// $Id: surfacing.java,v 1.165 2010/09/29 23:50:17 cmzmasek Exp $
//
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.application;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
import org.forester.go.GoUtils;
import org.forester.go.OBOparser;
import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.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.DomainSimilarityCalculator;
import org.forester.surfacing.GenomeWideCombinableDomains;
import org.forester.surfacing.MappingResults;
import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
import org.forester.surfacing.PairwiseGenomeComparator;
import org.forester.surfacing.PrintableDomainSimilarity;
import org.forester.surfacing.Protein;
import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
import org.forester.surfacing.Species;
import org.forester.surfacing.SurfacingUtil;
import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public class surfacing {
public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out";
public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot";
public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc";
// gain/loss:
public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d";
public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc";
public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d";
public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc";
// gain/loss counts:
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d";
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc";
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d";
public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc";
// tables:
public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d";
public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d";
public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex";
public final static String BDC_PRESENT_NEXUS = "_dc.nex";
// ---
public final static String PRG_NAME = "surfacing";
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
+ ForesterConstants.PHYLO_XML_SUFFIX;
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
+ ForesterConstants.PHYLO_XML_SUFFIX;
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
+ ForesterConstants.PHYLO_XML_SUFFIX;
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
+ ForesterConstants.PHYLO_XML_SUFFIX;
public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ ForesterConstants.PHYLO_XML_SUFFIX;
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
final static private String HELP_OPTION_1 = "help";
final static private String HELP_OPTION_2 = "h";
final static private String OUTPUT_DIR_OPTION = "out_dir";
final static private String SCORING_OPTION = "scoring";
private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
final static private String SCORING_COMBINATION_BASED = "combinations";
final static private String DETAILEDNESS_OPTION = "detail";
private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
final static private String SPECIES_MATRIX_OPTION = "smatrix";
final static private String DETAILEDNESS_BASIC = "basic";
final static private String DETAILEDNESS_LIST_IDS = "list_ids";
final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
final static private String MAX_E_VALUE_OPTION = "e";
final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
final static private String OUTPUT_FILE_OPTION = "o";
final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
final static private String GO_OBO_FILE_USE_OPTION = "obo";
final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML;
final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
// final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
final static private String JACKNIFE_OPTION = "jack";
final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
//final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh";
final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh";
final static private String FILTER_POSITIVE_OPTION = "pos_filter";
final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
final static private String PRG_VERSION = "2.002";
final static private String PRG_DATE = "2010.07.27";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
final static private double MAX_E_VALUE_DEFAULT = -1;
final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
final static private String DEFAULT_SEARCH_PARAMETER = "ls";
final private static boolean VERBOSE_DEFAULT = true;
private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
private static final String SEQ_EXTRACT_SUFFIX = ".prot";
private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
private static final boolean VERBOSE = false;
private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true;
public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
private static final String LOG_FILE_SUFFIX = "_log.txt";
private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
// final String error = ForesterUtil.isReadableFile( new File(
// input_file_properties[ i ][ 0 ] ) );
// if ( !ForesterUtil.isEmpty( error ) ) {
// ForesterUtil.fatalError( surfacing.PRG_NAME, error );
// }
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
final String automated_pairwise_comparison_suffix,
final File outdir ) {
for( int i = 0; i < input_file_properties.length; ++i ) {
for( int j = 0; j < i; ++j ) {
final String species_i = input_file_properties[ i ][ 1 ];
final String species_j = input_file_properties[ j ][ 1 ];
String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
+ species_j + automated_pairwise_comparison_suffix;
switch ( domain_similarity_print_option ) {
case HTML:
if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
pairwise_similarities_output_file_str += ".html";
}
break;
}
final String error = ForesterUtil
.isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+ ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, error );
}
}
}
}
private static StringBuilder createParametersAsString( final boolean ignore_dufs,
final double e_value_max,
final int max_allowed_overlap,
final boolean no_engulfing_overlaps,
final File cutoff_scores_file,
final BinaryDomainCombination.DomainCombinationType dc_type ) {
final StringBuilder parameters_sb = new StringBuilder();
parameters_sb.append( "E-value: " + e_value_max );
if ( cutoff_scores_file != null ) {
parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
}
else {
parameters_sb.append( ", Cutoff-scores-file: not-set" );
}
if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
}
else {
parameters_sb.append( ", Max-overlap: not-set" );
}
if ( no_engulfing_overlaps ) {
parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
}
else {
parameters_sb.append( ", Engulfing-overlaps: allowed" );
}
if ( ignore_dufs ) {
parameters_sb.append( ", Ignore-dufs: true" );
}
else {
parameters_sb.append( ", Ignore-dufs: false" );
}
parameters_sb.append( ", DC type (if applicable): " + dc_type );
return parameters_sb;
}
/**
* Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
*
*
* @param output_file
* @param all_bin_domain_combinations_changed
* @param sum_of_all_domains_encountered
* @param all_bin_domain_combinations_encountered
* @param is_gains_analysis
* @throws IOException
*/
private static void executeFitchGainsAnalysis( final File output_file,
final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
final int sum_of_all_domains_encountered,
final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
final boolean is_gains_analysis ) throws IOException {
SurfacingUtil.checkForOutputFileWriteability( output_file );
final Writer out = ForesterUtil.createBufferedWriter( output_file );
final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
.listToSortedCountsMap( all_bin_domain_combinations_changed );
final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
int above_one = 0;
int one = 0;
for( final Object bdc_object : bdc_to_counts.keySet() ) {
final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
final int count = bdc_to_counts.get( bdc_object );
if ( count < 1 ) {
ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
}
out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
if ( count > 1 ) {
all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
above_one++;
}
else if ( count == 1 ) {
all_domains_in_combination_changed_only_once.add( bdc.getId0() );
all_domains_in_combination_changed_only_once.add( bdc.getId1() );
one++;
}
}
final int all = all_bin_domain_combinations_encountered.size();
int never_lost = -1;
if ( !is_gains_analysis ) {
all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
never_lost = all_bin_domain_combinations_encountered.size();
for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
}
}
if ( is_gains_analysis ) {
out.write( "Sum of all distinct domain combinations appearing once : " + one
+ ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
}
else {
out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domain combinations lost once : " + one
+ ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domains in combinations lost only once : "
+ all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
out.write( "Sum of all distinct domains in combinations lost more than once: "
+ all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
}
out.write( "All binary combinations : " + all
+ ForesterUtil.LINE_SEPARATOR );
out.write( "All domains : "
+ sum_of_all_domains_encountered );
out.close();
ForesterUtil.programMessage( surfacing.PRG_NAME,
"Wrote fitch domain combination dynamics counts analysis to \"" + output_file
+ "\"" );
}
private static void executePlusMinusAnalysis( final File output_file,
final List<String> plus_minus_analysis_high_copy_base,
final List<String> plus_minus_analysis_high_copy_target,
final List<String> plus_minus_analysis_low_copy,
final List<GenomeWideCombinableDomains> gwcd_list,
final SortedMap<Species, List<Protein>> protein_lists_per_species,
final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final List<Object> plus_minus_analysis_numbers ) {
final Set<String> all_spec = new HashSet<String>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
all_spec.add( gwcd.getSpecies().getSpeciesId() );
}
final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
final File proteins_file_base = new File( output_file + "" );
final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
try {
DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
protein_lists_per_species,
plus_minus_analysis_high_copy_base,
plus_minus_analysis_high_copy_target,
plus_minus_analysis_low_copy,
min_diff,
factor,
plain_out_dom,
html_out_dom,
html_out_dc,
domain_id_to_go_ids_map,
go_id_to_term_map,
all_domains_go_ids_out_dom,
passing_domains_go_ids_out_dom,
proteins_file_base );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ html_out_dom + "\"" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ plain_out_dom + "\"" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
+ "\"" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
+ passing_domains_go_ids_out_dom + "\"" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
+ all_domains_go_ids_out_dom + "\"" );
}
private static Phylogeny[] getIntrees( final File[] intree_files,
final int number_of_genomes,
final String[][] input_file_properties ) {
final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
int i = 0;
for( final File intree_file : intree_files ) {
Phylogeny intree = null;
final String error = ForesterUtil.isReadableFile( intree_file );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
+ error );
}
try {
final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
.create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
if ( p_array.length < 1 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ "] does not contain any phylogeny in phyloXML format" );
}
else if ( p_array.length > 1 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ "] contains more than one phylogeny in phyloXML format" );
}
intree = p_array[ 0 ];
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
+ "]: " + error );
}
if ( ( intree == null ) || intree.isEmpty() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
}
if ( !intree.isRooted() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
}
if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "number of external nodes ["
+ intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file
+ "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" );
}
final StringBuilder parent_names = new StringBuilder();
final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
if ( nodes_lacking_name > 0 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
+ nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
}
preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
if ( !intree.isCompletelyBinary() ) {
ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
+ "] is not completely binary" );
}
intrees[ i++ ] = intree;
}
return intrees;
}
private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
final NeighborJoining nj = NeighborJoining.createInstance();
final List<Phylogeny> phylogenies = nj.execute( distances_list );
final PhylogenyWriter w = new PhylogenyWriter();
try {
w.toNewHampshire( phylogenies, true, true, outfile, ";" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
}
return phylogenies;
}
private static void log( final String msg, final Writer w ) {
try {
w.write( msg );
w.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
}
}
public static void main( final String args[] ) {
final long start_time = new Date().getTime();
// final StringBuffer log = new StringBuffer();
final StringBuilder html_desc = new StringBuilder();
ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
surfacing.PRG_VERSION,
surfacing.PRG_DATE,
surfacing.E_MAIL,
surfacing.WWW );
final String nl = ForesterUtil.LINE_SEPARATOR;
html_desc.append( "<table>" + nl );
html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
CommandLineArguments cla = null;
try {
cla = new CommandLineArguments( args );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
surfacing.printHelp();
System.exit( 0 );
}
if ( ( args.length < 1 ) ) {
surfacing.printHelp();
System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
allowed_options.add( surfacing.DETAILEDNESS_OPTION );
allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
allowed_options.add( surfacing.SCORING_OPTION );
allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
allowed_options.add( surfacing.DISPLAY_M_HISTOGRAMS_OPTION );
allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
allowed_options.add( JACKNIFE_OPTION );
allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
allowed_options.add( JACKNIFE_RATIO_OPTION );
allowed_options.add( INPUT_SPECIES_TREE_OPTION );
//allowed_options.add( INFER_SPECIES_TREES_OPTION );
allowed_options.add( FILTER_POSITIVE_OPTION );
allowed_options.add( FILTER_NEGATIVE_OPTION );
allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
allowed_options.add( IGNORE_VIRAL_IDS );
allowed_options.add( SEQ_EXTRACT_OPTION );
allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
boolean output_binary_domain_combinationsfor_graph_analysis = false;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
output_binary_domain_combinationsfor_graph_analysis = true;
}
if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
try {
e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
}
}
if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
try {
max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
}
}
boolean no_engulfing_overlaps = false;
if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
no_engulfing_overlaps = true;
}
boolean ignore_virus_like_ids = false;
if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
ignore_virus_like_ids = true;
}
if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
ignore_dufs = false;
}
if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
ignore_combination_with_same = true;
}
boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
ignore_domains_without_combs_in_all_spec = true;
}
boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
ignore_species_specific_domains = true;
}
File output_file = null;
if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"no value for domain combinations similarities output file: -"
+ surfacing.OUTPUT_FILE_OPTION + "=<file>" );
}
output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
SurfacingUtil.checkForOutputFileWriteability( output_file );
}
File cutoff_scores_file = null;
Map<String, Double> individual_score_cutoffs = null;
if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
+ surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
}
cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
+ error );
}
try {
final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
}
}
BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
}
if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
}
File out_dir = null;
if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
+ surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
}
out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
}
if ( !out_dir.exists() ) {
final boolean success = out_dir.mkdir();
if ( !success || !out_dir.exists() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
}
}
if ( !out_dir.canWrite() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
}
}
File positive_filter_file = null;
File negative_filter_file = null;
File negative_domains_filter_file = null;
if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
}
if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
&& ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
ForesterUtil
.fatalError( surfacing.PRG_NAME,
"attempt to use both negative or positive protein filter together wirh a negative domains filter" );
}
if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
+ surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
}
negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
final String msg = ForesterUtil.isReadableFile( negative_filter_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
+ msg );
}
}
else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
+ surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
}
positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
final String msg = ForesterUtil.isReadableFile( positive_filter_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
+ msg );
}
}
else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
+ surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
}
negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
+ "\": " + msg );
}
}
final List<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.INPUT_FILES_FROM_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
+ surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
}
input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
final String msg = ForesterUtil.isReadableFile( input_files_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
}
try {
input_file_names_from_file = ForesterUtil.file2array( input_files_file );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
}
}
if ( ( cla.getNumberOfNames() < 1 )
&& ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"No hmmpfam output file indicated is input: use comand line directly or "
+ surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
}
DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"no value for scoring method for domain combinations similarity calculation: -"
+ surfacing.SCORING_OPTION + "=<"
+ surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
+ surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
+ surfacing.SCORING_COMBINATION_BASED + ">\"" );
}
final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
}
else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
}
else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
+ "\" for scoring method for domain combinations similarity calculation: \"-"
+ surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
+ surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
}
}
boolean sort_by_species_count_first = false;
if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
sort_by_species_count_first = true;
}
boolean species_matrix = false;
if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
species_matrix = true;
}
boolean output_protein_lists_for_all_domains = false;
if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
output_protein_lists_for_all_domains = true;
}
Detailedness detailedness = DETAILEDNESS_DEFAULT;
if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
+ surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
+ surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
}
final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
}
else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
}
else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
+ surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
+ surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
}
}
String automated_pairwise_comparison_suffix = null;
boolean perform_pwc = false;
boolean write_pwc_files = false;
if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
perform_pwc = true;
if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
write_pwc_files = false;
}
else {
write_pwc_files = true;
automated_pairwise_comparison_suffix = "_"
+ cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
}
}
String query_domain_ids = null;
if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
ForesterUtil
.fatalError( surfacing.PRG_NAME,
"no domain ids given for sequences with given domains to be extracted : -"
+ surfacing.SEQ_EXTRACT_OPTION
+ "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
}
query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
}
DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
+ surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
+ ">\"" );
}
final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
}
else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
+ "\" for domain combinations similarities sorting: \"-"
+ surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
+ surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
+ ">\"" );
}
}
PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
}
final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
}
else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
// domain_similarity_print_option =
// DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
}
else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
}
}
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
+ surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
+ surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
}
final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
}
else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
}
else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
}
else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
+ "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
+ surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
}
}
String[][] input_file_properties = null;
if ( input_file_names_from_file != null ) {
input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
}
else {
input_file_properties = surfacing.processInputFileNames( cla.getNames() );
}
final int number_of_genomes = input_file_properties.length;
if ( number_of_genomes < 2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
}
if ( ( number_of_genomes < 3 ) && perform_pwc ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
+ surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ "=<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.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.PFAM_TO_GO_FILE_USE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
+ surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
}
pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
}
try {
final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
final List<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.PRG_NAME,
"parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
}
domain_id_to_go_ids_count = parser.getMappingCount();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
}
}
File go_obo_file = null;
List<GoTerm> go_terms = null;
if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
}
if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
+ surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
}
go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
final String error = ForesterUtil.isReadableFile( go_obo_file );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
}
try {
final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
go_terms = parser.parse();
if ( parser.getGoTermCount() != go_terms.size() ) {
ForesterUtil
.unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
}
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
}
}
Map<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.GO_NAMESPACE_LIMIT_OPTION ) ) {
if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
+ surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
}
if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
}
final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
.toLowerCase();
if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
go_namespace_limit = GoNameSpace.createMolecularFunction();
}
else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
go_namespace_limit = GoNameSpace.createBiologicalProcess();
}
else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
go_namespace_limit = GoNameSpace.createCellularComponent();
}
else {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
+ "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
}
}
if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
&& ( number_of_genomes > 2 ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
}
boolean jacknifed_distances = false;
int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) {
if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-"
+ surfacing.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
+ surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ "=<suffix for pairwise comparison output files>)" );
}
jacknifed_distances = true;
if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) {
try {
jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" );
}
if ( jacknife_resamplings < 2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" );
}
}
if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION )
&& cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) {
try {
jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" );
}
if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: "
+ jacknife_ratio );
}
}
if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION )
&& cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) {
try {
random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" );
}
}
}
// boolean infer_species_trees = false;
// if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
// if ( ( output_file == null ) || ( number_of_genomes < 3 )
// || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
// ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
// + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
// + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
// + "=<suffix for pairwise comparison output files>)" );
// }
// infer_species_trees = true;
// }
File[] intree_files = null;
Phylogeny[] intrees = null;
if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
// TODO FIXME if jacknife.... maybe not
if ( number_of_genomes < 3 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
+ surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
+ surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ "=<suffix for pairwise comparison output files>)" );
}
if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
+ surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
}
final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
if ( intrees_str.indexOf( "#" ) > 0 ) {
final String[] intrees_strs = intrees_str.split( "#" );
intree_files = new File[ intrees_strs.length ];
int i = 0;
for( final String s : intrees_strs ) {
intree_files[ i++ ] = new File( s.trim() );
}
}
else {
intree_files = new File[ 1 ];
intree_files[ 0 ] = new File( intrees_str );
}
intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
}
long random_number_seed_for_fitch_parsimony = 0l;
boolean radomize_fitch_parsimony = false;
if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
+ surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
}
try {
random_number_seed_for_fitch_parsimony = cla
.getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
radomize_fitch_parsimony = true;
}
SortedSet<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.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
+ surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
}
final String[] secondary_features_map_files_strs = cla
.getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
int i = 0;
for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
}
try {
domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
.createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: "
+ e.getMessage() );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
+ secondary_features_map_files[ i ] + "]: " + e.getMessage() );
}
i++;
}
}
if ( out_dir == null ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
+ surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
}
if ( output_file == null ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
+ surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
}
if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
+ surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
}
if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
}
boolean display_histograms = false;
if ( cla.isOptionSet( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
display_histograms = true;
}
System.out.println( "Output directory : " + out_dir );
if ( input_file_names_from_file != null ) {
System.out.println( "Input files names from : " + input_files_file + " ["
+ input_file_names_from_file.length + " input files]" );
html_desc.append( "<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.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.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.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.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.PRG_NAME, "unknown value for sorting for detailedness" );
}
System.out.print( " Print option : " );
switch ( domain_similarity_print_option ) {
case HTML:
System.out.println( "HTML" );
break;
case SIMPLE_TAB_DELIMITED:
System.out.println( "simple tab delimited" );
break;
default:
ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
}
System.out.print( " Species matrix : " + species_matrix );
System.out.println();
final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
System.out.println( "Domain comb data output : " + dc_data_file );
html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
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.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.SEQ_EXTRACT_SUFFIX;
if ( out_dir != null ) {
protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
}
try {
query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
+ e.getLocalizedMessage() );
}
}
}
SortedMap<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.PRG_NAME, e2.getMessage() );
}
final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
BufferedWriter log_writer = null;
try {
log_writer = new BufferedWriter( new FileWriter( log_file ) );
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
}
BufferedWriter dc_data_writer = null;
try {
dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
dc_data_writer.write( DATA_FILE_DESC );
dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
}
for( int i = 0; i < number_of_genomes; ++i ) {
System.out.println();
System.out.println( ( i + 1 ) + "/" + number_of_genomes );
log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
log( "Genome : " + input_file_properties[ i ][ 0 ], log_writer );
HmmscanPerDomainTableParser parser = null;
INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
if ( individual_score_cutoffs != null ) {
ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
}
if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
|| ( negative_domains_filter_file != null ) ) {
HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
if ( positive_filter_file != null ) {
filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
}
else if ( negative_filter_file != null ) {
filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
}
else if ( negative_domains_filter_file != null ) {
filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
}
parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
input_file_properties[ i ][ 1 ],
filter,
filter_type,
ind_score_cutoff );
}
else {
parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
input_file_properties[ i ][ 1 ],
ind_score_cutoff );
}
if ( e_value_max >= 0.0 ) {
parser.setEValueMaximum( e_value_max );
}
parser.setIgnoreDufs( ignore_dufs );
parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
parser.setMaxAllowedOverlap( max_allowed_overlap );
}
parser
.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
if ( individual_score_cutoffs != null ) {
parser.setIndividualScoreCutoffs( individual_score_cutoffs );
}
List<Protein> protein_list = null;
try {
protein_list = parser.parse();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
catch ( final Exception e ) {
ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
}
if ( VERBOSE ) {
System.out.println( "Domains ignored due to negative domain filter: " );
ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
System.out.println( "Domains ignored due to virus like id: " );
ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
}
System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
System.out.println( "Number of proteins stored : " + protein_list.size() );
log( "Number of proteins stored : " + protein_list.size(), log_writer );
System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
System.out.println( "Domains stored : " + parser.getDomainsStored() );
log( "Domains stored : " + parser.getDomainsStored(), log_writer );
System.out.println( "Distinct domains stored : "
+ parser.getDomainsStoredSet().size() );
log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), log_writer );
System.out.println( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
log( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer );
System.out.println( "Domains ignored due to E-value : "
+ parser.getDomainsIgnoredDueToEval() );
log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
System.out.println( "Domains ignored due to DUF designation : "
+ parser.getDomainsIgnoredDueToDuf() );
log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
if ( ignore_virus_like_ids ) {
System.out.println( "Domains ignored due virus like ids : "
+ parser.getDomainsIgnoredDueToVirusLikeIds() );
log( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
log_writer );
}
System.out.println( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter() );
log( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter(), log_writer );
System.out.println( "Domains ignored due to overlap : "
+ parser.getDomainsIgnoredDueToOverlap() );
log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
log_writer );
if ( negative_filter_file != null ) {
System.out.println( "Proteins ignored due to negative filter : "
+ parser.getProteinsIgnoredDueToFilter() );
log( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
if ( positive_filter_file != null ) {
System.out.println( "Proteins ignored due to positive filter : "
+ parser.getProteinsIgnoredDueToFilter() );
log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
System.out.println( "Time for processing : " + parser.getTime() + "ms" );
log( "", log_writer );
html_desc.append( "<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 ] );
try {
int count = 0;
for( final Protein protein : protein_list ) {
dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
.toString() );
++count;
}
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
}
gwcd_list.add( BasicGenomeWideCombinableDomains
.createInstance( protein_list,
ignore_combination_with_same,
new BasicSpecies( input_file_properties[ i ][ 1 ] ),
domain_id_to_go_ids_map,
dc_type ) );
domain_lengths_table.addLengths( protein_list );
if ( gwcd_list.get( i ).getSize() > 0 ) {
SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
out_dir,
per_genome_domain_promiscuity_statistics_writer,
gwcd_list.get( i ),
i,
dc_sort_order );
if ( output_binary_domain_combinationsfor_graph_analysis ) {
SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
out_dir,
gwcd_list.get( i ),
i,
dc_sort_order );
}
SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
all_bin_domain_combinations_encountered );
}
if ( query_domains_writer_ary != null ) {
for( int j = 0; j < query_domain_ids_array.length; j++ ) {
try {
SurfacingUtil.extractProteinNames( protein_list,
query_domain_ids_array[ j ],
query_domains_writer_ary[ j ],
"\t" );
query_domains_writer_ary[ j ].flush();
}
catch ( final IOException e ) {
e.printStackTrace();
}
}
}
if ( need_protein_lists_per_species ) {
protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
}
try {
log_writer.flush();
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
}
System.gc();
} // for( int i = 0; i < number_of_genomes; ++i ) {
try {
per_genome_domain_promiscuity_statistics_writer.flush();
per_genome_domain_promiscuity_statistics_writer.close();
dc_data_writer.flush();
dc_data_writer.close();
log_writer.flush();
log_writer.close();
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
}
ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ per_genome_domain_promiscuity_statistics_file );
if ( query_domains_writer_ary != null ) {
for( int j = 0; j < query_domain_ids_array.length; j++ ) {
try {
query_domains_writer_ary[ j ].close();
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
}
}
}
if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
try {
SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
number_of_genomes,
domain_lengths_table,
domain_lengths_analysis_outfile );
}
catch ( final IOException e1 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
}
System.out.println();
ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
System.out.println();
}
final long analysis_start_time = new Date().getTime();
PairwiseDomainSimilarityCalculator pw_calc = null;
// double[] values_for_all_scores_histogram = null;
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
number_of_genomes == 2 );
switch ( scoring ) {
case COMBINATIONS:
pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
break;
case DOMAINS:
pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
break;
case PROTEINS:
pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
break;
default:
ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
}
DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
if ( domain_id_to_go_ids_map != null ) {
go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
}
final SortedSet<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.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
+ e.getMessage() + "]" );
}
System.out.println();
// values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
final Species[] species = new Species[ number_of_genomes ];
for( int i = 0; i < number_of_genomes; ++i ) {
species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
}
List<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.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing.PRG_NAME,
display_histograms,
out_dir,
write_pwc_files );
String matrix_output_file = new String( output_file.toString() );
if ( matrix_output_file.indexOf( '.' ) > 1 ) {
matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
}
if ( out_dir != null ) {
matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
}
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedBinaryCombinationsBasedDistances() );
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedDomainsBasedDistances() );
final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
.get( 0 ) );
final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedBinaryCombinationsBasedDistances().get( 0 ) );
final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedDomainsBasedDistances().get( 0 ) );
inferred_trees = new ArrayList<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.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedBinaryCombinationsBasedDistances() );
SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
.getSharedDomainsBasedDistances() );
// if ( infer_species_trees ) {
// inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
// + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
// .getSharedBinaryCombinationsBasedDistances() );
// inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
// + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
// }
}
if ( display_histograms ) {
// final List<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.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
all_bin_domain_combinations_gained_fitch,
all_domains_encountered.size(),
all_bin_domain_combinations_encountered,
true );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
}
}
if ( all_bin_domain_combinations_lost_fitch != null ) {
try {
executeFitchGainsAnalysis( new File( output_file
+ surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
all_bin_domain_combinations_lost_fitch,
all_domains_encountered.size(),
all_bin_domain_combinations_encountered,
false );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
}
}
final Runtime rt = java.lang.Runtime.getRuntime();
final long free_memory = rt.freeMemory() / 1000000;
final long total_memory = rt.totalMemory() / 1000000;
System.out.println();
System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" );
System.out.println();
System.out.println( "If this application is useful to you, please cite:" );
System.out.println( surfacing.WWW );
System.out.println();
ForesterUtil.programMessage( PRG_NAME, "OK" );
System.out.println();
}
private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
final String[][] input_file_properties ) {
final String[] genomes = new String[ input_file_properties.length ];
for( int i = 0; i < input_file_properties.length; ++i ) {
if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ "] is not unique in input tree " + intree.getName() );
}
genomes[ i ] = input_file_properties[ i ][ 1 ];
}
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.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.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.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
+ DETAILEDNESS_DEFAULT + ")" );
System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
+ ": to ignore combinations with self (default: not to ignore)" );
System.out
.println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
+ ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
System.out
.println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
+ ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
+ ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
System.out
.println( surfacing.IGNORE_VIRAL_IDS
+ ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
+ DOMAIN_SORT_FILD_DEFAULT + ")" );
System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
+ DOMAINS_SORT_ORDER_DEFAULT + ")" );
System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
+ DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
+ ": sort by species count first" );
System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ ": species tree, to perform (Dollo, Fitch) parismony analyses" );
System.out
.println( surfacing.DISPLAY_M_HISTOGRAMS_OPTION + ": to display multiple histograms (using fluorite)" );
System.out
.println( JACKNIFE_OPTION
+ ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
+ JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
+ JACKNIFE_RATIO_DEFAULT + "]" );
System.out.println( JACKNIFE_RANDOM_SEED_OPTION
+ ": seed for random number generator for jacknife resampling [default: "
+ JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
// System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
// + ": to infer NJ species trees based on shared domains/binary domain combinations" );
System.out
.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
System.out.println( surfacing.FILTER_POSITIVE_OPTION
+ "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
System.out.println( surfacing.FILTER_NEGATIVE_OPTION
+ "=<file>: to filter out proteins containing at least one domain listed in <file>" );
System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
+ "=<file>: to filter out (ignore) domains listed in <file>" );
System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
System.out
.println( surfacing.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.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
+ ": to consider directedness in binary combinations: e.g. A-B != B-A" );
System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
+ ": to consider directedness and adjacency in binary combinations" );
System.out
.println( surfacing.SEQ_EXTRACT_OPTION
+ "=<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.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
+ "=<file>: to perfom parsimony analysis on secondary features" );
System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
+ ": to output binary domain combinations for (downstream) graph analysis" );
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
System.out.println();
System.out.println();
System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
+ "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
+ "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
+ "=50 human mouse brafl strpu" );
System.out.println();
}
private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
SortedSet<String> filter_str = null;
try {
filter_str = ForesterUtil.file2set( filter_file );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
}
if ( filter_str != null ) {
for( final String string : filter_str ) {
filter.add( new DomainId( string ) );
}
}
if ( VERBOSE ) {
System.out.println( "Filter:" );
for( final DomainId domainId : filter ) {
System.out.println( domainId.getId() );
}
}
}
private static String[][] processInputFileNames( final String[] names ) {
final String[][] input_file_properties = new String[ names.length ][];
for( int i = 0; i < names.length; ++i ) {
if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
input_file_properties[ i ] = new String[ 2 ];
input_file_properties[ i ][ 0 ] = names[ i ];
input_file_properties[ i ][ 1 ] = names[ i ];
}
else {
input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
if ( input_file_properties[ i ].length != 3 ) {
ForesterUtil
.fatalError( surfacing.PRG_NAME,
"properties for the input files (hmmpfam output) are expected "
+ "to be in the following format \"<hmmpfam output file>#<species>\" (or just one word, which is both the filename and the species id), instead received \""
+ names[ i ] + "\"" );
}
}
final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, error );
}
}
return input_file_properties;
}
private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
final List<String> high_copy_base,
final List<String> high_copy_target,
final List<String> low_copy,
final List<Object> numbers ) {
if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
+ surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
}
final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
final String msg = ForesterUtil.isReadableFile( plus_minus_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
}
processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
}
}
// First numbers is minimal difference, second is factor.
private static void processPlusMinusFile( final File plus_minus_file,
final List<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.PRG_NAME, e.getMessage() );
}
if ( species_set != null ) {
for( final String species : species_set ) {
final String species_trimmed = species.substring( 1 );
if ( species.startsWith( "+" ) ) {
if ( low_copy.contains( species_trimmed ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ species_trimmed + "\"" );
}
high_copy_base.add( species_trimmed );
}
else if ( species.startsWith( "*" ) ) {
if ( low_copy.contains( species_trimmed ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ species_trimmed + "\"" );
}
high_copy_target.add( species_trimmed );
}
else if ( species.startsWith( "-" ) ) {
if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ species_trimmed + "\"" );
}
low_copy.add( species_trimmed );
}
else if ( species.startsWith( "$D" ) ) {
try {
min_diff = Integer.parseInt( species.substring( 3 ) );
}
catch ( final NumberFormatException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME,
"could not parse integer value for minimal difference from: \""
+ species.substring( 3 ) + "\"" );
}
}
else if ( species.startsWith( "$F" ) ) {
try {
factor = Double.parseDouble( species.substring( 3 ) );
}
catch ( final NumberFormatException e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
+ species.substring( 3 ) + "\"" );
}
}
else if ( species.startsWith( "#" ) ) {
// Comment, ignore.
}
else {
ForesterUtil
.fatalError( surfacing.PRG_NAME,
"species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$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.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.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.PRG_NAME, e.getLocalizedMessage() );
}
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
}
}
}