+++ /dev/null
-// $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.HmmPfamOutputParser;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-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_old {
-
- 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 = "1.00";
- final static private String PRG_DATE = "2009.07.06";
- 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 ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT = true;
- 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";
-
- // 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_old.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_old.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<BinaryDomainCombination> all_bin_domain_combinations_changed,
- final int sum_of_all_domains_encountered,
- final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
- final boolean is_gains_analysis ) throws IOException {
- SurfacingUtil.checkForOutputFileWriteability( output_file );
- final Writer out = ForesterUtil.createBufferedWriter( output_file );
- final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
- .listToSortedCountsMap( all_bin_domain_combinations_changed );
- final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
- final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
- int above_one = 0;
- int one = 0;
- for( final Object bdc_object : bdc_to_counts.keySet() ) {
- final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
- final int count = bdc_to_counts.get( bdc_object );
- if ( count < 1 ) {
- ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
- }
- out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
- if ( count > 1 ) {
- all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
- all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
- above_one++;
- }
- else if ( count == 1 ) {
- all_domains_in_combination_changed_only_once.add( bdc.getId0() );
- all_domains_in_combination_changed_only_once.add( bdc.getId1() );
- one++;
- }
- }
- final int all = all_bin_domain_combinations_encountered.size();
- int never_lost = -1;
- if ( !is_gains_analysis ) {
- all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
- never_lost = all_bin_domain_combinations_encountered.size();
- for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
- out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
- }
- }
- if ( is_gains_analysis ) {
- out.write( "Sum of all distinct domain combinations appearing once : " + one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations apppearing only once : "
- + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations apppearing more than once: "
- + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
- }
- else {
- out.write( "Sum of all distinct domain combinations never lost : " + never_lost
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations lost once : " + one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations lost only once : "
- + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
- out.write( "Sum of all distinct domains in combinations lost more than once: "
- + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
- }
- out.write( "All binary combinations : " + all
- + ForesterUtil.LINE_SEPARATOR );
- out.write( "All domains : "
- + sum_of_all_domains_encountered );
- out.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
- "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
- + "\"" );
- }
-
- private static void executePlusMinusAnalysis( final File output_file,
- final List<String> plus_minus_analysis_high_copy_base,
- final List<String> plus_minus_analysis_high_copy_target,
- final List<String> plus_minus_analysis_low_copy,
- final List<GenomeWideCombinableDomains> gwcd_list,
- final SortedMap<Species, List<Protein>> protein_lists_per_species,
- final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final List<Object> plus_minus_analysis_numbers ) {
- final Set<String> all_spec = new HashSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- all_spec.add( gwcd.getSpecies().getSpeciesId() );
- }
- final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
- final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
- final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
- final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
- final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
- final File proteins_file_base = new File( output_file + "" );
- final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
- final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
- try {
- DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
- protein_lists_per_species,
- plus_minus_analysis_high_copy_base,
- plus_minus_analysis_high_copy_target,
- plus_minus_analysis_low_copy,
- min_diff,
- factor,
- plain_out_dom,
- html_out_dom,
- html_out_dc,
- domain_id_to_go_ids_map,
- go_id_to_term_map,
- all_domains_go_ids_out_dom,
- passing_domains_go_ids_out_dom,
- proteins_file_base );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
- + html_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
- + plain_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
- + html_out_dc + "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
- "Wrote plus minus domain analysis based passing GO ids to \""
- + passing_domains_go_ids_out_dom + "\"" );
- ForesterUtil.programMessage( surfacing_old.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_old.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_old.PRG_NAME, "file [" + intree_file
- + "] does not contain any phylogeny in phyloXML format" );
- }
- else if ( p_array.length > 1 ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "file [" + intree_file
- + "] contains more than one phylogeny in phyloXML format" );
- }
- intree = p_array[ 0 ];
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to read input tree from file [" + intree_file
- + "]: " + error );
- }
- if ( ( intree == null ) || intree.isEmpty() ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is empty" );
- }
- if ( !intree.isRooted() ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
- }
- if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
- ForesterUtil.fatalError( surfacing_old.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_old.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_old.PRG_NAME, "input tree [" + intree_file
- + "] is not completely binary" );
- }
- intrees[ i++ ] = intree;
- }
- return intrees;
- }
-
- private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
- final NeighborJoining nj = NeighborJoining.createInstance();
- final List<Phylogeny> phylogenies = nj.execute( distances_list );
- final PhylogenyWriter w = new PhylogenyWriter();
- try {
- w.toNewHampshire( phylogenies, true, true, outfile, ";" );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
- }
- return phylogenies;
- }
-
- 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_old.PRG_NAME,
- surfacing_old.PRG_VERSION,
- surfacing_old.PRG_DATE,
- surfacing_old.E_MAIL,
- surfacing_old.WWW );
- final String nl = ForesterUtil.LINE_SEPARATOR;
- html_desc.append( "<table>" + nl );
- html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing_old.PRG_NAME + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Version:</td><td>" + surfacing_old.PRG_VERSION + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing_old.PRG_DATE + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Contact:</td><td>" + surfacing_old.E_MAIL + "</td></tr>" + nl );
- html_desc.append( "<tr><td>WWW:</td><td>" + surfacing_old.WWW + "</td></tr>" + nl );
- CommandLineArguments cla = null;
- try {
- cla = new CommandLineArguments( args );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
- }
- if ( cla.isOptionSet( surfacing_old.HELP_OPTION_1 ) || cla.isOptionSet( surfacing_old.HELP_OPTION_2 ) ) {
- surfacing_old.printHelp();
- System.exit( 0 );
- }
- if ( ( args.length < 1 ) ) {
- surfacing_old.printHelp();
- System.exit( -1 );
- }
- final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( surfacing_old.NOT_IGNORE_DUFS_OPTION );
- allowed_options.add( surfacing_old.MAX_E_VALUE_OPTION );
- allowed_options.add( surfacing_old.DETAILEDNESS_OPTION );
- allowed_options.add( surfacing_old.OUTPUT_FILE_OPTION );
- allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION );
- allowed_options.add( surfacing_old.SPECIES_MATRIX_OPTION );
- allowed_options.add( surfacing_old.SCORING_OPTION );
- allowed_options.add( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION );
- allowed_options.add( surfacing_old.NO_ENGULFING_OVERLAP_OPTION );
- allowed_options.add( surfacing_old.DOMAIN_COUNT_SORT_OPTION );
- allowed_options.add( surfacing_old.CUTOFF_SCORE_FILE_OPTION );
- allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
- allowed_options.add( surfacing_old.OUTPUT_DIR_OPTION );
- allowed_options.add( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION );
- allowed_options.add( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION );
- allowed_options.add( surfacing_old.GO_OBO_FILE_USE_OPTION );
- allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION );
- allowed_options.add( surfacing_old.GO_NAMESPACE_LIMIT_OPTION );
- allowed_options.add( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
- allowed_options.add( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
- allowed_options.add( surfacing_old.DISPLAY_M_HISTOGRAMS_OPTION );
- allowed_options.add( surfacing_old.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_old.IGNORE_DUFS_DEFAULT;
- boolean ignore_combination_with_same = surfacing_old.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
- double e_value_max = surfacing_old.MAX_E_VALUE_DEFAULT;
- int max_allowed_overlap = surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT;
- final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
- if ( dissallowed_options.length() > 0 ) {
- ForesterUtil.fatalError( surfacing_old.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_old.MAX_E_VALUE_OPTION ) ) {
- try {
- e_value_max = cla.getOptionValueAsDouble( surfacing_old.MAX_E_VALUE_OPTION );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no acceptable value for E-value maximum" );
- }
- }
- if ( cla.isOptionSet( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION ) ) {
- try {
- max_allowed_overlap = cla.getOptionValueAsInt( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no acceptable value for maximal allowed domain overlap" );
- }
- }
- boolean no_engulfing_overlaps = false;
- if ( cla.isOptionSet( surfacing_old.NO_ENGULFING_OVERLAP_OPTION ) ) {
- no_engulfing_overlaps = true;
- }
- boolean ignore_virus_like_ids = false;
- if ( cla.isOptionSet( surfacing_old.IGNORE_VIRAL_IDS ) ) {
- ignore_virus_like_ids = true;
- }
- if ( cla.isOptionSet( surfacing_old.NOT_IGNORE_DUFS_OPTION ) ) {
- ignore_dufs = false;
- }
- if ( cla.isOptionSet( surfacing_old.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_old.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_old.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
- ignore_species_specific_domains = true;
- }
- File output_file = null;
- if ( cla.isOptionSet( surfacing_old.OUTPUT_FILE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_FILE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no value for domain combinations similarities output file: -"
- + surfacing_old.OUTPUT_FILE_OPTION + "=<file>" );
- }
- output_file = new File( cla.getOptionValue( surfacing_old.OUTPUT_FILE_OPTION ) );
- SurfacingUtil.checkForOutputFileWriteability( output_file );
- }
- File cutoff_scores_file = null;
- Map<String, String> individual_domain_score_cutoffs = null;
- if ( cla.isOptionSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for individual domain score cutoffs file: -"
- + surfacing_old.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
- }
- cutoff_scores_file = new File( cla.getOptionValue( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) );
- final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read individual domain score cutoffs file: "
- + error );
- }
- try {
- final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
- individual_domain_score_cutoffs = scores_table.getColumnsAsMap( 0, 1 );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "cannot read from individual domain score cutoffs file: " + e );
- }
- }
- BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
- if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
- dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
- }
- if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
- dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
- }
- File out_dir = null;
- if ( cla.isOptionSet( surfacing_old.OUTPUT_DIR_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_DIR_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for output directory: -"
- + surfacing_old.OUTPUT_DIR_OPTION + "=<dir>" );
- }
- out_dir = new File( cla.getOptionValue( surfacing_old.OUTPUT_DIR_OPTION ) );
- if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
- ForesterUtil.fatalError( surfacing_old.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_old.PRG_NAME, "failed to create \"" + out_dir + "\"" );
- }
- }
- if ( !out_dir.canWrite() ) {
- ForesterUtil.fatalError( surfacing_old.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_old.FILTER_NEGATIVE_OPTION )
- && cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
- ForesterUtil
- .fatalError( surfacing_old.PRG_NAME, "attempt to use both negative and positive protein filter" );
- }
- if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION )
- && ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) || cla
- .isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) ) {
- ForesterUtil
- .fatalError( surfacing_old.PRG_NAME,
- "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
- }
- if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative filter: -"
- + surfacing_old.FILTER_NEGATIVE_OPTION + "=<file>" );
- }
- negative_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( negative_filter_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
- + msg );
- }
- }
- else if ( cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for positive filter: -"
- + surfacing_old.FILTER_POSITIVE_OPTION + "=<file>" );
- }
- positive_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_POSITIVE_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( positive_filter_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
- + msg );
- }
- }
- else if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative domains filter: -"
- + surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
- }
- negative_domains_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_domains_filter_file
- + "\": " + msg );
- }
- }
- final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
- final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
- final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
- final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
- processPlusMinusAnalysisOption( cla,
- 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_old.INPUT_FILES_FROM_FILE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input files file: -"
- + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
- }
- input_files_file = new File( cla.getOptionValue( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( input_files_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing_old.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_old.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_old.PRG_NAME,
- "No hmmpfam output file indicated is input: use comand line directly or "
- + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
- }
- DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
- if ( cla.isOptionSet( surfacing_old.SCORING_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.SCORING_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no value for scoring method for domain combinations similarity calculation: -"
- + surfacing_old.SCORING_OPTION + "=<"
- + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|"
- + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|"
- + surfacing_old.SCORING_COMBINATION_BASED + ">\"" );
- }
- final String scoring_str = cla.getOptionValue( surfacing_old.SCORING_OPTION );
- if ( scoring_str.equals( surfacing_old.SCORING_DOMAIN_COUNT_BASED ) ) {
- scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
- }
- else if ( scoring_str.equals( surfacing_old.SCORING_COMBINATION_BASED ) ) {
- scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
- }
- else if ( scoring_str.equals( surfacing_old.SCORING_PROTEIN_COUNT_BASED ) ) {
- scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
- }
- else {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + scoring_str
- + "\" for scoring method for domain combinations similarity calculation: \"-"
- + surfacing_old.SCORING_OPTION + "=<" + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|"
- + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing_old.SCORING_COMBINATION_BASED
- + ">\"" );
- }
- }
- boolean sort_by_species_count_first = false;
- if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
- sort_by_species_count_first = true;
- }
- boolean species_matrix = false;
- if ( cla.isOptionSet( surfacing_old.SPECIES_MATRIX_OPTION ) ) {
- species_matrix = true;
- }
- boolean output_protein_lists_for_all_domains = false;
- if ( cla.isOptionSet( surfacing_old.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
- output_protein_lists_for_all_domains = true;
- }
- Detailedness detailedness = DETAILEDNESS_DEFAULT;
- if ( cla.isOptionSet( surfacing_old.DETAILEDNESS_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.DETAILEDNESS_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for -" + surfacing_old.DETAILEDNESS_OPTION
- + "=<" + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|"
- + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" );
- }
- final String detness = cla.getOptionValue( surfacing_old.DETAILEDNESS_OPTION ).toLowerCase();
- if ( detness.equals( surfacing_old.DETAILEDNESS_BASIC ) ) {
- detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
- }
- else if ( detness.equals( surfacing_old.DETAILEDNESS_LIST_IDS ) ) {
- detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
- }
- else if ( detness.equals( surfacing_old.DETAILEDNESS_PUNCTILIOUS ) ) {
- detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
- }
- else {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + detness
- + "\" for detailedness: \"-" + surfacing_old.DETAILEDNESS_OPTION + "=<"
- + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|"
- + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" );
- }
- }
- String automated_pairwise_comparison_suffix = null;
- boolean perform_pwc = false;
- boolean write_pwc_files = false;
- if ( cla.isOptionSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
- perform_pwc = true;
- if ( !cla.isOptionValueSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
- write_pwc_files = false;
- }
- else {
- write_pwc_files = true;
- automated_pairwise_comparison_suffix = "_"
- + cla.getOptionValue( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
- }
- }
- String query_domain_ids = null;
- if ( cla.isOptionSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) {
- ForesterUtil
- .fatalError( surfacing_old.PRG_NAME,
- "no domain ids given for sequences with given domains to be extracted : -"
- + surfacing_old.SEQ_EXTRACT_OPTION
- + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
- }
- query_domain_ids = cla.getOptionValue( surfacing_old.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_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no value for domain combinations similarities sorting: -"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
- }
- final String sort_str = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
- if ( sort_str.equals( surfacing_old.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_old.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_old.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_old.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_old.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_old.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_old.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_old.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_old.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_old.PRG_NAME, "unknown value \"" + sort_str
- + "\" for domain combinations similarities sorting: \"-"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX
- + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF
- + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
- + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
- }
- }
- PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
- if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for print option: -"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
- }
- final String sort = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
- if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
- domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
- }
- else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
- // domain_similarity_print_option =
- // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "simple HTML output not implemented yet :(" );
- }
- else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
- domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
- }
- else {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
- + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
- }
- }
- GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
- if ( cla.isOptionSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for sorting of domain counts: -"
- + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
- }
- final String sort = cla.getOptionValue( surfacing_old.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
- if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_ALPHA ) ) {
- dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
- }
- else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
- dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
- }
- else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
- dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
- }
- else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
- dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
- }
- else {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort
- + "\" for sorting of domain counts: \"-" + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<"
- + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
- + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
- }
- }
- String[][] input_file_properties = null;
- if ( input_file_names_from_file != null ) {
- input_file_properties = surfacing_old.processInputFileNames( input_file_names_from_file );
- }
- else {
- input_file_properties = surfacing_old.processInputFileNames( cla.getNames() );
- }
- final int number_of_genomes = input_file_properties.length;
- if ( number_of_genomes < 2 ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot analyze less than two files" );
- }
- if ( ( number_of_genomes < 3 ) && perform_pwc ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use : -"
- + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- + "=<suffix> 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_old.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<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
- int domain_id_to_go_ids_count = 0;
- if ( cla.isOptionSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for Pfam to GO mapping file: -"
- + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
- }
- pfam_to_go_file = new File( cla.getOptionValue( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) );
- final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
- }
- try {
- final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
- final List<PfamToGoMapping> 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_old.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_old.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
- }
- }
- File go_obo_file = null;
- List<GoTerm> go_terms = null;
- if ( cla.isOptionSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO OBO file: -"
- + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>" );
- }
- if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO OBO file (-"
- + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
- + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
- }
- go_obo_file = new File( cla.getOptionValue( surfacing_old.GO_OBO_FILE_USE_OPTION ) );
- final String error = ForesterUtil.isReadableFile( go_obo_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing_old.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_old.PRG_NAME,
- "parser.getGoTermCount() != go_terms.size()" );
- }
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "cannot read from GO OBO file: " + e.getLocalizedMessage() );
- }
- }
- Map<GoId, GoTerm> 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_old.GO_NAMESPACE_LIMIT_OPTION ) ) {
- if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO namespace limit (-"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
- + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
- + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>)" );
- }
- if ( !cla.isOptionValueSet( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO namespace limit: \"-"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
- }
- final String go_namespace_limit_str = cla.getOptionValue( surfacing_old.GO_NAMESPACE_LIMIT_OPTION )
- .toLowerCase();
- if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
- go_namespace_limit = GoNameSpace.createMolecularFunction();
- }
- else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
- go_namespace_limit = GoNameSpace.createBiologicalProcess();
- }
- else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
- go_namespace_limit = GoNameSpace.createCellularComponent();
- }
- else {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + go_namespace_limit_str
- + "\" for GO namespace limit: \"-" + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
- + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
- + surfacing_old.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_old.JACKNIFE_OPTION ) ) {
- if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use jacknife resampling analysis (-"
- + surfacing_old.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
- + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- + "=<suffix for pairwise comparison output files>)" );
- }
- jacknifed_distances = true;
- if ( cla.isOptionHasAValue( surfacing_old.JACKNIFE_OPTION ) ) {
- try {
- jacknife_resamplings = cla.getOptionValueAsInt( surfacing_old.JACKNIFE_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for number of resamplings" );
- }
- if ( jacknife_resamplings < 2 ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "attempt to use less than 2 resamplings" );
- }
- }
- if ( cla.isOptionSet( surfacing_old.JACKNIFE_RATIO_OPTION )
- && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RATIO_OPTION ) ) {
- try {
- jacknife_ratio = cla.getOptionValueAsDouble( surfacing_old.JACKNIFE_RATIO_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for jacknife ratio" );
- }
- if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "attempt to use illegal value for jacknife ratio: " + jacknife_ratio );
- }
- }
- if ( cla.isOptionSet( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION )
- && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION ) ) {
- try {
- random_seed = cla.getOptionValueAsLong( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.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
- // + "=<suffix for pairwise comparison output files>)" );
- // }
- // infer_species_trees = true;
- // }
- File[] intree_files = null;
- Phylogeny[] intrees = null;
- if ( cla.isOptionSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) {
- // TODO FIXME if jacknife.... maybe not
- if ( number_of_genomes < 3 ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "cannot infer gains and losses on input species trees (-"
- + surfacing_old.INPUT_SPECIES_TREE_OPTION
- + " without pairwise analyses ("
- + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- + "=<suffix for pairwise comparison output files>)" );
- }
- if ( !cla.isOptionValueSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input tree: -"
- + surfacing_old.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
- }
- final String intrees_str = cla.getOptionValue( surfacing_old.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_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for random number seed: -"
- + surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
- }
- try {
- random_number_seed_for_fitch_parsimony = cla
- .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
- }
- radomize_fitch_parsimony = true;
- }
- SortedSet<DomainId> filter = null;
- if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
- || ( negative_domains_filter_file != null ) ) {
- filter = new TreeSet<DomainId>();
- 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<DomainId, Set<String>>[] 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_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for secondary features map file: -"
- + surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
- }
- final String[] secondary_features_map_files_strs = cla
- .getOptionValue( surfacing_old.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_old.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_old.PRG_NAME,
- "cannot read secondary features map file: " + e.getMessage() );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "problem with contents of features map file ["
- + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
- }
- i++;
- }
- }
- if ( out_dir == null ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no output directory indicated (-"
- + surfacing_old.OUTPUT_DIR_OPTION + "=<dir>)" );
- }
- if ( output_file == null ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no name for (main) output file indicated (-"
- + surfacing_old.OUTPUT_FILE_OPTION + "=<file>)" );
- }
- if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
- + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
- }
- if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
- + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>)" );
- }
- boolean display_histograms = false;
- if ( cla.isOptionSet( surfacing_old.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( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
- + input_file_names_from_file.length + " input files]</td></tr>" + 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( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
- + " domain ids]</td></tr>" + 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( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
- + " domain ids]</td></tr>" + 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( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
- + filter_size + " domain ids]</td></tr>" + 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( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
- + "</td></tr>" + nl );
- }
- if ( cutoff_scores_file != null ) {
- System.out.println( "Cutoff scores file : " + cutoff_scores_file );
- html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
- }
- if ( e_value_max >= 0.0 ) {
- System.out.println( "E-value maximum (inclusive) : " + e_value_max );
- html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + 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( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
- + ignore_virus_like_ids + "</td></tr>" + nl );
- }
- html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
- if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) {
- System.out.println( "Max allowed domain overlap : " + max_allowed_overlap );
- html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
- }
- if ( no_engulfing_overlaps ) {
- System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps );
- html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
- + "</td></tr>" + nl );
- }
- System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec );
- html_desc
- .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
- + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
- System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
- html_desc
- .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
- + ignore_species_specific_domains + "</td></tr>" + nl );
- System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
- html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
- + ignore_combination_with_same + "</td></tr>" + nl );
- ;
- System.out.println( "Consider directedness : "
- + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
- html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
- + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
- if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
- System.out.println( "Consider adjacency : "
- + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
- html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
- + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
- + 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_old.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( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
- + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
- }
- if ( go_terms != null ) {
- System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" );
- html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
- + "</td></tr>" + nl );
- }
- if ( go_namespace_limit != null ) {
- System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() );
- html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
- }
- if ( perform_pwc ) {
- System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix );
- html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
- + "</td></tr>" + 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( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
- }
- System.out.println( "Write similarities to : " + output_file );
- System.out.print( " Scoring method : " );
- html_desc.append( "<tr><td>Scoring method:</td><td>" );
- switch ( scoring ) {
- case COMBINATIONS:
- System.out.println( "domain combinations based" );
- html_desc.append( "domain combinations based" + "</td></tr>" + nl );
- break;
- case DOMAINS:
- System.out.println( "domain counts based" );
- html_desc.append( "domain counts based" + "</td></tr>" + nl );
- break;
- case PROTEINS:
- System.out.println( "domain proteins counts based" );
- html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
- break;
- default:
- ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for scoring" );
- }
- System.out.print( " Sort by : " );
- html_desc.append( "<tr><td>Sort by:</td><td>" );
- 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_old.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( "</td></tr>" + 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_old.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_old.PRG_NAME, "unknown value for print option" );
- }
- System.out.print( " Species matrix : " + species_matrix );
- System.out.println();
- if ( perform_pwc ) {
- System.out.println( "Pairwise comparisons: " );
- html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
- System.out.print( " Sort by : " );
- html_desc.append( "<tr><td>Sort by:</td><td>" );
- 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_old.PRG_NAME,
- "unknown value for sorting for similarities" );
- }
- System.out.println();
- html_desc.append( "</td></tr>" + nl );
- if ( jacknifed_distances ) {
- html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
- html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
- + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + 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( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
- // System.out.println( " Infer species trees : true" );
- // }
- if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
- for( final File intree_file : intree_files ) {
- html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
- + "</td></tr>" + nl );
- System.out.println( " Intree for gain/loss pars.: " + intree_file );
- }
- }
- if ( radomize_fitch_parsimony ) {
- html_desc.append( "<tr><td> Random number seed for Fitch parsimony analysis:</td><td>"
- + random_number_seed_for_fitch_parsimony + "</td></tr>" + 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( "<tr><td>Secondary features map file:</td><td>"
- + secondary_features_map_files[ i ] + "</td></tr>" + 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( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
- System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
- BufferedWriter[] query_domains_writer_ary = null;
- List<DomainId>[] 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<DomainId> query = new ArrayList<DomainId>();
- 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_old.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_old.PRG_NAME, "Could not open [" + protein_names_writer_str
- + "]: " + e.getLocalizedMessage() );
- }
- }
- }
- SortedMap<Species, List<Protein>> 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<Species, List<Protein>>();
- }
- final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
- final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
- final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
- List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
- List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
- if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
- all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
- all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
- }
- 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_old.PRG_NAME, e2.getMessage() );
- }
- for( int i = 0; i < number_of_genomes; ++i ) {
- System.out.println();
- System.out.println( ( i + 1 ) + "/" + number_of_genomes );
- System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
- HmmPfamOutputParser parser = null;
- if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
- || ( negative_domains_filter_file != null ) ) {
- HmmPfamOutputParser.FilterType filter_type = HmmPfamOutputParser.FilterType.NONE;
- if ( positive_filter_file != null ) {
- filter_type = HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN;
- }
- else if ( negative_filter_file != null ) {
- filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN;
- }
- else if ( negative_domains_filter_file != null ) {
- filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN;
- }
- parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
- input_file_properties[ i ][ 1 ],
- input_file_properties[ i ][ 2 ],
- filter,
- filter_type );
- }
- else {
- parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
- input_file_properties[ i ][ 1 ],
- input_file_properties[ i ][ 2 ] );
- }
- 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_old.MAX_ALLOWED_OVERLAP_DEFAULT ) {
- parser.setMaxAllowedOverlap( max_allowed_overlap );
- }
- parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
- if ( individual_domain_score_cutoffs != null ) {
- parser.setIndividualDomainScoreCutoffs( individual_domain_score_cutoffs );
- }
- parser.setAllowNonUniqueQuery( ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT );
- parser.setVerbose( VERBOSE_DEFAULT );
- List<Protein> protein_list = null;
- try {
- protein_list = parser.parse();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
- }
- catch ( final Exception e ) {
- ForesterUtil.unexpectedFatalError( surfacing_old.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() );
- System.out.println( "Number of proteins stored : " + protein_list.size() );
- System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
- System.out.println( "Domains stored : " + parser.getDomainsStored() );
- System.out.println( "Distinct domains stored : "
- + parser.getDomainsStoredSet().size() );
- System.out.println( "Domains ignored due to individual score cutoffs: "
- + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
- System.out.println( "Domains ignored due to E-value : "
- + parser.getDomainsIgnoredDueToEval() );
- System.out.println( "Domains ignored due to DUF designation : "
- + parser.getDomainsIgnoredDueToDuf() );
- if ( ignore_virus_like_ids ) {
- System.out.println( "Domains ignored due virus like ids : "
- + parser.getDomainsIgnoredDueToVirusLikeIds() );
- }
- System.out.println( "Domains ignored due negative domain filter : "
- + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
- System.out.println( "Domains ignored due to overlap : "
- + parser.getDomainsIgnoredDueToOverlap() );
- if ( negative_filter_file != null ) {
- System.out.println( "Proteins ignored due to negative filter : "
- + parser.getProteinsIgnoredDueToFilter() );
- }
- if ( positive_filter_file != null ) {
- System.out.println( "Proteins ignored due to positive filter : "
- + parser.getProteinsIgnoredDueToFilter() );
- }
- System.out.println( "Time for processing : " + parser.getTime() + "ms" );
- html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
- + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>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( "</td></tr>" + nl );
- // domain_partner_counts_array[ i ] =
- // Methods.getDomainPartnerCounts( protein_domain_collections_array[
- // i ],
- // false, input_file_properties[ i ][ 1 ] );
- 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 );
- }
- System.gc();
- } // for( int i = 0; i < number_of_hmmpfam_files_to_analyze; ++i ) {
- try {
- per_genome_domain_promiscuity_statistics_writer.flush();
- per_genome_domain_promiscuity_statistics_writer.close();
- }
- catch ( final IOException e2 ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e2.toString() );
- }
- 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_old.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_old.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_old.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<DomainSimilarity> 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> species_order = null;
- if ( species_matrix ) {
- species_order = new ArrayList<Species>();
- for( int i = 0; i < number_of_genomes; i++ ) {
- species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
- }
- }
- html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
- + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
- + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Analysis date/time:</td><td>"
- + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
- + "</td></tr>" + nl );
- html_desc.append( "</table>" + 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_old.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_old.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<Phylogeny> 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_old.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
- surfacing_old.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_old.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getDomainDistanceScoresMeans() );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file
- + surfacing_old.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedBinaryCombinationsBasedDistances() );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file
- + surfacing_old.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedDomainsBasedDistances() );
- final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
- + surfacing_old.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getDomainDistanceScoresMeans().get( 0 ) );
- final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
- + surfacing_old.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_old.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
- .getSharedDomainsBasedDistances().get( 0 ) );
- inferred_trees = new ArrayList<Phylogeny>();
- inferred_trees.add( nj_gd );
- inferred_trees.add( nj_bc );
- inferred_trees.add( nj_d );
- // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
- // if ( infer_species_trees ) {
- // inferred_trees = new ArrayList<Phylogeny>();
- // final List<Phylogeny> inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
- // .getSharedBinaryCombinationsBasedDistances() );
- // final List<Phylogeny> 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_old.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_old.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<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
- // 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<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
- final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
- 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_old.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_old.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_old.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_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
- + "] is not unique in input tree " + intree.getName() );
- }
- genomes[ i ] = input_file_properties[ i ][ 1 ];
- }
- PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
- 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_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
- + "] not present/not unique in input tree" );
- }
- }
- }
-
- // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
- // final SortedMap<String, CombinableDomains> map ) {
- // final StringBuffer sb = new StringBuffer();
- // for( final Iterator<String> 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_old.PRG_NAME
- + " [options] <phylogen(y|ies) infile> [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_old.DETAILEDNESS_OPTION
- + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" );
- System.out.println( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION
- + ": to ignore combinations with self (default: not to ignore)" );
- System.out
- .println( surfacing_old.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_old.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_old.NOT_IGNORE_DUFS_OPTION
- + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
- System.out
- .println( surfacing_old.IGNORE_VIRAL_IDS
- + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
- System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
- + DOMAIN_SORT_FILD_DEFAULT + ")" );
- System.out.println( surfacing_old.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
- System.out.println( surfacing_old.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
- System.out.println( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
- System.out
- .println( surfacing_old.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
- System.out.println( surfacing_old.SPECIES_MATRIX_OPTION + ": species matrix" );
- System.out.println( surfacing_old.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
- System.out.println( surfacing_old.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
- + DOMAINS_SORT_ORDER_DEFAULT + ")" );
- System.out.println( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
- + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
- System.out.println( surfacing_old.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
- System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
- + ": sort by species count first" );
- System.out.println( surfacing_old.OUTPUT_DIR_OPTION + ": output directory" );
- System.out.println( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
- System.out.println( surfacing_old.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
- System.out.println( surfacing_old.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
- System.out.println( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
- System.out.println( surfacing_old.INPUT_SPECIES_TREE_OPTION
- + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
- System.out.println( surfacing_old.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_old.INPUT_SPECIES_TREE_OPTION
- + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
- System.out.println( surfacing_old.FILTER_POSITIVE_OPTION
- + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
- System.out.println( surfacing_old.FILTER_NEGATIVE_OPTION
- + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
- System.out.println( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION
- + "=<file>: to filter out (ignore) domains listed in <file>" );
- System.out.println( surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
- System.out
- .println( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
- + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
- System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
- + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
- System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
- + ": to consider directedness and adjacency in binary combinations" );
- System.out
- .println( surfacing_old.SEQ_EXTRACT_OPTION
- + "=<domain ids (Pfam names)>: 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_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
- + "=<file>: to perfom parsimony analysis on secondary features" );
- System.out.println( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
- System.out.println( surfacing_old.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
- + ": to output binary domain combinations for (downstream) graph analysis" );
- System.out.println( surfacing_old.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<DomainId> filter ) {
- SortedSet<String> filter_str = null;
- try {
- filter_str = ForesterUtil.file2set( filter_file );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.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[ 3 ];
- input_file_properties[ i ][ 0 ] = names[ i ];
- input_file_properties[ i ][ 1 ] = names[ i ];
- input_file_properties[ i ][ 2 ] = DEFAULT_SEARCH_PARAMETER;
- }
- else {
- input_file_properties[ i ] = names[ i ].split( surfacing_old.SEPARATOR_FOR_INPUT_VALUES + "" );
- if ( input_file_properties[ i ].length != 3 ) {
- ForesterUtil
- .fatalError( surfacing_old.PRG_NAME,
- "properties for the input files (hmmpfam output) are expected "
- + "to be in the following format \"<hmmpfam output file>#<species>#<search"
- + " parameter>\" (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_old.PRG_NAME, error );
- }
- }
- return input_file_properties;
- }
-
- private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
- final List<String> high_copy_base,
- final List<String> high_copy_target,
- final List<String> low_copy,
- final List<Object> numbers ) {
- if ( cla.isOptionSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for 'plus-minus' file: -"
- + surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
- }
- final File plus_minus_file = new File( cla.getOptionValue( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( plus_minus_file );
- if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + plus_minus_file + "\": "
- + msg );
- }
- processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
- }
- }
-
- // First numbers is minimal difference, second is factor.
- private static void processPlusMinusFile( final File plus_minus_file,
- final List<String> high_copy_base,
- final List<String> high_copy_target,
- final List<String> low_copy,
- final List<Object> numbers ) {
- Set<String> species_set = null;
- int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
- double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
- try {
- species_set = ForesterUtil.file2set( plus_minus_file );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.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_old.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_old.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_old.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_old.PRG_NAME,
- "could not parse integer value for minimal difference from: \""
- + species.substring( 3 ) + "\"" );
- }
- }
- else if ( species.startsWith( "$F" ) ) {
- try {
- factor = Double.parseDouble( species.substring( 3 ) );
- }
- catch ( final NumberFormatException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME,
- "could not parse double value for factor from: \""
- + species.substring( 3 ) + "\"" );
- }
- }
- else if ( species.startsWith( "#" ) ) {
- // Comment, ignore.
- }
- else {
- ForesterUtil
- .fatalError( surfacing_old.PRG_NAME,
- "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
- + species + "\"" );
- }
- numbers.add( new Integer( min_diff + "" ) );
- numbers.add( new Double( factor + "" ) );
- }
- }
- else {
- ForesterUtil.fatalError( surfacing_old.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<DomainId> filter,
- final List<GenomeWideCombinableDomains> gwcd_list ) {
- try {
- SurfacingUtil
- .writeMatrixToFile( DomainParsimonyCalculator
- .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
- : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
- SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
- .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
- + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
- }
- }
-
- private static void writeProteinListsForAllSpecies( final File output_dir,
- final SortedMap<Species, List<Protein>> protein_lists_per_species,
- final List<GenomeWideCombinableDomains> gwcd_list ) {
- final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
- 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_old.PRG_NAME, e.getLocalizedMessage() );
- }
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
- }
- }
-}
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.forester.application.surfacing_old;
+import org.forester.application.surfacing;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
public static void checkForOutputFileWriteability( final File outfile ) {
final String error = ForesterUtil.isWritableFile( outfile );
if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
}
}
domain_parsimony.executeDolloParsimonyOnDomainPresence();
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.LOSS,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
- SurfacingUtil
- .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
//HTML:
writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
go_id_to_term_map,
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Gains | Domains",
false,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Losses | Domains",
false,
domain_parsimony.getGainLossMatrix(),
null,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
sep,
ForesterUtil.LINE_SEPARATOR,
"Dollo Parsimony | Present | Domains",
"dollo_on_domains_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing_old.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
try {
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
}
catch ( final IOException e ) {
e.printStackTrace();
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
// FITCH DOMAIN COMBINATIONS
domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
- SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- null );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
- CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+ CharacterStateMatrix.GainLossStates.GAIN,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.LOSS,
+ outfile_name
+ + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
+ + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
if ( all_binary_domains_combination_gained_fitch != null ) {
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
dc_type,
.getGainLossMatrix(),
null,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
+ + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
sep,
ForesterUtil.LINE_SEPARATOR,
BinaryDomainCombination.OutputFormat.DOT );
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Gains | Domain Combinations",
true,
domain_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Losses | Domain Combinations",
true,
domain_parsimony.getGainLossMatrix(),
null,
- outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
+ outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
sep,
ForesterUtil.LINE_SEPARATOR,
"Fitch Parsimony | Present | Domain Combinations",
go_id_to_term_map,
outfile_name,
all_pfams_encountered );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX,
- all_pfams_gained_as_domains );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
all_pfams_gained_as_dom_combinations );
- writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DC_SUFFIX,
- all_pfams_lost_as_dom_combinations );
+ writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
"fitch_on_binary_domain_combinations_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
- + surfacing_old.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+ + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+ calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name
+ + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX );
+ }
+ }
+
+ private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
+ final String outfilename_for_counts,
+ final String outfilename_for_dc ) {
+ try {
+ final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
+ final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
+ final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
+ for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
+ for( final String dc : gained_dc ) {
+ if ( dc_gain_counts.containsKey( dc ) ) {
+ dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
+ }
+ else {
+ dc_gain_counts.put( dc, 1 );
+ }
+ }
+ }
+ final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
+ final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
+ final Set<String> dcs = dc_gain_counts.keySet();
+ for( final String dc : dcs ) {
+ final int count = dc_gain_counts.get( dc );
+ if ( histogram.containsKey( count ) ) {
+ histogram.put( count, histogram.get( count ) + 1 );
+ domain_lists.put( count, domain_lists.get( count ).append( ", " + dc ) );
+ }
+ else {
+ histogram.put( count, 1 );
+ domain_lists.put( count, new StringBuilder( dc ) );
+ }
+ }
+ final Set<Integer> histogram_keys = histogram.keySet();
+ for( final Integer histogram_key : histogram_keys ) {
+ final int count = histogram.get( histogram_key );
+ final StringBuilder dc = domain_lists.get( histogram_key );
+ out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
+ }
+ out_counts.close();
+ out_dc.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
+ + outfilename_for_counts + "]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
+ + outfilename_for_dc + "]" );
}
public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
System.out.println();
- writeToNexus( outfile_name + surfacing_old.NEXUS_SECONDARY_FEATURES,
+ writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
phylogeny );
final Phylogeny local_phylogeny_copy = phylogeny.copy();
secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+ + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
SurfacingUtil
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.GAIN,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
CharacterStateMatrix.GainLossStates.LOSS,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
.writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
null,
outfile_name
- + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
+ + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
sep,
ForesterUtil.LINE_SEPARATOR,
null );
"dollo_on_secondary_features_" + outfile_name,
parameters_str );
SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
- + surfacing_old.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+ + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
}
public static void extractProteinNames( final List<Protein> proteins,
if ( !get_gains ) {
state = CharacterStateMatrix.GainLossStates.LOSS;
}
- final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
+ final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
false,
state,
outdir );
final Map<GoId, GoTerm> go_id_to_term_map,
final String outfile_name,
final SortedSet<String> all_pfams_encountered ) {
- final File all_pfams_encountered_file = new File( outfile_name + surfacing_old.ALL_PFAMS_ENCOUNTERED_SUFFIX );
+ final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
- + surfacing_old.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
- final File encountered_pfams_summary_file = new File( outfile_name
- + surfacing_old.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
+ + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
+ final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
int biological_process_counter = 0;
int cellular_component_counter = 0;
int molecular_function_counter = 0;
}
all_pfams_encountered_writer.close();
all_pfams_encountered_with_go_annotation_writer.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
+ "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+ "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
+ "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote summary (including all ["
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
+ pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
+ encountered_pfams_summary_file + "\"" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Sum of Pfams encountered : "
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : "
+ all_pfams_encountered.size() );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without a mapping : "
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
+ pfams_without_mappings_counter + " ["
+ ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
"Pfams with a mapping : " + pfams_with_mappings_counter
+ " ["
+ ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
+ "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ pfams_with_mappings_to_bp_or_mf_counter + " ["
+ ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
"Pfams with mapping to biological process: " + biological_process_counter
+ " ["
+ ( 100 * biological_process_counter / all_pfams_encountered.size() )
+ "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
"Pfams with mapping to molecular function: " + molecular_function_counter
+ " ["
+ ( 100 * molecular_function_counter / all_pfams_encountered.size() )
+ "%]" );
- ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
"Pfams with mapping to cellular component: " + cellular_component_counter
+ " ["
+ ( 100 * cellular_component_counter / all_pfams_encountered.size() )
summary_writer.close();
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
}
final int i,
final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
- + surfacing_old.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
+ + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
if ( output_dir != null ) {
dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
}
out_dot.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote binary domain combination for \""
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
}
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
out.write( character_separator );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
}
try {
final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
+ final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
domain_combinations,
state,
filename );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
- + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
}
public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
}
try {
final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
+ final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
domain_combinations,
state,
filename );
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
- + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
}
public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
final int i,
final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
File dc_outfile = new File( input_file_properties[ i ][ 0 ]
- + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
if ( output_dir != null ) {
dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
}
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
try {
per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
if ( input_file_properties[ i ].length == 3 ) {
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+ input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
}
else {
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+ input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+ dc_outfile + "\"" );
}
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
}
public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
out.close();
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
}
private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
writer.write( ForesterUtil.LINE_SEPARATOR );
}
writer.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
+ "]" );
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
}
}
writer.toPhyloXML( new File( filename ), phylogeny, 1 );
}
catch ( final IOException e ) {
- ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "failed to write phylogeny to \"" + filename
- + "\": " + e );
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
+ + e );
}
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
}
public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
my_matrix.writeNexusBinaryChractersBlock( w );
w.flush();
w.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
}
PhylogenyWriter.writeNexusTreesBlock( w, phylogenies );
w.flush();
w.close();
- ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
}
private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony ) {
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
domain_parsimony.createMatrixOfDomainPresenceOrAbsence() );
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence() );
}
private static void writeToNexus( final String outfile_name,
final DomainParsimonyCalculator domain_parsimony,
final Phylogeny phylogeny ) {
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
phylogeny );
- writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
+ writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
phylogeny );
}
git://source.jalview.org / jalview.git / commitdiff