 0 ], 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 ] + "]" ); + 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; if ( individual_score_cutoffs != null ) { @@ -1788,8 +1505,11 @@ public class surfacing { ind_score_cutoff, true ); } - if ( e_value_max >= 0.0 ) { - parser.setEValueMaximum( e_value_max ); + if ( fs_e_value_max >= 0.0 ) { + parser.setFsEValueMaximum( fs_e_value_max ); + } + if ( ie_value_max >= 0.0 ) { + parser.setIEValueMaximum( ie_value_max ); } parser.setIgnoreDufs( ignore_dufs ); parser.setIgnoreVirusLikeIds( ignore_virus_like_ids ); @@ -1819,88 +1539,104 @@ public class surfacing { } final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered(); protein_coverage_stats.addValue( coverage ); + int distinct_das = -1; + if ( da_analysis ) { + final String genome = input_file_properties[ i ][ 0 ]; + distinct_das = SurfacingUtil.storeDomainArchitectures( genome, + distinct_domain_architecutures_per_genome, + protein_list, + 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 ) - + "%", log_writer ); + 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: " - + 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 individual score cutoffs: " + + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), + log_writer ); + System.out.println( "Domains ignored due to FS E-value : " + + parser.getDomainsIgnoredDueToFsEval() ); + SurfacingUtil.log( "Domains ignored due to FS E-value : " + + parser.getDomainsIgnoredDueToFsEval(), + log_writer ); + System.out.println( "Domains ignored due to iE-value : " + + parser.getDomainsIgnoredDueToIEval() ); + SurfacingUtil.log( "Domains ignored due to iE-value : " + + parser.getDomainsIgnoredDueToIEval(), + 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(), - log_writer ); + 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 : " - + parser.getDomainsIgnoredDueToNegativeDomainFilter(), - log_writer ); + 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(), - log_writer ); + 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(), - log_writer ); + 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(), - log_writer ); + SurfacingUtil.log( "Proteins ignored due to positive filter : " + + parser.getProteinsIgnoredDueToFilter(), + log_writer ); } - System.out.println( "Time for processing : " + parser.getTime() + "ms" ); - log( "", log_writer ); - html_desc.append( "" + input_file_properties[ i ][ 0 ] + " [species: " - + input_file_properties[ i ][ 1 ] + "]" + ":domains analyzed: " - + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: " - + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf() - + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds() - + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter() - + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" ); - if ( negative_filter_file != null ) { - html_desc.append( "; proteins ignored due to negative filter: " - + parser.getProteinsIgnoredDueToFilter() ); - } - if ( positive_filter_file != null ) { - html_desc.append( "; proteins ignored due to positive filter: " - + parser.getProteinsIgnoredDueToFilter() ); + if ( da_analysis ) { + System.out.println( "Distinct domain architectures stored : " + distinct_das ); + SurfacingUtil.log( "Distinct domain architectures stored : " + distinct_das, log_writer ); } - html_desc.append( "" + nl ); - // domain_partner_counts_array[ i ] = - // Methods.getDomainPartnerCounts( protein_domain_collections_array[ - // i ], - // false, input_file_properties[ i ][ 1 ] ); + System.out.println( "Time for processing : " + parser.getTime() + "ms" ); + SurfacingUtil.log( "", log_writer ); try { int count = 0; for( final Protein protein : protein_list ) { dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ) - .toString() ); + .toString() ); ++count; + for( final Domain d : protein.getProteinDomains() ) { + final String d_str = d.getDomainId().toString(); + if ( !domain_length_stats_by_domain.containsKey( d_str ) ) { + domain_length_stats_by_domain.put( d_str, new BasicDescriptiveStatistics() ); + } + domain_length_stats_by_domain.get( d_str ).addValue( d.getLength() ); + } } } catch ( final IOException e ) { @@ -1914,30 +1650,39 @@ public class surfacing { domains_which_are_sometimes_single_sometimes_not, domains_which_never_single, domains_per_potein_stats_writer ); - gwcd_list.add( BasicGenomeWideCombinableDomains - .createInstance( protein_list, - ignore_combination_with_same, - new BasicSpecies( input_file_properties[ i ][ 1 ] ), - domain_id_to_go_ids_map, - dc_type ) ); - domain_lengths_table.addLengths( protein_list ); - if ( gwcd_list.get( i ).getSize() > 0 ) { - SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties, - out_dir, - per_genome_domain_promiscuity_statistics_writer, - gwcd_list.get( i ), - i, - dc_sort_order ); - if ( output_binary_domain_combinationsfor_graph_analysis ) { - SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties, - out_dir, - gwcd_list.get( i ), - i, - dc_sort_order ); + if ( domain_length_analysis ) { + domain_lengths_table.addLengths( protein_list ); + } + if ( !da_analysis ) { + gwcd_list.add( BasicGenomeWideCombinableDomains + .createInstance( protein_list, + ignore_combination_with_same, + new BasicSpecies( input_file_properties[ i ][ 1 ] ), + domain_id_to_go_ids_map, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc ) ); + if ( gwcd_list.get( i ).getSize() > 0 ) { + if ( output_binary_domain_combinationsfor_counts ) { + SurfacingUtil + .writeDomainCombinationsCountsFile( input_file_properties, + out_dir, + per_genome_domain_promiscuity_statistics_writer, + gwcd_list.get( i ), + i, + dc_sort_order ); + } + if ( output_binary_domain_combinationsfor_graph_analysis ) { + SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties, + out_dir, + gwcd_list.get( i ), + i, + dc_sort_order ); + } + SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered ); + SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ), + all_bin_domain_combinations_encountered ); } - SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered ); - SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ), - all_bin_domain_combinations_encountered ); } if ( query_domains_writer_ary != null ) { for( int j = 0; j < query_domain_ids_array.length; j++ ) { @@ -1945,7 +1690,8 @@ public class surfacing { SurfacingUtil.extractProteinNames( protein_list, query_domain_ids_array[ j ], query_domains_writer_ary[ j ], - "\t" ); + "\t", + LIMIT_SPEC_FOR_PROT_EX ); query_domains_writer_ary[ j ].flush(); } catch ( final IOException e ) { @@ -1967,6 +1713,18 @@ public class surfacing { ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file ); // + if ( da_analysis ) { + SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome, + distinct_domain_architecuture_counts, + 10, + new File( out_dir.toString() + "/" + output_file + + "_DA_counts.txt" ), + new File( out_dir.toString() + "/" + output_file + + "_unique_DAs.txt" ) ); + distinct_domain_architecutures_per_genome.clear(); + distinct_domain_architecuture_counts.clear(); + System.gc(); + } try { domains_per_potein_stats_writer.write( "ALL" ); domains_per_potein_stats_writer.write( "\t" ); @@ -1974,8 +1732,10 @@ public class surfacing { domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" ); domains_per_potein_stats_writer.write( "\t" ); - domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); - domains_per_potein_stats_writer.write( "\t" ); + if ( all_genomes_domains_per_potein_stats.getN() <= 300 ) { + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + } domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" ); @@ -1983,25 +1743,32 @@ public class surfacing { 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 ); + all_genomes_domains_per_potein_stats = null; + 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" ); + + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); + + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); + + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__domains_always_combined.txt" ), domains_which_never_single, "\n" ); + + "_domains_always_combined.txt" ), domains_which_never_single, "\n" ); ForesterUtil.programMessage( PRG_NAME, "Average of proteins with a least one domain assigned: " + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" ); - ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " + 100 - * protein_coverage_stats.getMin() + "%-" + 100 * protein_coverage_stats.getMax() + "%" ); - log( "Average of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.arithmeticMean() ) - + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer ); - log( "Range of prot with a least one dom assigned : " + 100 * protein_coverage_stats.getMin() + "%-" - + 100 * protein_coverage_stats.getMax() + "%", log_writer ); + ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " + + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() ) + + "%" ); + SurfacingUtil.log( "Average of prot with a least one dom assigned : " + + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", + log_writer ); + SurfacingUtil.log( "Range of prot with a least one dom assigned : " + + ( 100 * protein_coverage_stats.getMin() ) + "%-" + + ( 100 * protein_coverage_stats.getMax() ) + "%", + log_writer ); + protein_coverage_stats = null; } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); @@ -2024,7 +1791,7 @@ public class surfacing { catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); } - if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { + if ( domain_length_analysis ) { try { SurfacingUtil.executeDomainLengthAnalysis( input_file_properties, number_of_genomes, @@ -2038,12 +1805,14 @@ public class surfacing { ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile ); System.out.println(); } + domain_lengths_table = null; final long analysis_start_time = new Date().getTime(); PairwiseDomainSimilarityCalculator pw_calc = null; - // double[] values_for_all_scores_histogram = null; final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field, sort_by_species_count_first, - number_of_genomes == 2 ); + number_of_genomes == 2, + CALC_SIMILARITY_SCORES, + true ); switch ( scoring ) { case COMBINATIONS: pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator(); @@ -2066,22 +1835,18 @@ public class surfacing { gwcd_list, ignore_domains_without_combs_in_all_spec, ignore_species_specific_domains ); - SurfacingUtil.decoratePrintableDomainSimilarities( similarities, - detailedness, - go_annotation_output, - go_id_to_term_map, - go_namespace_limit ); - DescriptiveStatistics pw_stats = null; + SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness ); + final Map tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] ); try { String my_outfile = output_file.toString(); Map split_writers = null; Writer writer = null; - if ( similarities.size() > 1000 ) { + if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) { if ( my_outfile.endsWith( ".html" ) ) { my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 ); } split_writers = new HashMap(); - createSplitWriters( out_dir, my_outfile, split_writers ); + SurfacingUtil.createSplitWriters( out_dir, my_outfile, split_writers ); } else if ( !my_outfile.endsWith( ".html" ) ) { my_outfile += ".html"; @@ -2097,23 +1862,28 @@ public class surfacing { html_desc.append( "Sum of all distinct binary combinations:" + all_bin_domain_combinations_encountered.size() + "" + nl ); html_desc.append( "Sum of all distinct domains:" + all_domains_encountered.size() - + "" + nl ); + + "" + nl ); html_desc.append( "Analysis date/time:" + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) + "" + nl ); html_desc.append( "" + nl ); - pw_stats = SurfacingUtil - .writeDomainSimilaritiesToFile( html_desc, - new StringBuilder( number_of_genomes + " genomes" ), - writer, - split_writers, - similarities, - number_of_genomes == 2, - species_order, - domain_similarity_print_option, - domain_similarity_sort_field, - scoring, - true ); + final Writer simple_tab_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + + my_outfile + ".tsv" ) ); + SurfacingUtil.writeDomainSimilaritiesToFile( html_desc, + new StringBuilder( number_of_genomes + " genomes" ), + simple_tab_writer, + writer, + split_writers, + similarities, + number_of_genomes == 2, + species_order, + domain_similarity_print_option, + scoring, + true, + tax_code_to_id_map, + intree_0_orig, + positive_filter_file != null ? filter : null ); + 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 ) + "\"" ); } @@ -2122,7 +1892,6 @@ public class surfacing { + e.getMessage() + "]" ); } System.out.println(); - // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray(); final Species[] species = new Species[ number_of_genomes ]; for( int i = 0; i < number_of_genomes; ++i ) { species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] ); @@ -2150,7 +1919,10 @@ public class surfacing { surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, surfacing.PRG_NAME, out_dir, - write_pwc_files ); + write_pwc_files, + tax_code_to_id_map, + CALC_SIMILARITY_SCORES, + 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( '.' ) ); @@ -2160,68 +1932,42 @@ public class surfacing { output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); } SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); + + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedBinaryCombinationsBasedDistances() ); + .writeMatrixToFile( new File( matrix_output_file + + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedDomainsBasedDistances() ); + + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() - .get( 0 ) ); + + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() + .get( 0 ) ); final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); + + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc + .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances().get( 0 ) ); + + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc + .getSharedDomainsBasedDistances().get( 0 ) ); inferred_trees = new ArrayList(); inferred_trees.add( nj_gd ); inferred_trees.add( nj_bc ); inferred_trees.add( nj_d ); - if ( jacknifed_distances ) { - pwgc.performPairwiseComparisonsJacknifed( species, - number_of_genomes, - gwcd_list, - true, - jacknife_resamplings, - jacknife_ratio, - random_seed ); - SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) - + "_" - + jacknife_resamplings - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 ) - + "_" + jacknife_resamplings - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedDomainsBasedDistances() ); - // if ( infer_species_trees ) { - // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings - // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc - // .getSharedBinaryCombinationsBasedDistances() ); - // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings - // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() ); - // } - } } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) ) if ( ( out_dir != null ) && ( !perform_pwc ) ) { output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); } - writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list ); + if ( write_to_nexus ) { + 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, - e_value_max, - max_allowed_overlap, - no_engulfing_overlaps, - cutoff_scores_file, - dc_type ); + final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs, + ie_value_max, + fs_e_value_max, + max_allowed_overlap, + no_engulfing_overlaps, + cutoff_scores_file, + dc_type ); String s = "_"; if ( radomize_fitch_parsimony ) { s += random_number_seed_for_fitch_parsimony + "_"; @@ -2243,26 +1989,34 @@ public class surfacing { parameters_sb.toString(), domain_id_to_secondary_features_maps, positive_filter_file == null ? null : filter, - output_binary_domain_combinationsfor_graph_analysis, - all_bin_domain_combinations_gained_fitch, - all_bin_domain_combinations_lost_fitch, - dc_type ); - // Listing of all domain combinations gained is only done if only one input tree is used. + output_binary_domain_combinationsfor_graph_analysis, + all_bin_domain_combinations_gained_fitch, + all_bin_domain_combinations_lost_fitch, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc, + domain_length_stats_by_domain, + tax_code_to_id_map, + write_to_nexus, + use_last_in_fitch_parsimony, + perform_dc_fich ); + // Listing of all domain combinations gained is only done if only one input tree is used. if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { int j = 0; - for( final Map> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) { + for( final Map> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) { final Map mapping_results_map = new TreeMap(); final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map ); SurfacingUtil - .executeParsimonyAnalysisForSecondaryFeatures( outfile_name - + "_" - + secondary_features_map_files[ j++ ], - secondary_features_parsimony, - intree, - parameters_sb.toString(), - mapping_results_map ); + .executeParsimonyAnalysisForSecondaryFeatures( outfile_name + + "_" + + secondary_features_map_files[ j++ ], + secondary_features_parsimony, + intree, + parameters_sb.toString(), + mapping_results_map, + use_last_in_fitch_parsimony ); if ( i == 0 ) { System.out.println(); System.out.println( "Mapping to secondary features:" ); @@ -2275,7 +2029,7 @@ public class surfacing { System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() ); if ( total_domains > 0 ) { System.out.println( ", mapped ratio = " - + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" ); + + ( ( 100 * mapping_results.getSumOfSuccesses() ) / total_domains ) + "%" ); } else { System.out.println( ", mapped ratio = n/a (total domains = 0 )" ); @@ -2288,58 +2042,33 @@ public class surfacing { } // for( final Phylogeny intree : intrees ) { } if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) { - executePlusMinusAnalysis( output_file, - plus_minus_analysis_high_copy_base_species, - plus_minus_analysis_high_copy_target_species, - plus_minus_analysis_high_low_copy_species, - gwcd_list, - protein_lists_per_species, - domain_id_to_go_ids_map, - go_id_to_term_map, - plus_minus_analysis_numbers ); + 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, + gwcd_list, + protein_lists_per_species, + domain_id_to_go_ids_map, + go_id_to_term_map, + plus_minus_analysis_numbers ); } if ( output_protein_lists_for_all_domains ) { - writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list ); - } - // if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) { - // final StringBuilder parameters_sb = createParametersAsString( ignore_dufs, - // e_value_max, - // max_allowed_overlap, - // no_engulfing_overlaps, - // cutoff_scores_file ); - // String s = "_"; - // if ( radomize_fitch_parsimony ) { - // s += random_number_seed_for_fitch_parsimony + "_"; - // } - // int i = 0; - // for( final Phylogeny inferred_tree : inferred_trees ) { - // if ( !inferred_tree.isRooted() ) { - // intrees[ 0 ].getRoot().getName(); - // inferred_tree.r - // } - // final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s; - // final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator - // .createInstance( inferred_tree, gwcd_list ); - // SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony, - // radomize_fitch_parsimony, - // outfile_name, - // domain_parsimony, - // inferred_tree, - // domain_id_to_go_ids_map, - // go_id_to_term_map, - // go_namespace_limit, - // parameters_sb.toString() ); - // i++; - // } - // } + SurfacingUtil.writeProteinListsForAllSpecies( out_dir, + protein_lists_per_species, + gwcd_list, + output_list_of_all_proteins_per_domain_e_value_max, + positive_filter_file != null ? filter : null ); + } + gwcd_list = null; if ( all_bin_domain_combinations_gained_fitch != null ) { try { - 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(), - all_bin_domain_combinations_encountered, - true ); + 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(), + all_bin_domain_combinations_encountered, + true ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2347,12 +2076,13 @@ public class surfacing { } if ( all_bin_domain_combinations_lost_fitch != null ) { try { - 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(), - all_bin_domain_combinations_encountered, - false ); + 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(), + all_bin_domain_combinations_encountered, + false ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2361,189 +2091,49 @@ public class surfacing { final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; - System.out.println(); - System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" ); - System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); - System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" ); - System.out.println(); - System.out.println( "If this application is useful to you, please cite:" ); - System.out.println( surfacing.WWW ); - System.out.println(); + ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + + "ms" ); + ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); + ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " + + total_memory + "MB" ); + ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" ); + ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); ForesterUtil.programMessage( PRG_NAME, "OK" ); System.out.println(); } - private static void createSplitWriters( File out_dir, String my_outfile, Map 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 - + "_09.html" ) ) ); - } - - private static void printOutPercentageOfMultidomainProteins( final SortedMap all_genomes_domains_per_potein_histo, - final Writer log_writer ) { - int sum = 0; - for( final Entry 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 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( int i = 0; i < input_file_properties.length; ++i ) { - try { - intree.getNode( input_file_properties[ i ][ 1 ] ); - } - catch ( final IllegalArgumentException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ] - + "] not present/not unique in input tree" ); - } - } - } - - // public static StringBuffer stringCombinableDomainsMapToStringBuffer( - // final SortedMap map ) { - // final StringBuffer sb = new StringBuffer(); - // for( final Iterator iter = map.keySet().iterator(); - // iter.hasNext(); ) { - // final Object key = iter.next(); - // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ', - // false ) ); - // final CombinableDomains domain_combination = map.get( key ); - // sb.append( ForesterUtil.pad( new StringBuffer( "" + - // domain_combination.getNumberOfCombiningDomains() ), 8, - // ' ', false ) ); - // sb.append( domain_combination.toStringBuffer() ); - // sb.append( ForesterUtil.getLineSeparator() ); - // } - // return sb; - // } private static void printHelp() { System.out.println(); System.out.println( "Usage:" ); System.out.println(); System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME - + " [options] [external node name 1] [name 2] ... [name n]" ); + + " [options] [external node name 1] [name 2] ... [name n]" ); System.out.println(); System.out.println( " Note: This software might need a significant amount of memory (heap space);" ); System.out - .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); + .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); System.out.println(); System.out.println( " Options: " ); System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" ); System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION - + ": to ignore combinations with self (default: not to ignore)" ); + + ": to ignore combinations with self (default: not to ignore)" ); System.out - .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION - + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION + + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); System.out - .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION - + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION + + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION - + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); + + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); System.out - .println( surfacing.IGNORE_VIRAL_IDS - + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); + .println( surfacing.IGNORE_VIRAL_IDS + + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: " + DOMAIN_SORT_FILD_DEFAULT + ")" ); System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" ); - System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" ); + System.out.println( surfacing.MAX_I_E_VALUE_OPTION + ": max (inclusive) iE-value" ); + System.out.println( surfacing.MAX_FS_E_VALUE_OPTION + ": max (inclusive) FS E-value" ); System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" ); System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" ); System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" ); @@ -2554,245 +2144,58 @@ public class surfacing { + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" ); System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION - + ": sort by species count first" ); + + ": sort by species count first" ); System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" ); System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" ); System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" ); System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" ); System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "[=]: to perform pairwise comparison based analyses" ); + + "[=]: to perform pairwise comparison based analyses" ); System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION - + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); - System.out - .println( JACKNIFE_OPTION - + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: " - + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" ); - System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: " - + JACKNIFE_RATIO_DEFAULT + "]" ); - System.out.println( JACKNIFE_RANDOM_SEED_OPTION - + ": seed for random number generator for jacknife resampling [default: " - + JACKNIFE_RANDOM_SEED_DEFAULT + "]" ); - // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION - // + ": to infer NJ species trees based on shared domains/binary domain combinations" ); + + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); System.out - .println( surfacing.INPUT_SPECIES_TREE_OPTION - + "=: to infer domain/binary domain combination gains/losses on given species trees" ); + .println( surfacing.INPUT_SPECIES_TREE_OPTION + + "=: to infer domain/binary domain combination gains/losses on given species trees" ); System.out.println( surfacing.FILTER_POSITIVE_OPTION - + "=: to filter out proteins not containing at least one domain listed in " ); + + "=: to filter out proteins not containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_OPTION - + "=: to filter out proteins containing at least one domain listed in " ); + + "=: to filter out proteins containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION - + "=: to filter out (ignore) domains listed in " ); - System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=: to read input files from " ); + + "=: to filter out (ignore) domains listed in " ); + System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=: to read input files from " ); System.out - .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION - + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); + .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS - + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); + + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY - + ": to consider directedness and adjacency in binary combinations" ); + + ": to consider directedness and adjacency in binary combinations" ); System.out - .println( surfacing.SEQ_EXTRACT_OPTION - + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); + .println( surfacing.SEQ_EXTRACT_OPTION + + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE - + "=: to perfom parsimony analysis on secondary features" ); + + "=: to perfom parsimony analysis on secondary features" ); System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); + System.out.println( surfacing.DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION + + ": to output binary domain counts (as individual files)" ); System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - + ": to output binary domain combinations for (downstream) graph analysis" ); + + ": to output binary domain combinations for (downstream) graph analysis" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" ); + System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION + + ": e value max per domain for output of all proteins per domain" ); + System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" ); + System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" ); + System.out.println( PERFORM_DC_FITCH + ": to perform DC Fitch parsimony" ); + System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" ); + System.out.println( DA_ANALYSIS_OPTION + ": to perform DA analysis" ); + System.out.println( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION + ": to perform domain length analysis" ); System.out.println(); System.out.println(); - System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar" - + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST" - + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo " - + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo " - + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION - + "=50 human mouse brafl strpu" ); + System.out + .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); + System.out.println(); + System.out + .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); System.out.println(); - } - - private static void processFilter( final File filter_file, final SortedSet filter ) { - SortedSet 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( new DomainId( string ) ); - } - } - if ( VERBOSE ) { - System.out.println( "Filter:" ); - for( final DomainId domainId : filter ) { - System.out.println( domainId.getId() ); - } - } - } - - private static String[][] processInputFileNames( final String[] names ) { - final String[][] input_file_properties = new String[ names.length ][]; - for( int i = 0; i < names.length; ++i ) { - if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) { - input_file_properties[ i ] = new String[ 2 ]; - input_file_properties[ i ][ 0 ] = names[ i ]; - input_file_properties[ i ][ 1 ] = names[ i ]; - } - else { - input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" ); - if ( input_file_properties[ i ].length != 3 ) { - ForesterUtil - .fatalError( surfacing.PRG_NAME, - "properties for the input files (hmmpfam output) are expected " - + "to be in the following format \"#\" (or just one word, which is both the filename and the species id), instead received \"" - + names[ i ] + "\"" ); - } - } - 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 high_copy_base, - final List high_copy_target, - final List low_copy, - final List 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 + "=" ); - } - 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 high_copy_base, - final List high_copy_target, - final List low_copy, - final List numbers ) { - Set 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), '$D=' minimal Difference (default is 1), '$F=' 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 filter, - final List 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> protein_lists_per_species, - final List gwcd_list ) { - final SortedSet all_domains = new TreeSet(); - for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { - all_domains.addAll( gwcd.getAllDomainIds() ); - } - for( final DomainId 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" ); - 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 + "\"" ); - } } }