import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
-import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
import org.forester.go.PfamToGoParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
-import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.BinaryDomainCombination;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.surfacing.BasicGenomeWideCombinableDomains;
import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
-import org.forester.surfacing.DomainCountsDifferenceUtil;
import org.forester.surfacing.DomainLengthsTable;
import org.forester.surfacing.DomainParsimonyCalculator;
import org.forester.surfacing.DomainSimilarity;
final static private String PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION = "dc_regain_stats";
final static private String DA_ANALYSIS_OPTION = "DA_analyis";
final static private String USE_LAST_IN_FITCH_OPTION = "last";
- final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
+ public final static String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
final static private String OUTPUT_FILE_OPTION = "o";
final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private String PRG_VERSION = "2.302";
- final static private String PRG_DATE = "130715";
+ final static private String PRG_VERSION = "2.304";
+ final static private String PRG_DATE = "131024";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
final static private double MAX_E_VALUE_DEFAULT = -1;
- final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+ public final static int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
- 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";
+ public static final String SEQ_EXTRACT_SUFFIX = ".prot";
+ public static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
+ public static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
+ public static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
+ public static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
+ public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
+ public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
+ public static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
+ public static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e";
- private static final boolean VERBOSE = false;
+ public static final boolean VERBOSE = false;
private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
private static final boolean CALC_SIMILARITY_SCORES = false;
- private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
- final String[][] input_file_properties,
- final String automated_pairwise_comparison_suffix,
- final File outdir ) {
- for( int i = 0; i < input_file_properties.length; ++i ) {
- for( int j = 0; j < i; ++j ) {
- final String species_i = input_file_properties[ i ][ 1 ];
- final String species_j = input_file_properties[ j ][ 1 ];
- String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
- + species_j + automated_pairwise_comparison_suffix;
- switch ( domain_similarity_print_option ) {
- case HTML:
- if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
- pairwise_similarities_output_file_str += ".html";
- }
- break;
- }
- final String error = ForesterUtil
- .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
- + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- }
- }
- }
- }
-
- private static StringBuilder createParametersAsString( final boolean ignore_dufs,
- final double e_value_max,
- final int max_allowed_overlap,
- final boolean no_engulfing_overlaps,
- final File cutoff_scores_file,
- final BinaryDomainCombination.DomainCombinationType dc_type ) {
- final StringBuilder parameters_sb = new StringBuilder();
- parameters_sb.append( "E-value: " + e_value_max );
- if ( cutoff_scores_file != null ) {
- parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
- }
- else {
- parameters_sb.append( ", Cutoff-scores-file: not-set" );
- }
- if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
- parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
- }
- else {
- parameters_sb.append( ", Max-overlap: not-set" );
- }
- if ( no_engulfing_overlaps ) {
- parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
- }
- else {
- parameters_sb.append( ", Engulfing-overlaps: allowed" );
- }
- if ( ignore_dufs ) {
- parameters_sb.append( ", Ignore-dufs: true" );
- }
- else {
- parameters_sb.append( ", Ignore-dufs: false" );
- }
- parameters_sb.append( ", DC type (if applicable): " + dc_type );
- return parameters_sb;
- }
-
- /**
- * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
- *
- *
- * @param output_file
- * @param all_bin_domain_combinations_changed
- * @param sum_of_all_domains_encountered
- * @param all_bin_domain_combinations_encountered
- * @param is_gains_analysis
- * @param protein_length_stats_by_dc
- * @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<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
- final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
- 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<String, 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, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
- if ( p_array.length < 1 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
- + "] does not contain any phylogeny in phyloXML format" );
- }
- else if ( p_array.length > 1 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
- + "] contains more than one phylogeny in phyloXML format" );
- }
- intree = p_array[ 0 ];
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
- + "]: " + error );
- }
- if ( ( intree == null ) || intree.isEmpty() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
- }
- if ( !intree.isRooted() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
- }
- if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "number of external nodes [" + intree.getNumberOfExternalNodes()
- + "] of input tree [" + intree_file
- + "] is smaller than the number of genomes the be analyzed ["
- + number_of_genomes + "]" );
- }
- final StringBuilder parent_names = new StringBuilder();
- final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
- if ( nodes_lacking_name > 0 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
- + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
- }
- preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
- if ( !intree.isCompletelyBinary() ) {
- ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
- + "] is not completely binary" );
- }
- intrees[ i++ ] = intree;
- }
- return intrees;
- }
-
- private static 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();
if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
ignore_species_specific_domains = true;
}
+ if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no input species tree file given: "
+ + surfacing.INPUT_SPECIES_TREE_OPTION + "=<file>" );
+ }
File output_file = null;
if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
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 );
+ SurfacingUtil.processPlusMinusAnalysisOption( cla,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ plus_minus_analysis_numbers );
File input_genomes_file = null;
if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
+ surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
}
}
- final String[][] input_file_properties = processInputGenomesFile( input_genomes_file );
+ final String[][] input_file_properties = SurfacingUtil.processInputGenomesFile( input_genomes_file );
final int number_of_genomes = input_file_properties.length;
if ( number_of_genomes < 2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
+ 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 );
+ SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
+ input_file_properties,
+ automated_pairwise_comparison_suffix,
+ out_dir );
for( int i = 0; i < number_of_genomes; i++ ) {
File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
+ surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
intree_files = new File[ 1 ];
intree_files[ 0 ] = new File( intrees_str );
}
- intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
+ intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, number_of_genomes, input_file_properties );
}
+ final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ] );
long random_number_seed_for_fitch_parsimony = 0l;
boolean radomize_fitch_parsimony = false;
if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
|| ( negative_domains_filter_file != null ) ) {
filter = new TreeSet<String>();
if ( positive_filter_file != null ) {
- processFilter( positive_filter_file, filter );
+ SurfacingUtil.processFilter( positive_filter_file, filter );
}
else if ( negative_filter_file != null ) {
- processFilter( negative_filter_file, filter );
+ SurfacingUtil.processFilter( negative_filter_file, filter );
}
else if ( negative_domains_filter_file != null ) {
- processFilter( negative_domains_filter_file, filter );
+ SurfacingUtil.processFilter( negative_domains_filter_file, filter );
}
}
Map<String, Set<String>>[] domain_id_to_secondary_features_maps = null;
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 );
+ SurfacingUtil.log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
System.out.println( "Processing : " + input_file_properties[ i ][ 1 ]
+ " [" + input_file_properties[ i ][ 0 ] + "]" );
- log( "Genome : " + input_file_properties[ i ][ 1 ] + " ["
- + input_file_properties[ i ][ 0 ] + "]", log_writer );
+ SurfacingUtil.log( "Genome : " + input_file_properties[ i ][ 1 ]
+ + " [" + input_file_properties[ i ][ 0 ] + "]", log_writer );
HmmscanPerDomainTableParser parser = null;
INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
if ( individual_score_cutoffs != null ) {
distinct_domain_architecuture_counts );
}
System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
- log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
+ SurfacingUtil.log( "Number of proteins encountered : " + parser.getProteinsEncountered(),
+ log_writer );
System.out.println( "Number of proteins stored : " + protein_list.size() );
- log( "Number of proteins stored : " + protein_list.size(), log_writer );
+ SurfacingUtil.log( "Number of proteins stored : " + protein_list.size(), log_writer );
System.out.println( "Coverage : "
+ ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
- log( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage )
- + "%", log_writer );
+ SurfacingUtil.log( "Coverage : "
+ + ForesterUtil.roundToInt( 100.0 * coverage ) + "%",
+ log_writer );
System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
- log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
+ SurfacingUtil.log( "Domains encountered : " + parser.getDomainsEncountered(),
+ log_writer );
System.out.println( "Domains stored : " + parser.getDomainsStored() );
- log( "Domains stored : " + parser.getDomainsStored(), log_writer );
+ SurfacingUtil.log( "Domains stored : " + parser.getDomainsStored(),
+ log_writer );
System.out.println( "Distinct domains stored : "
+ parser.getDomainsStoredSet().size() );
- log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), log_writer );
+ SurfacingUtil.log( "Distinct domains stored : "
+ + parser.getDomainsStoredSet().size(), log_writer );
System.out.println( "Domains ignored due to individual score cutoffs: "
+ parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
- log( "Domains ignored due to individual score cutoffs: "
- + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
- log_writer );
+ SurfacingUtil.log( "Domains ignored due to individual score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
+ log_writer );
System.out.println( "Domains ignored due to E-value : "
+ parser.getDomainsIgnoredDueToEval() );
- log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
+ SurfacingUtil.log( "Domains ignored due to 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 );
+ SurfacingUtil
+ .log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(),
+ log_writer );
if ( ignore_virus_like_ids ) {
System.out.println( "Domains ignored due virus like ids : "
+ parser.getDomainsIgnoredDueToVirusLikeIds() );
- log( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
- log_writer );
+ SurfacingUtil.log( "Domains ignored due virus like ids : "
+ + parser.getDomainsIgnoredDueToVirusLikeIds(),
+ log_writer );
}
System.out.println( "Domains ignored due negative domain filter : "
+ parser.getDomainsIgnoredDueToNegativeDomainFilter() );
- log( "Domains ignored due negative domain filter : "
- + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
- log_writer );
+ SurfacingUtil.log( "Domains ignored due negative domain filter : "
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
+ log_writer );
System.out.println( "Domains ignored due to overlap : "
+ parser.getDomainsIgnoredDueToOverlap() );
- log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
- log_writer );
+ SurfacingUtil.log( "Domains ignored due to overlap : "
+ + parser.getDomainsIgnoredDueToOverlap(),
+ log_writer );
if ( negative_filter_file != null ) {
System.out.println( "Proteins ignored due to negative filter : "
+ parser.getProteinsIgnoredDueToFilter() );
- log( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter(),
- log_writer );
+ SurfacingUtil.log( "Proteins ignored due to negative filter : "
+ + parser.getProteinsIgnoredDueToFilter(),
+ log_writer );
}
if ( positive_filter_file != null ) {
System.out.println( "Proteins ignored due to positive filter : "
+ parser.getProteinsIgnoredDueToFilter() );
- log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
- log_writer );
+ SurfacingUtil.log( "Proteins ignored due to positive filter : "
+ + parser.getProteinsIgnoredDueToFilter(),
+ log_writer );
}
if ( da_analysis ) {
System.out.println( "Distinct domain architectures stored : " + distinct_das );
- log( "Distinct domain architectures stored : " + distinct_das, log_writer );
+ SurfacingUtil.log( "Distinct domain architectures stored : " + distinct_das, log_writer );
}
System.out.println( "Time for processing : " + parser.getTime() + "ms" );
- log( "", log_writer );
+ SurfacingUtil.log( "", log_writer );
try {
int count = 0;
for( final Protein protein : protein_list ) {
domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
domains_per_potein_stats_writer.write( "\n" );
domains_per_potein_stats_writer.close();
- printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
+ SurfacingUtil.printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: "
+ ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() )
+ "%" );
- log( "Average of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.arithmeticMean() )
- + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
- log( "Range of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.getMin() ) + "%-"
- + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer );
+ SurfacingUtil.log( "Average of prot with a least one dom assigned : "
+ + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
+ + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)",
+ log_writer );
+ SurfacingUtil.log( "Range of prot with a least one dom assigned : "
+ + ( 100 * protein_coverage_stats.getMin() ) + "%-"
+ + ( 100 * protein_coverage_stats.getMax() ) + "%",
+ log_writer );
}
catch ( final IOException e2 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
}
split_writers = new HashMap<Character, Writer>();
- createSplitWriters( out_dir, my_outfile, split_writers );
+ SurfacingUtil.createSplitWriters( out_dir, my_outfile, split_writers );
}
else if ( !my_outfile.endsWith( ".html" ) ) {
my_outfile += ".html";
domain_similarity_print_option,
scoring,
true,
- tax_code_to_id_map );
+ tax_code_to_id_map,
+ intree_0_orig );
simple_tab_writer.close();
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
out_dir,
write_pwc_files,
tax_code_to_id_map,
- CALC_SIMILARITY_SCORES );
+ CALC_SIMILARITY_SCORES,
+ intree_0_orig );
String matrix_output_file = new String( output_file.toString() );
if ( matrix_output_file.indexOf( '.' ) > 1 ) {
matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
}
if ( write_to_nexus ) {
- writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ SurfacingUtil.writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
}
if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
- final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
- e_value_max,
- max_allowed_overlap,
- no_engulfing_overlaps,
- cutoff_scores_file,
- dc_type );
+ final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs,
+ 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 + "_";
} // for( final Phylogeny intree : intrees ) {
}
if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
- executePlusMinusAnalysis( output_file,
- plus_minus_analysis_high_copy_base_species,
- plus_minus_analysis_high_copy_target_species,
- plus_minus_analysis_high_low_copy_species,
- gwcd_list,
- protein_lists_per_species,
- domain_id_to_go_ids_map,
- go_id_to_term_map,
- plus_minus_analysis_numbers );
+ SurfacingUtil.executePlusMinusAnalysis( output_file,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ gwcd_list,
+ protein_lists_per_species,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ plus_minus_analysis_numbers );
}
if ( output_protein_lists_for_all_domains ) {
- writeProteinListsForAllSpecies( out_dir,
- protein_lists_per_species,
- gwcd_list,
- output_list_of_all_proteins_per_domain_e_value_max );
+ SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
+ protein_lists_per_species,
+ gwcd_list,
+ output_list_of_all_proteins_per_domain_e_value_max );
}
gwcd_list = null;
if ( all_bin_domain_combinations_gained_fitch != null ) {
try {
- executeFitchGainsAnalysis( new File( output_file
- + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
- all_bin_domain_combinations_gained_fitch,
- all_domains_encountered.size(),
- all_bin_domain_combinations_encountered,
- true );
+ SurfacingUtil
+ .executeFitchGainsAnalysis( new File( output_file
+ + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_gained_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ true );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
}
if ( all_bin_domain_combinations_lost_fitch != null ) {
try {
- executeFitchGainsAnalysis( new File( output_file
- + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
- all_bin_domain_combinations_lost_fitch,
- all_domains_encountered.size(),
- all_bin_domain_combinations_encountered,
- false );
+ SurfacingUtil
+ .executeFitchGainsAnalysis( new File( output_file
+ + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_lost_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ false );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
System.out.println();
}
- private static void createSplitWriters( final File out_dir,
- final String my_outfile,
- final Map<Character, Writer> split_writers ) throws IOException {
- split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_A.html" ) ) );
- split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_B.html" ) ) );
- split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_C.html" ) ) );
- split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_D.html" ) ) );
- split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_E.html" ) ) );
- split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_F.html" ) ) );
- split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_G.html" ) ) );
- split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_H.html" ) ) );
- split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_I.html" ) ) );
- split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_J.html" ) ) );
- split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_K.html" ) ) );
- split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_L.html" ) ) );
- split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_M.html" ) ) );
- split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_N.html" ) ) );
- split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_O.html" ) ) );
- split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_P.html" ) ) );
- split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_Q.html" ) ) );
- split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_R.html" ) ) );
- split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_S.html" ) ) );
- split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_T.html" ) ) );
- split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_U.html" ) ) );
- split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_V.html" ) ) );
- split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_W.html" ) ) );
- split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_X.html" ) ) );
- split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_Y.html" ) ) );
- split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_Z.html" ) ) );
- split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
- + "_domains_0.html" ) ) );
- }
-
- private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
- final Writer log_writer ) {
- int sum = 0;
- for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
- sum += entry.getValue();
- }
- final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
- ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
- log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer );
- }
-
- private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
- final String[][] input_file_properties ) {
- final String[] genomes = new String[ input_file_properties.length ];
- for( int i = 0; i < input_file_properties.length; ++i ) {
- if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
- + "] is not unique in input tree " + intree.getName() );
- }
- genomes[ i ] = input_file_properties[ i ][ 1 ];
- }
- //
- final PhylogenyNodeIterator it = intree.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( ForesterUtil.isEmpty( n.getName() ) ) {
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- else if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- n.setName( n.getNodeData().getTaxonomy().getScientificName() );
- }
- else if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
- n.setName( n.getNodeData().getTaxonomy().getCommonName() );
- }
- else {
- ForesterUtil
- .fatalError( surfacing.PRG_NAME,
- "node with no name, scientific name, common name, or taxonomy code present" );
- }
- }
- }
- //
- final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
- if ( igns.size() > 0 ) {
- System.out.println( "Not using the following " + igns.size() + " nodes:" );
- for( int i = 0; i < igns.size(); ++i ) {
- System.out.println( " " + i + ": " + igns.get( i ) );
- }
- System.out.println( "--" );
- }
- for( final String[] input_file_propertie : input_file_properties ) {
- try {
- intree.getNode( input_file_propertie[ 1 ] );
- }
- catch ( final IllegalArgumentException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
- + "] not present/not unique in input tree" );
- }
- }
- }
-
private static void printHelp() {
System.out.println();
System.out.println( "Usage:" );
+ "-ds_output=detailed_html -scoring=domains -sort=alpha " );
System.out.println();
}
-
- private static void processFilter( final File filter_file, final SortedSet<String> 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( string );
- }
- }
- if ( VERBOSE ) {
- System.out.println( "Filter:" );
- for( final String domainId : filter ) {
- System.out.println( domainId );
- }
- }
- }
-
- private static String[][] processInputGenomesFile( final File input_genomes ) {
- String[][] input_file_properties = null;
- try {
- input_file_properties = ForesterUtil.file22dArray( input_genomes );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
- + e.getLocalizedMessage() );
- }
- final Set<String> specs = new HashSet<String>();
- final Set<String> paths = new HashSet<String>();
- for( int i = 0; i < input_file_properties.length; ++i ) {
- if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
- + input_file_properties[ i ][ 1 ] );
- }
- if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
- + " is not unique" );
- }
- specs.add( input_file_properties[ i ][ 1 ] );
- if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
- + " is not unique" );
- }
- paths.add( input_file_properties[ i ][ 0 ] );
- final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, error );
- }
- }
- 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<String> 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 double domain_e_cutoff ) {
- final SortedSet<String> all_domains = new TreeSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- all_domains.addAll( gwcd.getAllDomainIds() );
- }
- for( final String domain : all_domains ) {
- final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
- SurfacingUtil.checkForOutputFileWriteability( out );
- try {
- final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
- SurfacingUtil.extractProteinNames( protein_lists_per_species,
- domain,
- proteins_file_writer,
- "\t",
- LIMIT_SPEC_FOR_PROT_EX,
- domain_e_cutoff );
- 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 + "\"" );
- }
- }
}
git://source.jalview.org / jalview.git / blobdiff