X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=fc98702421f0aebc64683317e0dbb2e1267c9f38;hb=7d5ee914b2beb6ec20aa906326113bba36551a4d;hp=12274f78d532b1476ed37aadaa583e35da563a69;hpb=756e207d17b773c707ff2315091bcef338ddcf85;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 12274f7..fc98702 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; @@ -33,6 +33,7 @@ import java.io.IOException; 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; @@ -43,9 +44,7 @@ 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; @@ -55,21 +54,23 @@ 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.phyloxml.PhyloXmlUtil; import org.forester.io.parsers.util.ParserUtils; -import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.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; @@ -84,9 +85,7 @@ 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; @@ -98,184 +97,187 @@ 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_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 = "2.200"; - final static private String PRG_DATE = "2011.10.18"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; - final static private boolean IGNORE_DUFS_DEFAULT = true; - final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false; - final static private double MAX_E_VALUE_DEFAULT = -1; - final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1; - private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj"; - private static final String SEQ_EXTRACT_SUFFIX = ".prot"; - private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus"; - private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt"; - private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html"; - private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html"; - private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0; - private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0; - private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; - private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; - private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; - private static final boolean VERBOSE = false; - private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; - private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; - private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis"; - private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true; - public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams"; - public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation"; - public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary"; - public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains"; - public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains"; - public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc"; - public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc"; - public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS"; - public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS"; - public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities"; - private static final String LOG_FILE_SUFFIX = "_log.txt"; - private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; - private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; - private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; + public 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 PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION = "dc_regain_stats"; + final static private String DA_ANALYSIS_OPTION = "DA_analyis"; + final static private String USE_LAST_IN_FITCH_OPTION = "last"; + final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; + 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 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 = "2.280"; + final static private String PRG_DATE = "130701"; + 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"; + final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e"; + 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 String WRITE_TO_NEXUS_OPTION = "nexus"; + 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 void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option, final String[][] input_file_properties, @@ -349,6 +351,7 @@ public class surfacing { * @param sum_of_all_domains_encountered * @param all_bin_domain_combinations_encountered * @param is_gains_analysis + * @param protein_length_stats_by_dc * @throws IOException */ private static void executeFitchGainsAnalysis( final File output_file, @@ -360,8 +363,8 @@ public class surfacing { 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(); + 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() ) { @@ -429,7 +432,7 @@ public class surfacing { 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> 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(); @@ -534,19 +537,6 @@ public class surfacing { 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 ); @@ -610,23 +600,27 @@ 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( 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( 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 ); 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; @@ -635,6 +629,22 @@ public class surfacing { 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_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; @@ -701,7 +711,7 @@ 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 ) { @@ -793,30 +803,22 @@ public class surfacing { 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 ); + 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 ) ) { @@ -854,8 +856,18 @@ 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 ) ) { @@ -980,8 +992,6 @@ public class surfacing { domain_similarity_print_option = PrintableDomainSimilarity.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 ) ) { @@ -1024,13 +1034,7 @@ public class surfacing { + 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 = 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" ); @@ -1045,7 +1049,7 @@ public class surfacing { 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 ); @@ -1053,7 +1057,7 @@ public class surfacing { SurfacingUtil.checkForOutputFileWriteability( dcc_outfile ); } File pfam_to_go_file = null; - Map> domain_id_to_go_ids_map = null; + Map> domain_id_to_go_ids_map = null; int domain_id_to_go_ids_count = 0; if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) { @@ -1151,67 +1155,9 @@ public class surfacing { && ( 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 (" @@ -1253,10 +1199,10 @@ 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 ); } @@ -1267,7 +1213,7 @@ public class surfacing { 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 ); @@ -1324,12 +1270,8 @@ 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 @@ -1376,6 +1318,11 @@ public class surfacing { System.out.println( "E-value maximum (inclusive) : " + e_value_max ); html_desc.append( "E-value maximum (inclusive):" + 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 ) { System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids ); @@ -1403,7 +1350,6 @@ public class surfacing { 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:" @@ -1415,19 +1361,34 @@ public class surfacing { + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "" + nl ); } + System.out.println( "Use last in Fitch parimony : " + use_last_in_fitch_parsimony ); + html_desc.append( "Use last in Fitch parimon:" + 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 ); + 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" ); @@ -1591,19 +1552,6 @@ public class surfacing { } 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 @@ -1625,8 +1573,8 @@ 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 ); @@ -1642,7 +1590,7 @@ public class surfacing { html_desc.append( "Command line:\n" + cla.getCommandLineArgsAsString() + "\n" + 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 ]; @@ -1650,9 +1598,9 @@ 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( '~', '_' ); @@ -1677,8 +1625,8 @@ 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; @@ -1731,7 +1679,7 @@ 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" ); @@ -1750,13 +1698,24 @@ 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(); + } // 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 ); + System.out.println( "Processing : " + input_file_properties[ i ][ 1 ] + + " [" + input_file_properties[ i ][ 0 ] + "]" ); + 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 ) { @@ -1778,12 +1737,14 @@ public class surfacing { input_file_properties[ i ][ 1 ], filter, filter_type, - ind_score_cutoff ); + ind_score_cutoff, + true ); } else { parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ), input_file_properties[ i ][ 1 ], - ind_score_cutoff ); + ind_score_cutoff, + true ); } if ( e_value_max >= 0.0 ) { parser.setEValueMaximum( e_value_max ); @@ -1816,6 +1777,14 @@ 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 ); System.out.println( "Number of proteins stored : " + protein_list.size() ); @@ -1869,6 +1838,10 @@ public class surfacing { log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(), log_writer ); } + if ( da_analysis ) { + System.out.println( "Distinct domain architectures stored : " + distinct_das ); + log( "Distinct domain architectures stored : " + distinct_das, log_writer ); + } System.out.println( "Time for processing : " + parser.getTime() + "ms" ); log( "", log_writer ); html_desc.append( "" + input_file_properties[ i ][ 0 ] + " [species: " @@ -1888,16 +1861,19 @@ public class surfacing { + parser.getProteinsIgnoredDueToFilter() ); } html_desc.append( "" + nl ); - // domain_partner_counts_array[ i ] = - // Methods.getDomainPartnerCounts( protein_domain_collections_array[ - // i ], - // false, input_file_properties[ i ][ 1 ] ); try { int count = 0; for( final Protein protein : protein_list ) { dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ) .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 ) { @@ -1911,30 +1887,34 @@ 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 ( !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 ) { + 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++ ) { @@ -1942,7 +1922,8 @@ 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 ) { @@ -1964,6 +1945,18 @@ 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" ); @@ -1982,23 +1975,24 @@ public class surfacing { domains_per_potein_stats_writer.close(); printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer ); ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); + + "_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() + "%" ); + 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 ); + log( "Range of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.getMin() ) + "%-" + + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); @@ -2068,14 +2062,22 @@ public class surfacing { go_annotation_output, go_id_to_term_map, go_namespace_limit ); - DescriptiveStatistics pw_stats = null; + final Map tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] ); try { String my_outfile = output_file.toString(); - if ( !my_outfile.endsWith( ".html" ) ) { + Map split_writers = null; + Writer writer = null; + if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) { + if ( my_outfile.endsWith( ".html" ) ) { + my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 ); + } + split_writers = new HashMap(); + createSplitWriters( out_dir, my_outfile, split_writers ); + } + else if ( !my_outfile.endsWith( ".html" ) ) { my_outfile += ".html"; + writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) ); } - final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir - + ForesterUtil.FILE_SEPARATOR + my_outfile ) ); List species_order = null; if ( species_matrix ) { species_order = new ArrayList(); @@ -2091,17 +2093,19 @@ public class surfacing { + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) + "" + nl ); html_desc.append( "" + nl ); - pw_stats = SurfacingUtil + final DescriptiveStatistics 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 ); + true, + tax_code_to_id_map ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \"" + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" ); } @@ -2110,7 +2114,6 @@ 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 ] ); @@ -2138,7 +2141,8 @@ public class surfacing { surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, surfacing.PRG_NAME, out_dir, - write_pwc_files ); + write_pwc_files, + tax_code_to_id_map ); 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( '.' ) ); @@ -2169,40 +2173,13 @@ public class surfacing { 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 ) { + 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, @@ -2234,12 +2211,18 @@ public class surfacing { output_binary_domain_combinationsfor_graph_analysis, all_bin_domain_combinations_gained_fitch, all_bin_domain_combinations_lost_fitch, - dc_type ); + 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 ); // 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 ); @@ -2250,7 +2233,8 @@ public class surfacing { secondary_features_parsimony, intree, parameters_sb.toString(), - mapping_results_map ); + mapping_results_map, + use_last_in_fitch_parsimony ); if ( i == 0 ) { System.out.println(); System.out.println( "Mapping to secondary features:" ); @@ -2263,7 +2247,7 @@ 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 )" ); @@ -2287,39 +2271,12 @@ public class surfacing { 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++; - // } - // } + writeProteinListsForAllSpecies( out_dir, + protein_lists_per_species, + gwcd_list, + output_list_of_all_proteins_per_domain_e_value_max ); + } + gwcd_list = null; if ( all_bin_domain_combinations_gained_fitch != null ) { try { executeFitchGainsAnalysis( new File( output_file @@ -2349,25 +2306,83 @@ 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( final File out_dir, + final String my_outfile, + final 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 + + "_domains_0.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; + 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 ); } @@ -2388,12 +2403,21 @@ public class surfacing { final PhylogenyNode n = it.next(); if ( ForesterUtil.isEmpty( n.getName() ) ) { if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + } + else if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { n.setName( n.getNodeData().getTaxonomy().getScientificName() ); } + else if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { + n.setName( n.getNodeData().getTaxonomy().getCommonName() ); + } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, - "node without both name and scientific taxonomy name found" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "node with no name, scientific name, common name, or taxonomy code present" ); } } } @@ -2406,34 +2430,17 @@ public class surfacing { } System.out.println( "--" ); } - for( int i = 0; i < input_file_properties.length; ++i ) { + for( final String[] input_file_propertie : input_file_properties ) { try { - intree.getNode( input_file_properties[ i ][ 1 ] ); + intree.getNode( input_file_propertie[ 1 ] ); } catch ( final IllegalArgumentException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ] + ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 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:" ); @@ -2485,17 +2492,6 @@ public class surfacing { 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" ); - System.out .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 @@ -2504,7 +2500,7 @@ public class surfacing { + "=: 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 " ); + 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" ); @@ -2521,18 +2517,27 @@ public class surfacing { System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_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_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" ); + System.out.println( DA_ANALYSIS_OPTION + ": to do DA analysis" ); System.out.println(); + System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar" + + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1" + + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o " + + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" ); System.out.println(); - System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar" + System.out.println( "Example 2: 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" ); + + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt " + + "-ds_output=detailed_html -scoring=domains -sort=alpha " ); System.out.println(); } - private static void processFilter( final File filter_file, final SortedSet filter ) { + private static void processFilter( final File filter_file, final SortedSet filter ) { SortedSet filter_str = null; try { filter_str = ForesterUtil.file2set( filter_file ); @@ -2542,35 +2547,44 @@ public class surfacing { } if ( filter_str != null ) { for( final String string : filter_str ) { - filter.add( new DomainId( string ) ); + filter.add( string ); } } if ( VERBOSE ) { System.out.println( "Filter:" ); - for( final DomainId domainId : filter ) { - System.out.println( domainId.getId() ); + for( final String domainId : filter ) { + System.out.println( domainId ); } } } - 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 ]; + private static String[][] processInputGenomesFile( final File input_genomes ) { + String[][] input_file_properties = null; + try { + input_file_properties = ForesterUtil.file22dArray( input_genomes ); + } + catch ( final IOException e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, + "genomes files is to be in the following format \" \": " + + e.getLocalizedMessage() ); + } + final Set specs = new HashSet(); + final Set paths = new HashSet(); + for( int i = 0; i < input_file_properties.length; ++i ) { + if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: " + + input_file_properties[ i ][ 1 ] ); } - 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 ] + "\"" ); - } + if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ] + + " is not unique" ); + } + specs.add( input_file_properties[ i ][ 1 ] ); + if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ] + + " is not unique" ); } + paths.add( input_file_properties[ i ][ 0 ] ); final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) ); if ( !ForesterUtil.isEmpty( error ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, error ); @@ -2679,7 +2693,7 @@ public class surfacing { private static void writePresentToNexus( final File output_file, final File positive_filter_file, - final SortedSet filter, + final SortedSet filter, final List gwcd_list ) { try { SurfacingUtil @@ -2697,17 +2711,23 @@ public class surfacing { private static void writeProteinListsForAllSpecies( final File output_dir, final SortedMap> protein_lists_per_species, - final List gwcd_list ) { - final SortedSet all_domains = new TreeSet(); + final List gwcd_list, + final double domain_e_cutoff ) { + final SortedSet all_domains = new TreeSet(); for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { all_domains.addAll( gwcd.getAllDomainIds() ); } - for( final DomainId domain : all_domains ) { + for( final String domain : all_domains ) { final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX ); SurfacingUtil.checkForOutputFileWriteability( out ); try { final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) ); - SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" ); + SurfacingUtil.extractProteinNames( protein_lists_per_species, + domain, + proteins_file_writer, + "\t", + LIMIT_SPEC_FOR_PROT_EX, + domain_e_cutoff ); proteins_file_writer.close(); } catch ( final IOException e ) {