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";
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 = "2.403";
- final static private String PRG_DATE = "131127";
+ final static private String PRG_VERSION = "2.404";
+ final static private String PRG_DATE = "140709";
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;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
output_binary_domain_combinationsfor_graph_analysis = true;
}
- final boolean output_binary_domain_combinationsfor_counts = false;
+ boolean output_binary_domain_combinationsfor_counts = false;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) {
- output_binary_domain_combinationsfor_graph_analysis = true;
+ output_binary_domain_combinationsfor_counts = true;
}
if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) {
try {
}
SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
}
- File pfam_to_go_file = null;
- Map<String, List<GoId>> domain_id_to_go_ids_map = null;
- int domain_id_to_go_ids_count = 0;
+ File pfam_to_go_file = new File( "pfam2go.txt" );
if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
+ surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
}
pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
- final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
- }
- try {
- final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
- final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
- domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
- if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
- ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
- "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
- }
- domain_id_to_go_ids_count = parser.getMappingCount();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ final String error1 = ForesterUtil.isReadableFile( pfam_to_go_file );
+ if ( !ForesterUtil.isEmpty( error1 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error1 );
+ }
+ Map<String, List<GoId>> domain_id_to_go_ids_map = null;
+ int domain_id_to_go_ids_count = 0;
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+ if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
+ "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
}
+ domain_id_to_go_ids_count = parser.getMappingCount();
}
- File go_obo_file = null;
- List<GoTerm> go_terms = null;
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ File go_obo_file = new File( "go.obo" );
if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
}
- if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
- + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
- + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
- }
go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
- final String error = ForesterUtil.isReadableFile( go_obo_file );
- if ( !ForesterUtil.isEmpty( error ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
- }
- try {
- final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
- go_terms = parser.parse();
- if ( parser.getGoTermCount() != go_terms.size() ) {
- ForesterUtil
- .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
- }
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
+ }
+ final String error2 = ForesterUtil.isReadableFile( go_obo_file );
+ if ( !ForesterUtil.isEmpty( error2 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error2 );
+ }
+ List<GoTerm> go_terms = null;
+ try {
+ final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
+ go_terms = parser.parse();
+ if ( parser.getGoTermCount() != go_terms.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
}
}
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
+ }
Map<GoId, GoTerm> go_id_to_term_map = null;
if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
&& ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
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();
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 ) {
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 -ie=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
- + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
+ System.out
+ .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" );
+ System.out.println();
+ System.out
+ .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -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();
}
}
git://source.jalview.org / jalview.git / blobdiff