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";
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 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 = "2.402";
+ final static private String PRG_DATE = "131126";
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;
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";
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
- allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
+ allowed_options.add( surfacing.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 );
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 );
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 ) {
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;
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 ) ) {
+ final boolean output_binary_domain_combinationsfor_counts = false;
+ if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) {
+ output_binary_domain_combinationsfor_graph_analysis = 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" );
System.out.println( "Cutoff scores file : " + cutoff_scores_file );
html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
}
- if ( e_value_max >= 0.0 ) {
- System.out.println( "E-value maximum (inclusive) : " + e_value_max );
- html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
+ if ( ie_value_max >= 0.0 ) {
+ System.out.println( "iE-value maximum (incl) : " + ie_value_max );
+ html_desc.append( "<tr><td>iE-value maximum (inclusive):</td><td>" + ie_value_max + "</td></tr>" + nl );
+ }
+ if ( fs_e_value_max >= 0.0 ) {
+ System.out.println( "FS E-value maximum (incl) : " + fs_e_value_max );
+ html_desc.append( "<tr><td>FS E-value maximum (inclusive):</td><td>" + fs_e_value_max + "</td></tr>" + 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 );
+ ( 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( "Fitch parsimony of DCs : " + perform_dc_fich );
+ html_desc.append( "<tr><td>Fitch parsimony of DCs:</td><td>" + perform_dc_fich + "</td></tr>" + nl );
+ if ( perform_dc_fich ) {
+ System.out.println( "Use last in Fitch parsimony : " + use_last_in_fitch_parsimony );
+ html_desc.append( "<tr><td>Use last in Fitch parsimony:</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 );
+ if ( perform_dc_fich ) {
+ 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 : " );
}
} // if ( perform_pwc ) {
System.out.println();
- html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
+ html_desc.append( "<tr><td>Command line:</td><td>" + nl + nl + cla.getCommandLineArgsAsString() + nl + nl
+ + "</td></tr>" + nl );
System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
BufferedWriter[] query_domains_writer_ary = null;
List<String>[] query_domain_ids_array = null;
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 );
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() );
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,
}
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,
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 ) ) {
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" );
System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
+ "=<file>: to perfom parsimony analysis on secondary features" );
System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
+ System.out.println( surfacing.DOMAIN_COMBINITONS_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" );
+ ": 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();
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 "
+ + "-dc_sort=dom -ignore_with_self -no_singles -ie=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
+ "-ds_output=detailed_html -scoring=domains -sort=alpha " );
System.out.println();
}
git://source.jalview.org / jalview.git / blobdiff