import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.protein.BasicProtein;
import org.forester.protein.BinaryDomainCombination;
import org.forester.protein.Domain;
import org.forester.protein.DomainId;
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 INFER_SPECIES_TREES_OPTION = "species_tree_inference";
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_FILES_FROM_FILE_OPTION = "input";
+ 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 char SEPARATOR_FOR_INPUT_VALUES = '#';
- final static private String PRG_VERSION = "2.252";
- final static private String PRG_DATE = "2012.08.01";
+ final static private String PRG_VERSION = "2.260";
+ final static private String PRG_DATE = "130721";
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;
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 = 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,
allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
allowed_options.add( JACKNIFE_RATIO_OPTION );
allowed_options.add( INPUT_SPECIES_TREE_OPTION );
- //allowed_options.add( INFER_SPECIES_TREES_OPTION );
allowed_options.add( FILTER_POSITIVE_OPTION );
allowed_options.add( FILTER_NEGATIVE_OPTION );
- allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
+ allowed_options.add( INPUT_GENOMES_FILE_OPTION );
allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
allowed_options.add( IGNORE_VIRAL_IDS );
plus_minus_analysis_high_copy_target_species,
plus_minus_analysis_high_low_copy_species,
plus_minus_analysis_numbers );
- File input_files_file = null;
- String[] input_file_names_from_file = null;
- if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
- if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
- + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
- }
- input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
- final String msg = ForesterUtil.isReadableFile( input_files_file );
+ File input_genomes_file = null;
+ if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -"
+ + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
+ }
+ input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( input_genomes_file );
if ( !ForesterUtil.isEmpty( msg ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
- }
- try {
- input_file_names_from_file = ForesterUtil.file2array( input_files_file );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg );
}
}
- if ( ( cla.getNumberOfNames() < 1 )
- && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME,
- "No hmmpfam output file indicated is input: use comand line directly or "
- + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
+ + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
}
DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
double output_list_of_all_proteins_per_domain_e_value_max = -1;
if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
output_protein_lists_for_all_domains = true;
- //
if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
try {
output_list_of_all_proteins_per_domain_e_value_max = cla
ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
}
}
- //
}
Detailedness detailedness = DETAILEDNESS_DEFAULT;
if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
}
else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
- // domain_similarity_print_option =
- // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
}
else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
+ surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
}
}
- String[][] input_file_properties = null;
- if ( input_file_names_from_file != null ) {
- input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
- }
- else {
- input_file_properties = surfacing.processInputFileNames( cla.getNames() );
+ 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 ) {
automated_pairwise_comparison_suffix,
out_dir );
for( int i = 0; i < number_of_genomes; i++ ) {
- File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
+ File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
+ surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
if ( out_dir != null ) {
dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
}
}
}
- // boolean infer_species_trees = false;
- // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
- // if ( ( output_file == null ) || ( number_of_genomes < 3 )
- // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
- // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
- // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
- // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- // + "=<suffix for pairwise comparison output files>)" );
- // }
- // infer_species_trees = true;
- // }
File[] intree_files = null;
Phylogeny[] intrees = null;
if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
+ surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
}
System.out.println( "Output directory : " + out_dir );
- if ( input_file_names_from_file != null ) {
- System.out.println( "Input files names from : " + input_files_file + " ["
- + input_file_names_from_file.length + " input files]" );
- html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
- + input_file_names_from_file.length + " input files]</td></tr>" + nl );
- }
+ System.out.println( "Input genomes from : " + input_genomes_file );
+ html_desc.append( "<tr><td>Input genomes from:</td><td>" + input_genomes_file + "</td></tr>" + nl );
if ( positive_filter_file != null ) {
final int filter_size = filter.size();
System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size
System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) );
System.out.println( " Random number seed : " + random_seed );
}
- // if ( infer_species_trees ) {
- // html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
- // System.out.println( " Infer species trees : true" );
- // }
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
BufferedWriter domains_per_potein_stats_writer = null;
try {
domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
- + output_file + "__domains_per_potein_stats.txt" ) );
+ + output_file + "_domains_per_potein_stats.txt" ) );
domains_per_potein_stats_writer.write( "Genome" );
domains_per_potein_stats_writer.write( "\t" );
domains_per_potein_stats_writer.write( "Mean" );
System.out.println();
System.out.println( ( i + 1 ) + "/" + number_of_genomes );
log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
- System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
- log( "Genome : " + input_file_properties[ i ][ 0 ], 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 );
HmmscanPerDomainTableParser parser = null;
INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
if ( individual_score_cutoffs != null ) {
int distinct_das = -1;
if ( DA_ANALYSIS ) {
final String genome = input_file_properties[ i ][ 0 ];
- distinct_das = storeDomainArchitectures( genome,
- distinct_domain_architecutures_per_genome,
- protein_list,
- distinct_domain_architecuture_counts );
+ distinct_das = SurfacingUtil.storeDomainArchitectures( genome,
+ distinct_domain_architecutures_per_genome,
+ protein_list,
+ distinct_domain_architecuture_counts );
}
System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
+ parser.getProteinsIgnoredDueToFilter() );
}
html_desc.append( "</td></tr>" + nl );
- // domain_partner_counts_array[ i ] =
- // Methods.getDomainPartnerCounts( protein_domain_collections_array[
- // i ],
- // false, input_file_properties[ i ][ 1 ] );
try {
int count = 0;
for( final Protein protein : protein_list ) {
domains_which_are_sometimes_single_sometimes_not,
domains_which_never_single,
domains_per_potein_stats_writer );
- gwcd_list.add( BasicGenomeWideCombinableDomains
- .createInstance( protein_list,
- ignore_combination_with_same,
- new BasicSpecies( input_file_properties[ i ][ 1 ] ),
- domain_id_to_go_ids_map,
- dc_type,
- protein_length_stats_by_dc,
- domain_number_stats_by_dc ) );
domain_lengths_table.addLengths( protein_list );
- 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_graph_analysis ) {
- SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
- out_dir,
- gwcd_list.get( i ),
- i,
- dc_sort_order );
+ if ( !DA_ANALYSIS ) {
+ gwcd_list.add( BasicGenomeWideCombinableDomains
+ .createInstance( protein_list,
+ ignore_combination_with_same,
+ new BasicSpecies( input_file_properties[ i ][ 1 ] ),
+ domain_id_to_go_ids_map,
+ dc_type,
+ 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_graph_analysis ) {
+ SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
+ out_dir,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ }
+ SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
+ SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
+ all_bin_domain_combinations_encountered );
}
- SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
- SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
- all_bin_domain_combinations_encountered );
}
if ( query_domains_writer_ary != null ) {
for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ per_genome_domain_promiscuity_statistics_file );
//
if ( DA_ANALYSIS ) {
- performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
- distinct_domain_architecuture_counts,
- ForesterUtil.roundToInt( number_of_genomes / 2.0 ) );
+ SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
+ distinct_domain_architecuture_counts,
+ 10,
+ new File( out_dir.toString() + "/" + output_file
+ + "_DA_counts.txt" ),
+ new File( out_dir.toString() + "/" + output_file
+ + "_unique_DAs.txt" ) );
distinct_domain_architecutures_per_genome.clear();
distinct_domain_architecuture_counts.clear();
System.gc();
domains_per_potein_stats_writer.close();
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" );
+ + "_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
- + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
+ + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
- + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
+ + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
- + "__domains_always_combined.txt" ), domains_which_never_single, "\n" );
+ + "_domains_always_combined.txt" ), domains_which_never_single, "\n" );
ForesterUtil.programMessage( PRG_NAME,
"Average of proteins with a least one domain assigned: "
+ ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
System.out.println();
}
- private static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
- final SortedMap<String, Integer> domain_architecuture_counts,
- final int min_count ) {
- final StringBuilder unique_das = new StringBuilder();
- final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
- System.out.println( "Domain Architecture Counts (min count: " + min_count + " ):" );
- while ( it.hasNext() ) {
- final Map.Entry<String, Integer> e = it.next();
- final String da = e.getKey();
- final int count = e.getValue();
- if ( count >= min_count ) {
- System.out.println( da + "\t" + count );
- }
- if ( count == 1 ) {
- final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
- while ( it2.hasNext() ) {
- final Map.Entry<String, Set<String>> e2 = it2.next();
- final String genome = e2.getKey();
- final Set<String> das = e2.getValue();
- if ( das.contains( da ) ) {
- unique_das.append( genome + "\t" + da + ForesterUtil.LINE_SEPARATOR );
- }
- }
- }
- }
- System.out.println();
- System.out.println();
- System.out.println( "Unique Domain Architectures:" );
- System.out.println( unique_das );
- System.out.println();
- System.out.println();
- }
-
- private static int storeDomainArchitectures( final String genome,
- final SortedMap<String, Set<String>> domain_architecutures,
- final List<Protein> protein_list,
- final Map<String, Integer> distinct_domain_architecuture_counts ) {
- final Set<String> da = new HashSet<String>();
- domain_architecutures.put( genome, da );
- for( final Protein protein : protein_list ) {
- final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~" );
- if ( !da.contains( da_str ) ) {
- if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
- distinct_domain_architecuture_counts.put( da_str, 1 );
- }
- else {
- distinct_domain_architecuture_counts.put( da_str,
- distinct_domain_architecuture_counts.get( da_str ) + 1 );
- }
- da.add( da_str );
- }
- }
- return da.size();
- }
-
private static void createSplitWriters( final File out_dir,
final String my_outfile,
final Map<Character, Writer> split_writers ) throws IOException {
+ "=<file>: to filter out proteins containing at least one domain listed in <file>" );
System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
+ "=<file>: to filter out (ignore) domains listed in <file>" );
- System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
+ System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>: to read input files from <file>" );
System.out
.println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
+ "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
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 -input=genomes_limited.txt -out_dir=out -o=o "
+ + " -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 "
- + "-ds_output=detailed_html -scoring=domains -sort=alpha human mouse brafl strpu" );
+ + "-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();
}
}
}
- private static String[][] processInputFileNames( final String[] names ) {
- final String[][] input_file_properties = new String[ names.length ][];
- for( int i = 0; i < names.length; ++i ) {
- if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
- input_file_properties[ i ] = new String[ 2 ];
- input_file_properties[ i ][ 0 ] = names[ i ];
- input_file_properties[ i ][ 1 ] = names[ i ];
- }
- else {
- input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
- if ( input_file_properties[ i ].length != 3 ) {
- ForesterUtil
- .fatalError( surfacing.PRG_NAME,
- "properties for the input files (hmmpfam output) are expected "
- + "to be in the following format \"<hmmpfam output file>#<species>\" (or just one word, which is both the filename and the species id), instead received \""
- + names[ i ] + "\"" );
- }
- }
+ 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() );
+ }
+ for( int i = 0; i < input_file_properties.length; ++i ) {
final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, error );
git://source.jalview.org / jalview.git / blobdiff