// $Id: // // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: www.phylosoft.org/forester package org.forester.application; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.io.Writer; import java.util.ArrayList; import java.util.Date; import java.util.HashSet; import java.util.List; import java.util.Map; 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; import org.forester.go.GoUtils; import org.forester.go.OBOparser; 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.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.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.DomainSimilarityCalculator; import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; import org.forester.surfacing.GenomeWideCombinableDomains; import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder; 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.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; 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"; // 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"; // 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"; // 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_GOID_D = "_dollo_gains_goid_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_GOID_D = "_dollo_present_goid_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_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d"; public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d"; public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d"; 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_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc"; public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc"; public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc"; 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 DISPLAY_M_HISTOGRAMS_OPTION = "mhisto"; // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false; 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 = "2.003"; final static private String PRG_DATE = "2010.12.03"; 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; final static private String DEFAULT_SEARCH_PARAMETER = "ls"; final private static boolean VERBOSE_DEFAULT = true; 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; // final String error = ForesterUtil.isReadableFile( new File( // input_file_properties[ i ][ 0 ] ) ); // if ( !ForesterUtil.isEmpty( error ) ) { // ForesterUtil.fatalError( surfacing.PRG_NAME, error ); // } 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 sideeffects '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, ForesterUtil.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 static void main( final String args[] ) { final long start_time = new Date().getTime(); // final StringBuffer log = new StringBuffer(); final StringBuilder html_desc = new StringBuilder(); ForesterUtil.printProgramInformation( surfacing.PRG_NAME, surfacing.PRG_VERSION, surfacing.PRG_DATE, surfacing.E_MAIL, surfacing.WWW ); final String nl = ForesterUtil.LINE_SEPARATOR; html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + nl ); CommandLineArguments cla = null; try { cla = new CommandLineArguments( args ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) { surfacing.printHelp(); System.exit( 0 ); } if ( ( args.length < 1 ) ) { surfacing.printHelp(); System.exit( -1 ); } 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.DETAILEDNESS_OPTION ); allowed_options.add( surfacing.OUTPUT_FILE_OPTION ); allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ); allowed_options.add( surfacing.SPECIES_MATRIX_OPTION ); allowed_options.add( surfacing.SCORING_OPTION ); allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION ); allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION ); allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION ); allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION ); allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ); allowed_options.add( surfacing.OUTPUT_DIR_OPTION ); allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ); allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION ); allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION ); allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ); allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION ); allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ); allowed_options.add( surfacing.DISPLAY_M_HISTOGRAMS_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( 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( 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 ); 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; 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 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 ) ) { try { e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" ); } } if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) { try { max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" ); } } boolean no_engulfing_overlaps = false; if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) { no_engulfing_overlaps = true; } boolean ignore_virus_like_ids = false; if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) { ignore_virus_like_ids = true; } if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) { ignore_dufs = false; } if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) { ignore_combination_with_same = 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; } boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT; if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) { ignore_species_specific_domains = true; } File output_file = null; if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities output file: -" + surfacing.OUTPUT_FILE_OPTION + "=" ); } output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) ); SurfacingUtil.checkForOutputFileWriteability( output_file ); } File cutoff_scores_file = null; Map individual_score_cutoffs = null; if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -" + surfacing.CUTOFF_SCORE_FILE_OPTION + "=" ); } cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) ); final String error = ForesterUtil.isReadableFile( cutoff_scores_file ); if ( !ForesterUtil.isEmpty( error ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: " + error ); } try { final BasicTable scores_table = BasicTableParser.parse( cutoff_scores_file, " " ); individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 ); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e ); } } BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC; if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) { dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED; } if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) { dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT; } File out_dir = null; if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -" + surfacing.OUTPUT_DIR_OPTION + "=" ); } out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) ); if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" ); } if ( !out_dir.exists() ) { final boolean success = out_dir.mkdir(); if ( !success || !out_dir.exists() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" ); } } if ( !out_dir.canWrite() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" ); } } File positive_filter_file = null; File negative_filter_file = null; File negative_domains_filter_file = null; if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) && ( 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" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -" + surfacing.FILTER_NEGATIVE_OPTION + "=" ); } negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) ); final String msg = ForesterUtil.isReadableFile( negative_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": " + msg ); } } else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -" + surfacing.FILTER_POSITIVE_OPTION + "=" ); } positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) ); final String msg = ForesterUtil.isReadableFile( positive_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": " + msg ); } } else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -" + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=" ); } negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ); 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 ); } } 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 ); 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 ); } } 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 + "=" ); } DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT; if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value 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 + ">\"" ); } final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION ); if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) { scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS; } else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) { scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; } else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) { scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS; } 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 + ">\"" ); } } boolean sort_by_species_count_first = false; if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) { sort_by_species_count_first = true; } boolean species_matrix = false; if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) { species_matrix = true; } boolean output_protein_lists_for_all_domains = false; if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) { output_protein_lists_for_all_domains = true; } Detailedness detailedness = DETAILEDNESS_DEFAULT; if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); } final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase(); if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) { detailedness = DomainSimilarityCalculator.Detailedness.BASIC; } else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) { detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES; } else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) { detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-" + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" ); } } String automated_pairwise_comparison_suffix = null; boolean perform_pwc = false; boolean write_pwc_files = false; if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) { perform_pwc = true; if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) { write_pwc_files = false; } else { write_pwc_files = true; automated_pairwise_comparison_suffix = "_" + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); } } String query_domain_ids = null; 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 + "=" ); } query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION ); } DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT; DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value 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 + ">\"" ); } final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase(); if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; } else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) { domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE; domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE; } 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 + ">\"" ); } } PrintableDomainSimilarity.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: -" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); } 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; } 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; } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); } } GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT; if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value 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 + ">\"" ); } final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase(); if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) { dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; } else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) { dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT; } else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) { dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT; } else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) { dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT; } 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 + ">\"" ); } } 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 int number_of_genomes = input_file_properties.length; if ( number_of_genomes < 2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" ); } if ( ( number_of_genomes < 3 ) && perform_pwc ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -" + 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 ); for( int i = 0; i < number_of_genomes; i++ ) { File dcc_outfile = new File( input_file_properties[ i ][ 0 ] + 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; 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 ); } } File go_obo_file = null; List go_terms = null; 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 ); } } 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 ) ) ) { go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms ); } GoNameSpace go_namespace_limit = null; if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) { if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=) without Pfam to GO mapping file (" + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=) and GO OBO file (-" + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); } if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value 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 + ">\"" ); } final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION ) .toLowerCase(); if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) { go_namespace_limit = GoNameSpace.createMolecularFunction(); } else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) { go_namespace_limit = GoNameSpace.createBiologicalProcess(); } else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) { go_namespace_limit = GoNameSpace.createCellularComponent(); } 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 + ">\"" ); } } 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 (" + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION + "=)" ); } if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -" + surfacing.INPUT_SPECIES_TREE_OPTION + "=" ); } final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION ); if ( intrees_str.indexOf( "#" ) > 0 ) { final String[] intrees_strs = intrees_str.split( "#" ); intree_files = new File[ intrees_strs.length ]; int i = 0; for( final String s : intrees_strs ) { intree_files[ i++ ] = new File( s.trim() ); } } else { intree_files = new File[ 1 ]; intree_files[ 0 ] = new File( intrees_str ); } intrees = getIntrees( intree_files, number_of_genomes, input_file_properties ); } long random_number_seed_for_fitch_parsimony = 0l; boolean radomize_fitch_parsimony = false; if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -" + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=" ); } try { random_number_seed_for_fitch_parsimony = cla .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } radomize_fitch_parsimony = true; } SortedSet filter = null; if ( ( positive_filter_file != null ) || ( negative_filter_file != null ) || ( negative_domains_filter_file != null ) ) { filter = new TreeSet(); if ( positive_filter_file != null ) { processFilter( positive_filter_file, filter ); } else if ( negative_filter_file != null ) { processFilter( negative_filter_file, filter ); } else if ( negative_domains_filter_file != null ) { processFilter( negative_domains_filter_file, filter ); } } 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 ) { SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); } if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -" + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=" ); } final String[] secondary_features_map_files_strs = cla .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" ); secondary_features_map_files = new File[ secondary_features_map_files_strs.length ]; domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ]; int i = 0; for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) { secondary_features_map_files[ i ] = new File( secondary_features_map_files_str ); final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] ); if ( !ForesterUtil.isEmpty( error ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error ); } try { domain_id_to_secondary_features_maps[ i ] = SurfacingUtil .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] ); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + e.getMessage() ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file [" + secondary_features_map_files[ i ] + "]: " + e.getMessage() ); } i++; } } if ( out_dir == null ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-" + surfacing.OUTPUT_DIR_OPTION + "=)" ); } if ( output_file == null ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-" + surfacing.OUTPUT_FILE_OPTION + "=)" ); } if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-" + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=)" ); } if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no (acceptable) go id to term mapping file provided ('GO OBO file') (-" + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); } boolean display_histograms = false; if ( cla.isOptionSet( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ) ) { display_histograms = true; } 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( "" + 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]" ); html_desc.append( "" + 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]" ); html_desc.append( "" + 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]" ); html_desc.append( "" + nl ); } if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) { String plus0 = ""; for( final String s : plus_minus_analysis_high_copy_base_species ) { plus0 += "+" + s + " "; } String plus1 = ""; for( final String s : plus_minus_analysis_high_copy_target_species ) { plus1 += "*" + s + " "; } String minus = ""; for( final String s : plus_minus_analysis_high_low_copy_species ) { minus += "-" + s + " "; } System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus ); html_desc.append( "" + nl ); } if ( cutoff_scores_file != null ) { System.out.println( "Cutoff scores file : " + cutoff_scores_file ); html_desc.append( "" + nl ); } if ( e_value_max >= 0.0 ) { System.out.println( "E-value maximum (inclusive) : " + e_value_max ); html_desc.append( "" + nl ); } System.out.println( "Ignore DUFs : " + ignore_dufs ); if ( ignore_virus_like_ids ) { System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids ); html_desc.append( "" + nl ); } html_desc.append( "" + nl ); if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { System.out.println( "Max allowed domain overlap : " + max_allowed_overlap ); html_desc.append( "" + nl ); } if ( no_engulfing_overlaps ) { System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps ); html_desc.append( "" + nl ); } System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec ); html_desc .append( "" + nl ); System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains ); html_desc .append( "" + nl ); System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); html_desc.append( "" + nl ); ; System.out.println( "Consider directedness : " + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) ); html_desc.append( "" + nl ); if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) { System.out.println( "Consider adjacency : " + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) ); html_desc.append( "" + nl ); } System.out.print( "Domain counts sort order : " ); switch ( dc_sort_order ) { case ALPHABETICAL_KEY_ID: System.out.println( "alphabetical" ); break; case KEY_DOMAIN_COUNT: System.out.println( "domain count" ); break; case KEY_DOMAIN_PROTEINS_COUNT: System.out.println( "domain proteins count" ); break; case COMBINATIONS_COUNT: System.out.println( "domain combinations count" ); 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]" ); html_desc.append( "" + nl ); } if ( go_terms != null ) { System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" ); html_desc.append( "" + nl ); } if ( go_namespace_limit != null ) { System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() ); html_desc.append( "" + nl ); } if ( perform_pwc ) { System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix ); html_desc.append( "" + nl ); } if ( out_dir != null ) { System.out.println( "Output directory : " + out_dir ); } if ( query_domain_ids != null ) { System.out.println( "Query domains (ordered) : " + query_domain_ids ); html_desc.append( "" + nl ); } System.out.println( "Write similarities to : " + output_file ); System.out.print( " Scoring method : " ); html_desc.append( "" + nl ); break; case DOMAINS: System.out.println( "domain counts based" ); html_desc.append( "domain counts based" + "" + nl ); break; case PROTEINS: System.out.println( "domain proteins counts based" ); html_desc.append( "domain proteins counts based" + "" + nl ); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" ); } System.out.print( " Sort by : " ); html_desc.append( "" + nl ); System.out.print( " Detailedness : " ); switch ( detailedness ) { case BASIC: System.out.println( "basic" ); break; case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES: System.out.println( "list combining domains for each species" ); break; case PUNCTILIOUS: System.out.println( "punctilious" ); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" ); } System.out.print( " Print option : " ); switch ( domain_similarity_print_option ) { case HTML: System.out.println( "HTML" ); break; case SIMPLE_TAB_DELIMITED: System.out.println( "simple tab delimited" ); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" ); } System.out.print( " Species matrix : " + species_matrix ); System.out.println(); final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX ); System.out.println( "Domain comb data output : " + dc_data_file ); html_desc.append( "" ); System.out.println(); if ( perform_pwc ) { System.out.println( "Pairwise comparisons: " ); html_desc.append( "" ); System.out.print( " Sort by : " ); html_desc.append( "" + nl ); if ( jacknifed_distances ) { html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + 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( "" + nl ); // System.out.println( " Infer species trees : true" ); // } if ( ( intrees != null ) && ( intrees.length > 0 ) ) { for( final File intree_file : intree_files ) { html_desc.append( "" + nl ); System.out.println( " Intree for gain/loss pars.: " + intree_file ); } } if ( radomize_fitch_parsimony ) { html_desc.append( "" + nl ); System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony ); } if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { for( int i = 0; i < secondary_features_map_files.length; i++ ) { html_desc.append( "" + nl ); System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ] + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" ); 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() ); System.out.print( " => " ); for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) { System.out.print( sec ); System.out.print( " " ); } System.out.println(); } } } } } // if ( perform_pwc ) { System.out.println(); html_desc.append( "" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = 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 ]; query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ]; 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(); for( final String element : query_domain_ids_str_ary ) { query.add( new DomainId( element ) ); } query_domain_ids_array[ i ] = query; query_domain_ids_str = query_domain_ids_str.replace( '~', '_' ); String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX; if ( out_dir != null ) { protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str; } try { query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) ); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: " + e.getLocalizedMessage() ); } } } SortedMap> protein_lists_per_species = null; //This will only be created if neede. boolean need_protein_lists_per_species = false; if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) { need_protein_lists_per_species = true; } 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(); 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; if ( ( intrees != null ) && ( intrees.length == 1 ) ) { 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 ); 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 ) ); per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "N:\t" ); per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:" + ForesterUtil.LINE_SEPARATOR ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX ); BufferedWriter log_writer = null; try { log_writer = new BufferedWriter( new FileWriter( log_file ) ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } BufferedWriter dc_data_writer = null; try { dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) ); dc_data_writer.write( DATA_FILE_DESC ); dc_data_writer.write( ForesterUtil.LINE_SEPARATOR ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } 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 ); HmmscanPerDomainTableParser parser = null; INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE; if ( individual_score_cutoffs != null ) { ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT; } if ( ( positive_filter_file != null ) || ( negative_filter_file != null ) || ( negative_domains_filter_file != null ) ) { HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE; if ( positive_filter_file != null ) { filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN; } else if ( negative_filter_file != null ) { filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN; } else if ( negative_domains_filter_file != null ) { filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN; } parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ), input_file_properties[ i ][ 1 ], filter, filter_type, ind_score_cutoff ); } else { parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ), input_file_properties[ i ][ 1 ], ind_score_cutoff ); } if ( e_value_max >= 0.0 ) { parser.setEValueMaximum( e_value_max ); } parser.setIgnoreDufs( ignore_dufs ); parser.setIgnoreVirusLikeIds( ignore_virus_like_ids ); parser.setIgnoreEngulfedDomains( no_engulfing_overlaps ); if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { parser.setMaxAllowedOverlap( max_allowed_overlap ); } parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); if ( individual_score_cutoffs != null ) { parser.setIndividualScoreCutoffs( individual_score_cutoffs ); } List protein_list = null; try { protein_list = parser.parse(); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } catch ( final Exception e ) { ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e ); } if ( VERBOSE ) { System.out.println( "Domains ignored due to negative domain filter: " ); ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() ); System.out.println( "Domains ignored due to virus like id: " ); ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() ); } System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() ); log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer ); System.out.println( "Number of proteins stored : " + protein_list.size() ); log( "Number of proteins stored : " + protein_list.size(), log_writer ); System.out.println( "Domains encountered : " + parser.getDomainsEncountered() ); log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer ); System.out.println( "Domains stored : " + parser.getDomainsStored() ); 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 ); 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 ); System.out.println( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf() ); 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 ); } System.out.println( "Domains ignored due negative domain filter : " + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); 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 ); 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 ); } 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 ); } System.out.println( "Time for processing : " + parser.getTime() + "ms" ); log( "", log_writer ); 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; } } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() ); } 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 ); } 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++ ) { try { SurfacingUtil.extractProteinNames( protein_list, query_domain_ids_array[ j ], query_domains_writer_ary[ j ], "\t" ); query_domains_writer_ary[ j ].flush(); } catch ( final IOException e ) { e.printStackTrace(); } } } if ( need_protein_lists_per_species ) { protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list ); } try { log_writer.flush(); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); } System.gc(); } // for( int i = 0; i < number_of_genomes; ++i ) { try { per_genome_domain_promiscuity_statistics_writer.flush(); per_genome_domain_promiscuity_statistics_writer.close(); dc_data_writer.flush(); dc_data_writer.close(); log_writer.flush(); log_writer.close(); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); } ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file ); if ( query_domains_writer_ary != null ) { for( int j = 0; j < query_domain_ids_array.length; j++ ) { try { query_domains_writer_ary[ j ].close(); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() ); } } } if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { try { SurfacingUtil.executeDomainLengthAnalysis( input_file_properties, number_of_genomes, domain_lengths_table, domain_lengths_analysis_outfile ); } catch ( final IOException e1 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() ); } System.out.println(); ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile ); System.out.println(); } 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 ); switch ( scoring ) { case COMBINATIONS: pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator(); break; case DOMAINS: pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator(); break; case PROTEINS: pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator(); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" ); } DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE; if ( domain_id_to_go_ids_map != null ) { go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL; } final SortedSet similarities = calc .calculateSimilarities( pw_calc, 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; try { String my_outfile = output_file.toString(); if ( !my_outfile.endsWith( ".html" ) ) { my_outfile += ".html"; } 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(); for( int i = 0; i < number_of_genomes; i++ ) { species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) ); } } html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "" + nl ); html_desc.append( "
Produced by:" + surfacing.PRG_NAME + "
Version:" + surfacing.PRG_VERSION + "
Release Date:" + surfacing.PRG_DATE + "
Contact:" + surfacing.E_MAIL + "
WWW:" + surfacing.WWW + "
Input files names from:" + input_files_file + " [" + input_file_names_from_file.length + " input files]
Positive protein filter:" + positive_filter_file + " [" + filter_size + " domain ids]
Negative protein filter:" + negative_filter_file + " [" + filter_size + " domain ids]
Negative domain filter:" + negative_domains_filter_file + " [" + filter_size + " domain ids]
Plus-minus analysis:" + plus1 + "&& " + plus0 + "&& " + minus + "
Cutoff scores file:" + cutoff_scores_file + "
E-value maximum (inclusive):" + e_value_max + "
Ignore virus, phage, transposition related ids:" + ignore_virus_like_ids + "
Ignore DUFs:" + ignore_dufs + "
Max allowed domain overlap:" + max_allowed_overlap + "
Ignore (lower confidence) engulfed domains:" + no_engulfing_overlaps + "
Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" + ignore_domains_without_combs_in_all_spec + "
Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" + ignore_species_specific_domains + "
Ignore combination with self for domain combination similarity analyses:" + ignore_combination_with_same + "
Consider directedness of binary domain combinations:" + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "
Consider djacency of binary domain combinations:" + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "
Pfam to GO mappings from:" + pfam_to_go_file + " [" + domain_id_to_go_ids_count + " mappings]" + "
GO terms from:" + go_obo_file + " [" + go_terms.size() + " terms]" + "
Limit GO terms to" + go_namespace_limit + "
Suffix for PWC files" + automated_pairwise_comparison_suffix + "
" + query_domain_ids + "
Scoring method:" ); switch ( scoring ) { case COMBINATIONS: System.out.println( "domain combinations based" ); html_desc.append( "domain combinations based" + "
Sort by:" ); switch ( domain_similarity_sort_field ) { case MIN: System.out.print( "score minimum" ); html_desc.append( "score minimum" ); break; case MAX: System.out.print( "score maximum" ); html_desc.append( "score maximum" ); break; case MEAN: System.out.print( "score mean" ); html_desc.append( "score mean" ); break; case SD: System.out.print( "score standard deviation" ); html_desc.append( "score standard deviation" ); break; case SPECIES_COUNT: System.out.print( "species number" ); html_desc.append( "species number" ); break; case DOMAIN_ID: System.out.print( "alphabetical domain identifier" ); html_desc.append( "alphabetical domain identifier" ); break; case MAX_DIFFERENCE: System.out.print( "(maximal) difference" ); html_desc.append( "(maximal) difference" ); break; case ABS_MAX_COUNTS_DIFFERENCE: System.out.print( "absolute (maximal) counts difference" ); html_desc.append( "absolute (maximal) counts difference" ); break; case MAX_COUNTS_DIFFERENCE: System.out.print( "(maximal) counts difference" ); html_desc.append( "(maximal) counts difference" ); break; default: ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); } if ( sort_by_species_count_first ) { System.out.println( " (sort by species count first)" ); html_desc.append( " (sort by species count first)" ); } else { System.out.println(); } html_desc.append( "
Domain combination data output: " + dc_data_file + "
Pairwise comparisons:
Sort by:" ); switch ( domain_similarity_sort_field_for_automated_pwc ) { case MEAN: System.out.print( "score mean" ); html_desc.append( "score mean" ); break; case DOMAIN_ID: System.out.print( "alphabetical domain identifier" ); html_desc.append( "alphabetical domain identifier" ); break; case MAX_DIFFERENCE: System.out.print( "difference" ); html_desc.append( "difference" ); break; case ABS_MAX_COUNTS_DIFFERENCE: System.out.print( "absolute counts difference" ); html_desc.append( "absolute counts difference" ); break; case MAX_COUNTS_DIFFERENCE: System.out.print( "counts difference" ); html_desc.append( "counts difference" ); break; default: ForesterUtil .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); } System.out.println(); html_desc.append( "
Jacknife:" + jacknife_resamplings + " resamplings
Jacknife ratio:" + ForesterUtil.round( jacknife_ratio, 2 ) + "
Jacknife random number seed:" + random_seed + "
Infer species trees:true
Intree for gain/loss parsimony analysis:" + intree_file + "
Random number seed for Fitch parsimony analysis:" + random_number_seed_for_fitch_parsimony + "
Secondary features map file:" + secondary_features_map_files[ i ] + "
Command line:" + cla.getCommandLineArgsAsString() + "
" + 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() ); } html_desc.append( "
Sum of all distinct binary combinations:" + all_bin_domain_combinations_encountered.size() + "
Sum of all distinct domains:" + all_domains_encountered.size() + "
Analysis date/time:" + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) + "
" + nl ); pw_stats = SurfacingUtil .writeDomainSimilaritiesToFile( html_desc, new StringBuilder( number_of_genomes + " genomes" ), writer, similarities, number_of_genomes == 2, species_order, domain_similarity_print_option, domain_similarity_sort_field, scoring, true ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \"" + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" ); } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" [" + 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 ] ); } List inferred_trees = null; if ( ( number_of_genomes > 2 ) && perform_pwc ) { final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator(); pwgc.performPairwiseComparisons( html_desc, sort_by_species_count_first, detailedness, ignore_domains_without_combs_in_all_spec, ignore_species_specific_domains, domain_similarity_sort_field_for_automated_pwc, domain_similarity_print_option, scoring, domain_id_to_go_ids_map, go_id_to_term_map, go_namespace_limit, species, number_of_genomes, gwcd_list, pw_calc, automated_pairwise_comparison_suffix, true, surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, surfacing.PRG_NAME, display_histograms, out_dir, write_pwc_files ); 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( '.' ) ); } if ( out_dir != null ) { matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file; 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() ); SurfacingUtil .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() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file + 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 ) ); final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file + 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 ); // final List histogram_datas = pwgc.getHistogramDatas(); // if ( infer_species_trees ) { // inferred_trees = new ArrayList(); // final List inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc // .getSharedBinaryCombinationsBasedDistances() ); // final List inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc // .getSharedDomainsBasedDistances() ); // inferred_trees.addAll( inferred_trees_bc ); // inferred_trees.addAll( inferred_trees_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 ( display_histograms ) { // final List histogram_datas_all = new ArrayList(); // histogram_datas_all.add( new HistogramData( "all", // values_for_all_scores_histogram, // null, // 20 ) ); // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all ); // final HistogramsFrame hf = new HistogramsFrame( histogram_datas ); // hf_all.setVisible( true ); // hf.setVisible( true ); } } // 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 ( ( ( 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 ); String s = "_"; if ( radomize_fitch_parsimony ) { s += random_number_seed_for_fitch_parsimony + "_"; } int i = 0; for( final Phylogeny intree : intrees ) { final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s + ForesterUtil.removeSuffix( intree_files[ i ].toString() ); final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree, gwcd_list ); SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony, radomize_fitch_parsimony, outfile_name, domain_parsimony, intree, domain_id_to_go_ids_map, go_id_to_term_map, go_namespace_limit, 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. 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 ) { 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 ); if ( i == 0 ) { System.out.println(); System.out.println( "Mapping to secondary features:" ); for( final Species spec : mapping_results_map.keySet() ) { final MappingResults mapping_results = mapping_results_map.get( spec ); final int total_domains = mapping_results.getSumOfFailures() + mapping_results.getSumOfSuccesses(); System.out.print( spec + ":" ); System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() ); System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() ); if ( total_domains > 0 ) { System.out.println( ", mapped ratio = " + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" ); } else { System.out.println( ", mapped ratio = n/a (total domains = 0 )" ); } } } } } i++; } // 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 ); } 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++; // } // } 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 ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); } } 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 ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); } } 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, "OK" ); System.out.println(); } 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().getScientificName() ) ) { n.setName( n.getNodeData().getTaxonomy().getScientificName() ); } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "node without both name and scientific taxonomy name found" ); } } } // 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]" ); 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\"." ); 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)" ); 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)" ); 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)" ); System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION + ": 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_'" ); 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_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" ); System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" ); System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:" + DOMAINS_SORT_ORDER_DEFAULT + ")" ); System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:" + 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" ); 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" ); System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); System.out .println( surfacing.DISPLAY_M_HISTOGRAMS_OPTION + ": to display multiple histograms (using fluorite)" ); 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 + "=: 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 " ); 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.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" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY + ": 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')" ); System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=: 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_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(); 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(); } 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 + "\"" ); } } }