2 package org.forester.surfacing;
4 import java.io.BufferedWriter;
6 import java.io.FileWriter;
7 import java.io.IOException;
9 import java.util.ArrayList;
10 import java.util.Arrays;
11 import java.util.HashSet;
12 import java.util.List;
13 import java.util.Map.Entry;
15 import java.util.SortedMap;
16 import java.util.SortedSet;
17 import java.util.TreeMap;
18 import java.util.TreeSet;
20 import org.forester.application.surfacing;
21 import org.forester.phylogeny.Phylogeny;
22 import org.forester.phylogeny.PhylogenyNode;
23 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
24 import org.forester.protein.Domain;
25 import org.forester.protein.Protein;
26 import org.forester.species.BasicSpecies;
27 import org.forester.species.Species;
28 import org.forester.surfacing.SurfacingUtil.DomainComparator;
29 import org.forester.util.ForesterUtil;
31 public final class MinimalDomainomeCalculator {
33 static final public void calcOme( final boolean use_domain_architectures,
35 final SortedMap<Species, List<Protein>> protein_lists_per_species,
36 final String separator,
37 final double ie_cutoff,
38 final String outfile_base )
40 final SortedMap<String, SortedSet<String>> species_to_features_map = new TreeMap<String, SortedSet<String>>();
41 if ( protein_lists_per_species == null || tre == null ) {
42 throw new IllegalArgumentException( "argument is null" );
44 if ( protein_lists_per_species.size() < 2 ) {
45 throw new IllegalArgumentException( "not enough genomes" );
48 if ( use_domain_architectures ) {
54 final File outfile = new File( outfile_base + "_minimal_" + x + "ome.tsv" );
55 final File outfile_table = new File( outfile_base + "_minimal_" + x + "ome_matrix.tsv" );
56 SurfacingUtil.checkForOutputFileWriteability( outfile );
57 SurfacingUtil.checkForOutputFileWriteability( outfile_table );
58 final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
59 final BufferedWriter out_table = new BufferedWriter( new FileWriter( outfile_table ) );
60 out.write( "SPECIES\tCOMMON NAME\tCODE\tRANK\t#EXT NODES\tEXT NODE CODES\t#" + x + "\t" + x + "" );
61 out.write( ForesterUtil.LINE_SEPARATOR );
62 for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) {
63 final PhylogenyNode node = iter.next();
64 final String species_name = node.getNodeData().isHasTaxonomy()
65 ? node.getNodeData().getTaxonomy().getScientificName() : node.getName();
66 final String common = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getCommonName()
68 final String tcode = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getTaxonomyCode()
70 final String rank = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getRank() : "";
71 out.write( species_name );
72 if ( !ForesterUtil.isEmpty( common ) ) {
73 out.write( "\t" + common );
78 if ( !ForesterUtil.isEmpty( tcode ) ) {
79 out.write( "\t" + tcode );
84 if ( !ForesterUtil.isEmpty( rank ) ) {
85 out.write( "\t" + rank );
90 final List<PhylogenyNode> external_descs = node.getAllExternalDescendants();
91 if ( node.isInternal() ) {
92 out.write( "\t" + external_descs.size() + "\t" );
97 final List<Set<String>> features_per_genome_list = new ArrayList<Set<String>>();
99 for( final PhylogenyNode external_desc : external_descs ) {
100 final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
101 if ( node.isInternal() ) {
110 final List<Protein> proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) );
111 if ( proteins_per_species != null ) {
112 final SortedSet<String> features_per_genome = new TreeSet<String>();
113 for( final Protein protein : proteins_per_species ) {
114 if ( use_domain_architectures ) {
115 final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
116 features_per_genome.add( da );
119 List<Domain> domains = protein.getProteinDomains();
120 for( final Domain domain : domains ) {
121 if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
122 features_per_genome.add( domain.getDomainId() );
127 if ( features_per_genome.size() > 0 ) {
128 features_per_genome_list.add( features_per_genome );
132 if ( features_per_genome_list.size() > 0 ) {
133 SortedSet<String> intersection = calcIntersection( features_per_genome_list );
134 out.write( "\t" + intersection.size() + "\t" );
136 for( final String s : intersection ) {
145 out.write( ForesterUtil.LINE_SEPARATOR );
146 species_to_features_map.put( species_name, intersection );
149 final SortedSet<String> all_species_names = new TreeSet<String>();
150 final SortedSet<String> all_features = new TreeSet<String>();
151 for( final Entry<String, SortedSet<String>> e : species_to_features_map.entrySet() ) {
152 all_species_names.add( e.getKey() );
153 for( final String f : e.getValue() ) {
154 all_features.add( f );
157 out_table.write( '\t' );
158 boolean first = true;
159 for( final String species_name : all_species_names ) {
164 out_table.write( '\t' );
166 out_table.write( species_name );
168 out_table.write( ForesterUtil.LINE_SEPARATOR );
169 for( final String das : all_features ) {
170 out_table.write( das );
171 out_table.write( '\t' );
173 for( final String species_name : all_species_names ) {
178 out_table.write( '\t' );
180 if ( species_to_features_map.get( species_name ).contains( das ) ) {
181 out_table.write( '1' );
184 out_table.write( '0' );
187 out_table.write( ForesterUtil.LINE_SEPARATOR );
193 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to : " + outfile );
194 ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to (as table): " + outfile_table );
195 for( String f : all_features ) {
197 if ( use_domain_architectures ) {
203 final File prot_dir = new File( outfile_base + "_prot" );
205 final File outt = new File( outfile_base + "_prot/" + a + f + surfacing.SEQ_EXTRACT_SUFFIX );
206 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( outt ) );
207 extractProteinFeatures( use_domain_architectures,
208 protein_lists_per_species,
210 proteins_file_writer,
213 proteins_file_writer.close();
217 private final static SortedSet<String> calcIntersection( final List<Set<String>> features_per_genome_list ) {
218 final Set<String> first = features_per_genome_list.get( 0 );
219 final SortedSet<String> my_first = new TreeSet<String>();
220 for( final String s : first ) {
223 for( int i = 1; i < features_per_genome_list.size(); ++i ) {
224 my_first.retainAll( features_per_genome_list.get( i ) );
229 public static void extractProteinFeatures( final boolean use_domain_architectures,
230 final SortedMap<Species, List<Protein>> protein_lists_per_species,
231 final String domain_id,
233 final double ie_cutoff,
234 final String domain_separator )
236 final String separator_for_output = "\t";
237 for( final Species species : protein_lists_per_species.keySet() ) {
238 final List<Protein> proteins_per_species = protein_lists_per_species.get( species );
239 for( final Protein protein : proteins_per_species ) {
240 if ( use_domain_architectures ) {
241 if ( domain_id.equals( protein.toDomainArchitectureString( domain_separator, ie_cutoff ) ) ) {
242 int from = Integer.MAX_VALUE;
244 for( final Domain d : protein.getProteinDomains() ) {
245 if ( ( ie_cutoff <= -1 ) || ( d.getPerDomainEvalue() <= ie_cutoff ) ) {
246 if ( d.getFrom() < from ) {
249 if ( d.getTo() > to ) {
254 out.write( protein.getSpecies().getSpeciesId() );
255 out.write( separator_for_output );
256 out.write( protein.getProteinId().getId() );
257 out.write( separator_for_output );
258 out.write( domain_id );
259 out.write( separator_for_output );
261 out.write( from + "-" + to );
263 out.write( SurfacingConstants.NL );
267 final List<Domain> domains = protein.getProteinDomains( domain_id );
268 if ( domains.size() > 0 ) {
269 out.write( protein.getSpecies().getSpeciesId() );
270 out.write( separator_for_output );
271 out.write( protein.getProteinId().getId() );
272 out.write( separator_for_output );
273 out.write( domain_id );
274 out.write( separator_for_output );
275 for( final Domain domain : domains ) {
276 if ( ( ie_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
278 out.write( domain.getFrom() + "-" + domain.getTo() );
282 out.write( separator_for_output );
283 final List<Domain> domain_list = new ArrayList<Domain>();
284 for( final Domain domain : protein.getProteinDomains() ) {
285 if ( ( ie_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
286 domain_list.add( domain );
289 final Domain domain_ary[] = new Domain[ domain_list.size() ];
290 for( int i = 0; i < domain_list.size(); ++i ) {
291 domain_ary[ i ] = domain_list.get( i );
293 Arrays.sort( domain_ary, new DomainComparator( true ) );
295 boolean first = true;
296 for( final Domain domain : domain_ary ) {
303 out.write( domain.getDomainId().toString() );
304 out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
305 out.write( ":" + domain.getPerDomainEvalue() );
308 if ( !( ForesterUtil.isEmpty( protein.getDescription() )
309 || protein.getDescription().equals( SurfacingConstants.NONE ) ) ) {
310 out.write( protein.getDescription() );
312 out.write( separator_for_output );
313 if ( !( ForesterUtil.isEmpty( protein.getAccession() )
314 || protein.getAccession().equals( SurfacingConstants.NONE ) ) ) {
315 out.write( protein.getAccession() );
317 out.write( SurfacingConstants.NL );
325 public static void main( final String[] args ) {
326 Set<String> a = new HashSet<String>();
327 Set<String> b = new HashSet<String>();
328 Set<String> c = new HashSet<String>();
329 Set<String> d = new HashSet<String>();
344 List<Set<String>> domains_per_genome_list = new ArrayList<Set<String>>();
345 domains_per_genome_list.add( a );
346 domains_per_genome_list.add( b );
347 domains_per_genome_list.add( c );
348 domains_per_genome_list.add( d );
349 Set<String> x = calcIntersection( domains_per_genome_list );
350 System.out.println( x );