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 = "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;
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";
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 fs_e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
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 {
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;
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 ) ) {
all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
}
- 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;
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<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
}
+ DomainLengthsTable domain_lengths_table = null;
+ if ( domain_length_analysis ) {
+ domain_lengths_table = new DomainLengthsTable();
+ }
// Main loop:
final SortedMap<String, Set<String>> distinct_domain_architecutures_per_genome = new TreeMap<String, Set<String>>();
final SortedMap<String, Integer> distinct_domain_architecuture_counts = new TreeMap<String, Integer>();
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,
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() + "" );
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" );
+ ( 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() );
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,
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( 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 -ie=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();
}
}
git://source.jalview.org / jalview.git / blobdiff