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.iterators.PhylogenyNodeIterator;
import org.forester.protein.BinaryDomainCombination;
import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
import org.forester.protein.Protein;
import org.forester.species.BasicSpecies;
import org.forester.species.Species;
final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ final static private String PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION = "dc_regain_stats";
+ final static private String DA_ANALYSIS_OPTION = "DA_analyis";
+ final static private String USE_LAST_IN_FITCH_OPTION = "last";
final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
final static private String OUTPUT_FILE_OPTION = "o";
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String JACKNIFE_OPTION = "jack";
- final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
- final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
- private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
- final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
- final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
final static private String FILTER_POSITIVE_OPTION = "pos_filter";
final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private String PRG_VERSION = "2.260";
- final static private String PRG_DATE = "130721";
+ final static private String PRG_VERSION = "2.280";
+ final static private String PRG_DATE = "130701";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
private static final String LOG_FILE_SUFFIX = "_log.txt";
private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
+ private static final String WRITE_TO_NEXUS_OPTION = "nexus";
private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change?
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
- private static final boolean PERFORM_DC_REGAIN_PROTEINS_STATS = true;
- private static final boolean DA_ANALYSIS = false;
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
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>();
+ 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 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<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>();
allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
- allowed_options.add( JACKNIFE_OPTION );
- allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
- allowed_options.add( JACKNIFE_RATIO_OPTION );
+ //allowed_options.add( JACKNIFE_OPTION );
+ // allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
+ // allowed_options.add( JACKNIFE_RATIO_OPTION );
allowed_options.add( INPUT_SPECIES_TREE_OPTION );
allowed_options.add( FILTER_POSITIVE_OPTION );
allowed_options.add( FILTER_NEGATIVE_OPTION );
allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
+ allowed_options.add( WRITE_TO_NEXUS_OPTION );
+ allowed_options.add( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION );
+ allowed_options.add( DA_ANALYSIS_OPTION );
+ allowed_options.add( USE_LAST_IN_FITCH_OPTION );
boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
+ boolean use_last_in_fitch_parsimony = false;
+ if ( cla.isOptionSet( USE_LAST_IN_FITCH_OPTION ) ) {
+ use_last_in_fitch_parsimony = true;
+ }
+ boolean write_to_nexus = false;
+ if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) {
+ write_to_nexus = true;
+ }
+ boolean perform_dc_regain_proteins_stats = false;
+ if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) {
+ perform_dc_regain_proteins_stats = true;
+ }
+ boolean da_analysis = false;
+ if ( cla.isOptionSet( DA_ANALYSIS_OPTION ) ) {
+ da_analysis = true;
+ }
boolean output_binary_domain_combinationsfor_graph_analysis = false;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
output_binary_domain_combinationsfor_graph_analysis = true;
}
}
final String[][] input_file_properties = processInputGenomesFile( input_genomes_file );
- for( final String[] input_file_propertie : input_file_properties ) {
- for( final String element : input_file_propertie ) {
- System.out.print( element + " " );
- }
- System.out.println();
- }
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" );
SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
}
File pfam_to_go_file = null;
- Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
+ Map<String, 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 ) ) {
&& ( 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" );
- }
- }
- }
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 ("
}
radomize_fitch_parsimony = true;
}
- SortedSet<DomainId> filter = null;
+ SortedSet<String> filter = null;
if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
|| ( negative_domains_filter_file != null ) ) {
- filter = new TreeSet<DomainId>();
+ filter = new TreeSet<String>();
if ( positive_filter_file != null ) {
processFilter( positive_filter_file, filter );
}
processFilter( negative_domains_filter_file, filter );
}
}
- Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
+ Map<String, 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 );
+ ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
+ nl );
}
+ System.out.println( "Use last in Fitch parimony : " + use_last_in_fitch_parsimony );
+ html_desc.append( "<tr><td>Use last in Fitch parimon:</td><td>" + use_last_in_fitch_parsimony + "</td></tr>"
+ + nl );
+ System.out.println( "Write to Nexus files : " + write_to_nexus );
+ html_desc.append( "<tr><td>Write to Nexus files:</td><td>" + write_to_nexus + "</td></tr>" + nl );
+ System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats );
+ html_desc.append( "<tr><td>DC regain prot stats:</td><td>" + perform_dc_regain_proteins_stats + "</td></tr>"
+ + nl );
+ System.out.println( "DA analysis : " + da_analysis );
+ html_desc.append( "<tr><td>DA analysis :</td><td>" + da_analysis + "</td></tr>" + nl );
System.out.print( "Domain counts sort order : " );
+ html_desc.append( "<tr><td>Domain counts sort order:</td><td>" );
switch ( dc_sort_order ) {
case ALPHABETICAL_KEY_ID:
System.out.println( "alphabetical" );
+ html_desc.append( "alphabetical" + "</td></tr>" + nl );
break;
case KEY_DOMAIN_COUNT:
System.out.println( "domain count" );
+ html_desc.append( "domain count" + "</td></tr>" + nl );
break;
case KEY_DOMAIN_PROTEINS_COUNT:
System.out.println( "domain proteins count" );
+ html_desc.append( "domain proteins count" + "</td></tr>" + nl );
break;
case COMBINATIONS_COUNT:
System.out.println( "domain combinations count" );
+ html_desc.append( "domain combinations count" + "</td></tr>" + nl );
break;
default:
ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
}
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 ( ( 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
if ( VERBOSE ) {
System.out.println();
System.out.println( "Domain ids to secondary features map:" );
- for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
- System.out.print( domain_id.getId() );
+ for( final String domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
+ System.out.print( domain_id );
System.out.print( " => " );
for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
System.out.print( sec );
html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
BufferedWriter[] query_domains_writer_ary = null;
- List<DomainId>[] query_domain_ids_array = null;
+ List<String>[] 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 ];
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>();
+ final List<String> query = new ArrayList<String>();
for( final String element : query_domain_ids_str_ary ) {
- query.add( new DomainId( element ) );
+ query.add( element );
}
query_domain_ids_array[ i ] = query;
query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
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>();
+ List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
+ final SortedSet<String> all_domains_encountered = new TreeSet<String>();
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;
Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
- if ( PERFORM_DC_REGAIN_PROTEINS_STATS ) {
+ if ( perform_dc_regain_proteins_stats ) {
protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
}
final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
protein_coverage_stats.addValue( coverage );
int distinct_das = -1;
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
final String genome = input_file_properties[ i ][ 0 ];
distinct_das = SurfacingUtil.storeDomainArchitectures( genome,
distinct_domain_architecutures_per_genome,
log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
System.out.println( "Distinct domain architectures stored : " + distinct_das );
log( "Distinct domain architectures stored : " + distinct_das, log_writer );
}
domains_which_never_single,
domains_per_potein_stats_writer );
domain_lengths_table.addLengths( protein_list );
- if ( !DA_ANALYSIS ) {
+ if ( !da_analysis ) {
gwcd_list.add( BasicGenomeWideCombinableDomains
.createInstance( protein_list,
ignore_combination_with_same,
ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ per_genome_domain_promiscuity_statistics_file );
//
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
distinct_domain_architecuture_counts,
10,
go_annotation_output,
go_id_to_term_map,
go_namespace_limit );
- DescriptiveStatistics pw_stats = null;
+ final Map<String, Integer> tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] );
try {
String my_outfile = output_file.toString();
Map<Character, Writer> split_writers = null;
+ 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
+ final DescriptiveStatistics pw_stats = SurfacingUtil
.writeDomainSimilaritiesToFile( html_desc,
new StringBuilder( number_of_genomes + " genomes" ),
writer,
domain_similarity_print_option,
domain_similarity_sort_field,
scoring,
- true );
+ true,
+ tax_code_to_id_map );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
}
+ 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 ] );
surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
surfacing.PRG_NAME,
out_dir,
- write_pwc_files );
+ write_pwc_files,
+ tax_code_to_id_map );
String matrix_output_file = new String( output_file.toString() );
if ( matrix_output_file.indexOf( '.' ) > 1 ) {
matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
inferred_trees.add( nj_gd );
inferred_trees.add( nj_bc );
inferred_trees.add( nj_d );
- if ( jacknifed_distances ) {
- pwgc.performPairwiseComparisonsJacknifed( species,
- number_of_genomes,
- gwcd_list,
- true,
- jacknife_resamplings,
- jacknife_ratio,
- random_seed );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file
- + "_"
- + ForesterUtil.round( jacknife_ratio, 2 )
- + "_"
- + jacknife_resamplings
- + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedBinaryCombinationsBasedDistances() );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 )
- + "_" + jacknife_resamplings
- + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedDomainsBasedDistances() );
- // if ( infer_species_trees ) {
- // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
- // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
- // .getSharedBinaryCombinationsBasedDistances() );
- // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
- // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
- // }
- }
} // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
if ( ( out_dir != null ) && ( !perform_pwc ) ) {
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
}
- writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ if ( write_to_nexus ) {
+ writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ }
if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
e_value_max,
dc_type,
protein_length_stats_by_dc,
domain_number_stats_by_dc,
- domain_length_stats_by_domain );
+ domain_length_stats_by_domain,
+ tax_code_to_id_map,
+ write_to_nexus,
+ use_last_in_fitch_parsimony );
// Listing of all domain combinations gained is only done if only one input tree is used.
if ( ( domain_id_to_secondary_features_maps != null )
&& ( domain_id_to_secondary_features_maps.length > 0 ) ) {
int j = 0;
- for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
+ for( final Map<String, 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 );
secondary_features_parsimony,
intree,
parameters_sb.toString(),
- mapping_results_map );
+ mapping_results_map,
+ use_last_in_fitch_parsimony );
if ( i == 0 ) {
System.out.println();
System.out.println( "Mapping to secondary features:" );
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
System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ ": species tree, to perform (Dollo, Fitch) parismony analyses" );
System.out
- .println( JACKNIFE_OPTION
- + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
- + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
- System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
- + JACKNIFE_RATIO_DEFAULT + "]" );
- System.out.println( JACKNIFE_RANDOM_SEED_OPTION
- + ": seed for random number generator for jacknife resampling [default: "
- + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
- // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
- // + ": to infer NJ species trees based on shared domains/binary domain combinations" );
- System.out
.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ "=<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
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
+ ": e value max per domain for output of all proteins per domain" );
+ System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" );
+ System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" );
+ System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" );
+ System.out.println( DA_ANALYSIS_OPTION + ": to do DA analysis" );
System.out.println();
System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
System.out.println();
}
- private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
+ private static void processFilter( final File filter_file, final SortedSet<String> filter ) {
SortedSet<String> filter_str = null;
try {
filter_str = ForesterUtil.file2set( filter_file );
}
if ( filter_str != null ) {
for( final String string : filter_str ) {
- filter.add( new DomainId( string ) );
+ filter.add( string );
}
}
if ( VERBOSE ) {
System.out.println( "Filter:" );
- for( final DomainId domainId : filter ) {
- System.out.println( domainId.getId() );
+ for( final String domainId : filter ) {
+ System.out.println( domainId );
}
}
}
"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 );
private static void writePresentToNexus( final File output_file,
final File positive_filter_file,
- final SortedSet<DomainId> filter,
+ final SortedSet<String> filter,
final List<GenomeWideCombinableDomains> gwcd_list ) {
try {
SurfacingUtil
final SortedMap<Species, List<Protein>> protein_lists_per_species,
final List<GenomeWideCombinableDomains> gwcd_list,
final double domain_e_cutoff ) {
- final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+ final SortedSet<String> all_domains = new TreeSet<String>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
all_domains.addAll( gwcd.getAllDomainIds() );
}
- for( final DomainId domain : all_domains ) {
+ for( final String domain : all_domains ) {
final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
SurfacingUtil.checkForOutputFileWriteability( out );
try {
git://source.jalview.org / jalview.git / blobdiff