X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=89ce71cf657f01e2468767cee00bdc861a99537f;hb=df171fce4381e27fd4d969e9456062ddbbec388f;hp=162ef57c0bcc9f0f7ab91ffe6ad62a1876669cb5;hpb=4aaa7b9109d4a4d7ed9c2f6cbba7c960a81a9ed0;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 162ef57..89ce71c 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -87,6 +87,7 @@ public class surfacing { private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; + public final static String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION = "dcc"; 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"; @@ -171,12 +172,13 @@ public class surfacing { 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_FS_E_VALUE_OPTION = "fs_e"; + final static private String MAX_I_E_VALUE_OPTION = "ie"; 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 DA_ANALYSIS_OPTION = "da_analyis"; final static private String USE_LAST_IN_FITCH_OPTION = "last"; public final static String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc"; @@ -213,8 +215,8 @@ public class surfacing { 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 = "2.401"; - final static private String PRG_DATE = "131125"; + final static private String PRG_VERSION = "2.404"; + final static private String PRG_DATE = "140319"; 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; @@ -239,7 +241,7 @@ public class surfacing { 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; + private static final String PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION = "dla"; 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"; @@ -254,6 +256,7 @@ public class surfacing { 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 String PERFORM_DC_FITCH = "dc_pars"; 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"; @@ -301,7 +304,8 @@ public class surfacing { } final List allowed_options = new ArrayList(); allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION ); - allowed_options.add( surfacing.MAX_E_VALUE_OPTION ); + allowed_options.add( surfacing.MAX_FS_E_VALUE_OPTION ); + allowed_options.add( surfacing.MAX_I_E_VALUE_OPTION ); allowed_options.add( surfacing.DETAILEDNESS_OPTION ); allowed_options.add( surfacing.OUTPUT_FILE_OPTION ); allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ); @@ -333,15 +337,19 @@ public class surfacing { 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( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ); 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 ); + allowed_options.add( PERFORM_DC_FITCH ); + allowed_options.add( PERFORM_DOMAIN_LENGTH_ANALYSIS_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; + double fs_e_value_max = surfacing.MAX_E_VALUE_DEFAULT; + double ie_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 ) { @@ -355,6 +363,10 @@ public class surfacing { if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) { write_to_nexus = true; } + boolean perform_dc_fich = false; + if ( cla.isOptionSet( PERFORM_DC_FITCH ) ) { + perform_dc_fich = true; + } boolean perform_dc_regain_proteins_stats = false; if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) { perform_dc_regain_proteins_stats = true; @@ -367,9 +379,21 @@ public class surfacing { 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 ) ) { + boolean output_binary_domain_combinationsfor_counts = false; + if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) { + output_binary_domain_combinationsfor_counts = true; + } + if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) { + try { + fs_e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_FS_E_VALUE_OPTION ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" ); + } + } + if ( cla.isOptionSet( surfacing.MAX_I_E_VALUE_OPTION ) ) { try { - e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION ); + ie_value_max = cla.getOptionValueAsDouble( surfacing.MAX_I_E_VALUE_OPTION ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" ); @@ -397,6 +421,10 @@ public class surfacing { if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) { ignore_combination_with_same = true; } + boolean domain_length_analysis = false; + if ( cla.isOptionSet( surfacing.PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION ) ) { + domain_length_analysis = 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; @@ -940,7 +968,7 @@ public class surfacing { 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 ) { + if ( domain_length_analysis ) { SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); } if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { @@ -1037,9 +1065,13 @@ public class surfacing { System.out.println( "Cutoff scores file : " + cutoff_scores_file ); html_desc.append( "Cutoff scores file:" + cutoff_scores_file + "" + nl ); } - if ( e_value_max >= 0.0 ) { - System.out.println( "E-value maximum (inclusive) : " + e_value_max ); - html_desc.append( "E-value maximum (inclusive):" + e_value_max + "" + nl ); + if ( ie_value_max >= 0.0 ) { + System.out.println( "iE-value maximum (incl) : " + ie_value_max ); + html_desc.append( "iE-value maximum (inclusive):" + ie_value_max + "" + nl ); + } + if ( fs_e_value_max >= 0.0 ) { + System.out.println( "FS E-value maximum (incl) : " + fs_e_value_max ); + html_desc.append( "FS E-value maximum (inclusive):" + fs_e_value_max + "" + nl ); } if ( output_protein_lists_for_all_domains ) { System.out.println( "Domain E-value max : " + output_list_of_all_proteins_per_domain_e_value_max ); @@ -1084,14 +1116,20 @@ public class surfacing { + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "" + nl ); } - System.out.println( "Use last in Fitch parimony : " + use_last_in_fitch_parsimony ); - html_desc.append( "Use last in Fitch parimon:" + use_last_in_fitch_parsimony + "" - + nl ); + System.out.println( "Fitch parsimony of DCs : " + perform_dc_fich ); + html_desc.append( "Fitch parsimony of DCs:" + perform_dc_fich + "" + nl ); + if ( perform_dc_fich ) { + System.out.println( "Use last in Fitch parsimony : " + use_last_in_fitch_parsimony ); + html_desc.append( "Use last in Fitch parsimony:" + use_last_in_fitch_parsimony + + "" + nl ); + } System.out.println( "Write to Nexus files : " + write_to_nexus ); html_desc.append( "Write to Nexus files:" + write_to_nexus + "" + nl ); - System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats ); - html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats + "" - + nl ); + if ( perform_dc_fich ) { + System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats ); + html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats + + "" + nl ); + } System.out.println( "DA analysis : " + da_analysis ); html_desc.append( "DA analysis :" + da_analysis + "" + nl ); System.out.print( "Domain counts sort order : " ); @@ -1310,7 +1348,8 @@ public class surfacing { } } // if ( perform_pwc ) { System.out.println(); - html_desc.append( "Command line:\n" + cla.getCommandLineArgsAsString() + "\n" + nl ); + html_desc.append( "Command line:" + nl + nl + cla.getCommandLineArgsAsString() + nl + nl + + "" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = null; List[] query_domain_ids_array = null; @@ -1357,7 +1396,6 @@ public class surfacing { all_bin_domain_combinations_gained_fitch = new ArrayList(); all_bin_domain_combinations_lost_fitch = new ArrayList(); } - 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; @@ -1393,8 +1431,8 @@ public class surfacing { catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } - final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics(); - final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics(); + DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics(); + DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics(); final SortedMap all_genomes_domains_per_potein_histo = new TreeMap(); final SortedSet domains_which_are_always_single = new TreeSet(); final SortedSet domains_which_are_sometimes_single_sometimes_not = new TreeSet(); @@ -1428,6 +1466,10 @@ public class surfacing { protein_length_stats_by_dc = new HashMap(); domain_number_stats_by_dc = new HashMap(); } + DomainLengthsTable domain_lengths_table = null; + if ( domain_length_analysis ) { + domain_lengths_table = new DomainLengthsTable(); + } // Main loop: final SortedMap> distinct_domain_architecutures_per_genome = new TreeMap>(); final SortedMap distinct_domain_architecuture_counts = new TreeMap(); @@ -1469,8 +1511,11 @@ public class surfacing { ind_score_cutoff, true ); } - if ( e_value_max >= 0.0 ) { - parser.setEValueMaximum( e_value_max ); + if ( fs_e_value_max >= 0.0 ) { + parser.setFsEValueMaximum( fs_e_value_max ); + } + if ( ie_value_max >= 0.0 ) { + parser.setIEValueMaximum( ie_value_max ); } parser.setIgnoreDufs( ignore_dufs ); parser.setIgnoreVirusLikeIds( ignore_virus_like_ids ); @@ -1533,10 +1578,15 @@ public class surfacing { SurfacingUtil.log( "Domains ignored due to individual score cutoffs: " + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer ); - System.out.println( "Domains ignored due to E-value : " - + parser.getDomainsIgnoredDueToEval() ); - SurfacingUtil.log( "Domains ignored due to E-value : " - + parser.getDomainsIgnoredDueToEval(), + System.out.println( "Domains ignored due to FS E-value : " + + parser.getDomainsIgnoredDueToFsEval() ); + SurfacingUtil.log( "Domains ignored due to FS E-value : " + + parser.getDomainsIgnoredDueToFsEval(), + log_writer ); + System.out.println( "Domains ignored due to iE-value : " + + parser.getDomainsIgnoredDueToIEval() ); + SurfacingUtil.log( "Domains ignored due to iE-value : " + + parser.getDomainsIgnoredDueToIEval(), log_writer ); System.out.println( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf() ); @@ -1606,7 +1656,9 @@ public class surfacing { domains_which_are_sometimes_single_sometimes_not, domains_which_never_single, domains_per_potein_stats_writer ); - domain_lengths_table.addLengths( protein_list ); + if ( domain_length_analysis ) { + domain_lengths_table.addLengths( protein_list ); + } if ( !da_analysis ) { gwcd_list.add( BasicGenomeWideCombinableDomains .createInstance( protein_list, @@ -1617,12 +1669,15 @@ public class surfacing { protein_length_stats_by_dc, domain_number_stats_by_dc ) ); 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_counts ) { + 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, @@ -1683,8 +1738,10 @@ public class surfacing { domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" ); domains_per_potein_stats_writer.write( "\t" ); - domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); - domains_per_potein_stats_writer.write( "\t" ); + if ( all_genomes_domains_per_potein_stats.getN() <= 300 ) { + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + } domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" ); @@ -1692,6 +1749,7 @@ public class surfacing { 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(); + all_genomes_domains_per_potein_stats = null; 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" ); @@ -1716,6 +1774,7 @@ public class surfacing { + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer ); + protein_coverage_stats = null; } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); @@ -1738,7 +1797,7 @@ public class surfacing { catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); } - if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { + if ( domain_length_analysis ) { try { SurfacingUtil.executeDomainLengthAnalysis( input_file_properties, number_of_genomes, @@ -1758,7 +1817,8 @@ public class surfacing { final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field, sort_by_species_count_first, number_of_genomes == 2, - CALC_SIMILARITY_SCORES ); + CALC_SIMILARITY_SCORES, + true ); switch ( scoring ) { case COMBINATIONS: pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator(); @@ -1908,7 +1968,8 @@ public class surfacing { } if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) { final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs, - e_value_max, + ie_value_max, + fs_e_value_max, max_allowed_overlap, no_engulfing_overlaps, cutoff_scores_file, @@ -1943,7 +2004,8 @@ public class surfacing { domain_length_stats_by_domain, tax_code_to_id_map, write_to_nexus, - use_last_in_fitch_parsimony ); + use_last_in_fitch_parsimony, + perform_dc_fich ); // 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 ) ) { @@ -2000,7 +2062,8 @@ public class surfacing { SurfacingUtil.writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list, - output_list_of_all_proteins_per_domain_e_value_max ); + output_list_of_all_proteins_per_domain_e_value_max, + positive_filter_file != null ? filter : null ); } gwcd_list = null; if ( all_bin_domain_combinations_gained_fitch != null ) { @@ -2075,7 +2138,8 @@ public class surfacing { 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_I_E_VALUE_OPTION + ": max (inclusive) iE-value" ); + System.out.println( surfacing.MAX_FS_E_VALUE_OPTION + ": max (inclusive) FS 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" ); @@ -2118,6 +2182,8 @@ public class surfacing { System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=: to perfom parsimony analysis on secondary features" ); System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); + System.out.println( surfacing.DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION + + ": to output binary domain counts (as individual files)" ); 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" ); @@ -2125,19 +2191,14 @@ public class surfacing { + ": 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_FITCH + ": to perform DC Fitch parsimony" ); 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( DA_ANALYSIS_OPTION + ": to perform DA analysis" ); + System.out.println( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION + ": to perform domain length 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" - + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o " - + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" ); System.out.println(); - System.out.println( "Example 2: 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 -genomes=eukaryotes.txt " - + "-ds_output=detailed_html -scoring=domains -sort=alpha " ); + System.out + .println( "Example: surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_156.xml -last -detail=punctilious -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); System.out.println(); } }