package org.forester.surfacing;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import org.forester.application.surfacing;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.species.BasicSpecies;
import org.forester.species.Species;
+import org.forester.surfacing.SurfacingUtil.DomainComparator;
+import org.forester.util.ForesterUtil;
public final class MinimalDomainomeCalculator {
+ public final static void calc( final boolean use_domain_architectures,
+ final Phylogeny tre,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final String separator,
+ final double ie_cutoff,
+ final String outfile_base,
+ final boolean write_protein_files )
+ throws IOException {
+ final SortedMap<String, SortedSet<String>> species_to_features_map = new TreeMap<String, SortedSet<String>>();
+ if ( protein_lists_per_species == null || tre == null ) {
+ throw new IllegalArgumentException( "argument is null" );
+ }
+ if ( protein_lists_per_species.size() < 2 ) {
+ throw new IllegalArgumentException( "not enough genomes" );
+ }
+ final String x;
+ if ( use_domain_architectures ) {
+ x = "DA";
+ }
+ else {
+ x = "domain";
+ }
+ final File outfile = new File( outfile_base + "_minimal_" + x + "ome.tsv" );
+ final File outfile_table = new File( outfile_base + "_minimal_" + x + "ome_matrix.tsv" );
+ SurfacingUtil.checkForOutputFileWriteability( outfile );
+ SurfacingUtil.checkForOutputFileWriteability( outfile_table );
+ final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+ final BufferedWriter out_table = new BufferedWriter( new FileWriter( outfile_table ) );
+ out.write( "SPECIES\tCOMMON NAME\tCODE\tRANK\t#EXT NODES\tEXT NODE CODES\t#" + x + "\t" + x + "" );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final String species_name = node.getNodeData().isHasTaxonomy()
+ ? node.getNodeData().getTaxonomy().getScientificName() : node.getName();
+ final String common = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getCommonName()
+ : "";
+ final String tcode = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getTaxonomyCode()
+ : "";
+ final String rank = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getRank() : "";
+ out.write( species_name );
+ if ( !ForesterUtil.isEmpty( common ) ) {
+ out.write( "\t" + common );
+ }
+ else {
+ out.write( "\t" );
+ }
+ if ( !ForesterUtil.isEmpty( tcode ) ) {
+ out.write( "\t" + tcode );
+ }
+ else {
+ out.write( "\t" );
+ }
+ if ( !ForesterUtil.isEmpty( rank ) ) {
+ out.write( "\t" + rank );
+ }
+ else {
+ out.write( "\t" );
+ }
+ final List<PhylogenyNode> external_descs = node.getAllExternalDescendants();
+ if ( node.isInternal() ) {
+ out.write( "\t" + external_descs.size() + "\t" );
+ }
+ else {
+ out.write( "\t\t" );
+ }
+ final List<Set<String>> features_per_genome_list = new ArrayList<Set<String>>();
+ boolean first = true;
+ for( final PhylogenyNode external_desc : external_descs ) {
+ final String code = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
+ if ( node.isInternal() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out.write( ", " );
+ }
+ out.write( code );
+ }
+ final List<Protein> proteins_per_species = protein_lists_per_species.get( new BasicSpecies( code ) );
+ if ( proteins_per_species != null ) {
+ final SortedSet<String> features_per_genome = new TreeSet<String>();
+ for( final Protein protein : proteins_per_species ) {
+ if ( use_domain_architectures ) {
+ final String da = protein.toDomainArchitectureString( separator, ie_cutoff );
+ features_per_genome.add( da );
+ }
+ else {
+ List<Domain> domains = protein.getProteinDomains();
+ for( final Domain domain : domains ) {
+ if ( ( ie_cutoff <= -1 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
+ features_per_genome.add( domain.getDomainId() );
+ }
+ }
+ }
+ }
+ if ( features_per_genome.size() > 0 ) {
+ features_per_genome_list.add( features_per_genome );
+ }
+ }
+ }
+ if ( features_per_genome_list.size() > 0 ) {
+ SortedSet<String> intersection = calcIntersection( features_per_genome_list );
+ out.write( "\t" + intersection.size() + "\t" );
+ first = true;
+ for( final String s : intersection ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out.write( ", " );
+ }
+ out.write( s );
+ }
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ species_to_features_map.put( species_name, intersection );
+ }
+ }
+ final SortedSet<String> all_species_names = new TreeSet<String>();
+ final SortedSet<String> all_features = new TreeSet<String>();
+ for( final Entry<String, SortedSet<String>> e : species_to_features_map.entrySet() ) {
+ all_species_names.add( e.getKey() );
+ for( final String f : e.getValue() ) {
+ all_features.add( f );
+ }
+ }
+ out_table.write( '\t' );
+ boolean first = true;
+ for( final String species_name : all_species_names ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out_table.write( '\t' );
+ }
+ out_table.write( species_name );
+ }
+ out_table.write( ForesterUtil.LINE_SEPARATOR );
+ for( final String das : all_features ) {
+ out_table.write( das );
+ out_table.write( '\t' );
+ first = true;
+ for( final String species_name : all_species_names ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out_table.write( '\t' );
+ }
+ if ( species_to_features_map.get( species_name ).contains( das ) ) {
+ out_table.write( '1' );
+ }
+ else {
+ out_table.write( '0' );
+ }
+ }
+ out_table.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ out.flush();
+ out.close();
+ out_table.flush();
+ out_table.close();
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to : " + outfile );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote minimal DAome data to (as table): " + outfile_table );
+ if ( write_protein_files ) {
+ final String protdirname;
+ final String a;
+ final String b;
+ if ( use_domain_architectures ) {
+ a = "_DA";
+ b = "domain architectures (DAs)";
+ protdirname = "_DAS";
+ }
+ else {
+ a = "_domain";
+ b = "domains";
+ protdirname = "_DOMAINS";
+ }
+ final File prot_dir = new File( outfile_base + protdirname );
+ final boolean success = prot_dir.mkdir();
+ if ( !success ) {
+ throw new IOException( "failed to create dir " + prot_dir );
+ }
+ int total = 0;
+ final String dir = outfile_base + protdirname + "/";
+ for( final String feat : all_features ) {
+ final File extract_outfile = new File( dir + feat + a + surfacing.SEQ_EXTRACT_SUFFIX );
+ SurfacingUtil.checkForOutputFileWriteability( extract_outfile );
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( extract_outfile ) );
+ final int counter = extractProteinFeatures( use_domain_architectures,
+ protein_lists_per_species,
+ feat,
+ proteins_file_writer,
+ ie_cutoff,
+ separator );
+ if ( counter < 1 ) {
+ ForesterUtil.printWarningMessage( "surfacing", feat + " not present (in " + b + " extraction)" );
+ }
+ total += counter;
+ proteins_file_writer.close();
+ }
+ ForesterUtil.programMessage( "surfacing",
+ "Wrote " + total + " individual " + b + " from a total of "
+ + all_features.size() + " into: " + dir );
+ }
+ }
+
+ private final static SortedSet<String> calcIntersection( final List<Set<String>> features_per_genome_list ) {
+ final Set<String> first = features_per_genome_list.get( 0 );
+ final SortedSet<String> my_first = new TreeSet<String>();
+ for( final String s : first ) {
+ my_first.add( s );
+ }
+ for( int i = 1; i < features_per_genome_list.size(); ++i ) {
+ my_first.retainAll( features_per_genome_list.get( i ) );
+ }
+ return my_first;
+ }
+
+ private final static int extractProteinFeatures( final boolean use_domain_architectures,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final String domain_id,
+ final Writer out,
+ final double ie_cutoff,
+ final String domain_separator )
+ throws IOException {
+ int counter = 0;
+ final String separator_for_output = "\t";
+ for( final Species species : protein_lists_per_species.keySet() ) {
+ final List<Protein> proteins_per_species = protein_lists_per_species.get( species );
+ for( final Protein protein : proteins_per_species ) {
+ if ( use_domain_architectures ) {
+ if ( domain_id.equals( protein.toDomainArchitectureString( domain_separator, ie_cutoff ) ) ) {
+ int from = Integer.MAX_VALUE;
+ int to = -1;
+ for( final Domain d : protein.getProteinDomains() ) {
+ if ( ( ie_cutoff <= -1 ) || ( d.getPerDomainEvalue() <= ie_cutoff ) ) {
+ if ( d.getFrom() < from ) {
+ from = d.getFrom();
+ }
+ if ( d.getTo() > to ) {
+ to = d.getTo();
+ }
+ }
+ }
+ out.write( protein.getSpecies().getSpeciesId() );
+ out.write( separator_for_output );
+ out.write( protein.getProteinId().getId() );
+ out.write( separator_for_output );
+ out.write( domain_id );
+ out.write( separator_for_output );
+ out.write( "/" );
+ out.write( from + "-" + to );
+ out.write( "/" );
+ out.write( SurfacingConstants.NL );
+ ++counter;
+ }
+ }
+ else {
+ final List<Domain> domains = protein.getProteinDomains( domain_id );
+ if ( domains.size() > 0 ) {
+ out.write( protein.getSpecies().getSpeciesId() );
+ out.write( separator_for_output );
+ out.write( protein.getProteinId().getId() );
+ out.write( separator_for_output );
+ out.write( domain_id );
+ out.write( separator_for_output );
+ for( final Domain domain : domains ) {
+ if ( ( ie_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
+ out.write( "/" );
+ out.write( domain.getFrom() + "-" + domain.getTo() );
+ }
+ }
+ out.write( "/" );
+ out.write( separator_for_output );
+ final List<Domain> domain_list = new ArrayList<Domain>();
+ for( final Domain domain : protein.getProteinDomains() ) {
+ if ( ( ie_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= ie_cutoff ) ) {
+ domain_list.add( domain );
+ }
+ }
+ final Domain domain_ary[] = new Domain[ domain_list.size() ];
+ for( int i = 0; i < domain_list.size(); ++i ) {
+ domain_ary[ i ] = domain_list.get( i );
+ }
+ Arrays.sort( domain_ary, new DomainComparator( true ) );
+ out.write( "{" );
+ boolean first = true;
+ for( final Domain domain : domain_ary ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ out.write( "," );
+ }
+ out.write( domain.getDomainId().toString() );
+ out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
+ out.write( ":" + domain.getPerDomainEvalue() );
+ }
+ out.write( "}" );
+ if ( !( ForesterUtil.isEmpty( protein.getDescription() )
+ || protein.getDescription().equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getDescription() );
+ }
+ out.write( separator_for_output );
+ if ( !( ForesterUtil.isEmpty( protein.getAccession() )
+ || protein.getAccession().equals( SurfacingConstants.NONE ) ) ) {
+ out.write( protein.getAccession() );
+ }
+ out.write( SurfacingConstants.NL );
+ ++counter;
+ }
+ }
+ }
+ }
+ out.flush();
+ return counter;
+ }
+
public static void main( final String[] args ) {
Set<String> a = new HashSet<String>();
Set<String> b = new HashSet<String>();
d.add( "a" );
d.add( "c" );
d.add( "d" );
- List<Set<String>> domains_per_genome_list = new ArrayList();
+ List<Set<String>> domains_per_genome_list = new ArrayList<Set<String>>();
domains_per_genome_list.add( a );
domains_per_genome_list.add( b );
domains_per_genome_list.add( c );
domains_per_genome_list.add( d );
- Set<String> x = x( domains_per_genome_list );
+ Set<String> x = calcIntersection( domains_per_genome_list );
System.out.println( x );
}
-
- static final public void calc( Phylogeny tre, SortedMap<Species, List<Protein>> protein_lists_per_species ) {
- for( final PhylogenyNodeIterator iter = tre.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.isInternal() ) {
- System.out.println();
- if ( node.getNodeData().isHasTaxonomy() ) {
- System.out.println( node.getNodeData().getTaxonomy().getScientificName() + ":" );
- }
- else {
- System.out.println( node.getName() + ":" );
- }
- final List<PhylogenyNode> e = node.getAllExternalDescendants();
- final List<Set<String>> domains_per_genome_list = new ArrayList();
- for( PhylogenyNode en : e ) {
- final String code = en.getNodeData().getTaxonomy().getTaxonomyCode();
- System.out.print( code + " " );
- //System.out.println( protein_lists_per_species );
- final List<Protein> x = protein_lists_per_species.get( new BasicSpecies( code ) );
- if ( x != null ) {
- final Set<String> d = new HashSet<String>();
- for( Protein protein : x ) {
- List<Domain> domains = protein.getProteinDomains();
- for( Domain domain : domains ) {
- d.add( domain.getDomainId() );
- }
- }
- domains_per_genome_list.add( d );
- }
- }
- System.out.println();
- Set<String> x = x( domains_per_genome_list );
- System.out.println( x );
- }
- }
- }
-
- static final Set<String> x( List<Set<String>> domains_per_genome_list ) {
- Set<String> first = domains_per_genome_list.get( 0 );
- for( int i = 1; i < domains_per_genome_list.size(); ++i ) {
- first.retainAll( domains_per_genome_list.get( i ) );
- }
- return first;
- }
}
git://source.jalview.org / jalview.git / blobdiff