import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sequence.MolecularSequence.TYPE;
import org.forester.util.ForesterUtil;
import org.forester.util.SequenceAccessionTools;
public final class SequenceDbWsTools {
- public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
- public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
- public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
- //public final static String EMBL_DBS_EMBL = "embl";
- public final static String EMBL_DBS_REFSEQ_N = "refseqn";
- public final static String EMBL_DBS_REFSEQ_P = "refseqp";
- private final static boolean DEBUG = true;
- private final static String URL_ENC = "UTF-8";
- public final static int DEFAULT_LINES_TO_RETURN = 4000;
-
- final static String extractFrom( final String target, final String a ) {
- final int i_a = target.indexOf( a );
- return target.substring( i_a + a.length() ).trim();
- }
-
- final static String extractFromTo( final String target, final String a, final String b ) {
- final int i_a = target.indexOf( a );
- final int i_b = target.indexOf( b );
- if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
- throw new IllegalArgumentException( "attempt to extract from \"" + target + "\" between \"" + a
- + "\" and \"" + b + "\"" );
- }
- return target.substring( i_a + a.length(), i_b ).trim();
- }
-
- final static String extractTo( final String target, final String b ) {
- final int i_b = target.indexOf( b );
- return target.substring( 0, i_b ).trim();
- }
+ public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
+ public final static int DEFAULT_LINES_TO_RETURN = 4000;
+ public final static String EMBL_DBS_REFSEQ_N = "refseqn";
+ public final static String EMBL_DBS_REFSEQ_P = "refseqp";
+ public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
+ public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
+ public final static String EMBL_EMBL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
+ private final static boolean DEBUG = true;
+ private final static String URL_ENC = "UTF-8";
+ private final static int SLEEP = 200;
+ private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false;
public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
* Does not return "sub-types".
* For example, for "Mus musculus" only returns "Mus musculus"
* and not "Mus musculus", "Mus musculus bactrianus", ...
- *
+ *
*/
public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict( final String sn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final String my_code = new String( code );
final List<String> result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
if ( result.size() > 0 ) {
return null;
}
+ public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc ) throws IOException {
+ return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
+ }
+
public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc, final int max_lines_to_return )
throws IOException {
final List<String> lines = queryEmblDb( acc, max_lines_to_return );
return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
}
- public static SequenceDatabaseEntry obtainEmblEntry( final Accession acc ) throws IOException {
- return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
+ public static SequenceDatabaseEntry obtainEntry( final String acc_str ) throws IOException {
+ if ( ForesterUtil.isEmpty( acc_str ) ) {
+ throw new IllegalArgumentException( "cannot not extract sequence db accessor from null or empty string" );
+ }
+ final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str );
+ if ( acc == null ) {
+ throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str
+ + "\"" );
+ }
+ if ( acc.getSource().equals( Source.REFSEQ.toString() ) || acc.getSource().equals( Source.EMBL.toString() )
+ || acc.getSource().equals( Source.NCBI.toString() ) ) {
+ return obtainEmblEntry( acc, DEFAULT_LINES_TO_RETURN );
+ }
+ else if ( acc.getSource().equals( Source.UNIPROT.toString() ) ) {
+ return obtainUniProtEntry( acc.getValue(), DEFAULT_LINES_TO_RETURN );
+ }
+ else {
+ throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource()
+ + "\"" );
+ }
}
- public final static Accession obtainSeqAccession( final PhylogenyNode node ) {
- Accession acc = SequenceAccessionTools.obtainFromSeqAccession( node );
- if ( !isAccessionAcceptable( acc ) ) {
- acc = SequenceAccessionTools.obtainAccessorFromDataFields( node );
- }
- return acc;
+ public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc ) throws IOException {
+ return obtainRefSeqEntryFromEmbl( acc, DEFAULT_LINES_TO_RETURN );
}
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc, final int max_lines_to_return )
return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
}
- public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Accession acc ) throws IOException {
- return obtainRefSeqEntryFromEmbl( acc, DEFAULT_LINES_TO_RETURN );
+ public final static Accession obtainSeqAccession( final PhylogenyNode node ) {
+ Accession acc = SequenceAccessionTools.obtainFromSeqAccession( node );
+ if ( !isAccessionAcceptable( acc ) ) {
+ acc = SequenceAccessionTools.obtainAccessorFromDataFields( node );
+ }
+ return acc;
}
public final static void obtainSeqInformation( final boolean allow_to_set_taxonomic_data,
obtainSeqInformation( allow_to_set_taxonomic_data, DEFAULT_LINES_TO_RETURN, not_found, node );
}
- public final static void obtainSeqInformation( final PhylogenyNode node ) throws IOException {
- obtainSeqInformation( true, DEFAULT_LINES_TO_RETURN, new TreeSet<String>(), node );
- }
-
public final static SortedSet<String> obtainSeqInformation( final Phylogeny phy,
final boolean ext_nodes_only,
final boolean allow_to_set_taxonomic_data,
return not_found;
}
- public static SequenceDatabaseEntry obtainUniProtEntry( final String query, final int max_lines_to_return )
- throws IOException {
- final List<String> lines = queryUniprot( "uniprot/" + query + ".txt", max_lines_to_return );
- return UniProtEntry.createInstanceFromPlainText( lines );
+ public final static void obtainSeqInformation( final PhylogenyNode node ) throws IOException {
+ obtainSeqInformation( true, DEFAULT_LINES_TO_RETURN, new TreeSet<String>(), node );
}
public static SequenceDatabaseEntry obtainUniProtEntry( final String query ) throws IOException {
return obtainUniProtEntry( query, DEFAULT_LINES_TO_RETURN );
}
+ public static SequenceDatabaseEntry obtainUniProtEntry( final String query, final int max_lines_to_return )
+ throws IOException {
+ final List<String> lines = queryUniprot( "uniprot/" + query + ".txt", max_lines_to_return );
+ return UniProtEntry.createInstanceFromPlainText( lines );
+ }
+
public static List<String> queryDb( final String query, int max_lines_to_return, final String base_url )
throws IOException {
if ( ForesterUtil.isEmpty( query ) ) {
}
in.close();
try {
- // To prevent accessing online dbs in too quick succession.
- Thread.sleep( 20 );
+ // To prevent accessing online dbs in too quick succession.
+ Thread.sleep( SLEEP );
}
catch ( final InterruptedException e ) {
e.printStackTrace();
return result;
}
- public static List<String> queryEmblDbForRefSeqEntry( final Accession id, final int max_lines_to_return )
- throws IOException {
- final StringBuilder url_sb = new StringBuilder();
- url_sb.append( EMBL_REFSEQ );
- return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
- }
-
- public static List<String> queryEmblDb( final Accession id, final int max_lines_to_return ) throws IOException {
+ public static List<String> queryEmblDb( final Accession acc, final int max_lines_to_return ) throws IOException {
final StringBuilder url_sb = new StringBuilder();
// url_sb.append( BASE_EMBL_DB_URL );
- if ( id.getSource().equals( Source.NCBI.toString() ) ) {
+ System.out.println( "source: " + acc.getSource() );
+ if ( acc.getSource().equals( Source.NCBI.toString() ) ) {
url_sb.append( EMBL_GENBANK );
//url_sb.append( '/' );
}
- else if ( id.getSource().equals( Source.REFSEQ.toString() ) ) {
+ else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
url_sb.append( EMBL_REFSEQ );
- // if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) {
- // url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_P );
- // url_sb.append( '/' );
- // }
- // else {
- // url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N );
- // url_sb.append( '/' );
- // }
+ }
+ else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
+ url_sb.append( EMBL_EMBL );
}
else {
- throw new IllegalArgumentException( "unable to handle source: " + id.getSource() );
+ throw new IllegalArgumentException( "unable to handle source: " + acc.getSource() );
}
+ return queryDb( acc.getValue(), max_lines_to_return, url_sb.toString() );
+ }
+
+ public static List<String> queryEmblDbForRefSeqEntry( final Accession id, final int max_lines_to_return )
+ throws IOException {
+ final StringBuilder url_sb = new StringBuilder();
+ url_sb.append( EMBL_REFSEQ );
return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
}
return queryDb( query, max_lines_to_return, BASE_UNIPROT_URL );
}
+ final static String extractFrom( final String target, final String a ) {
+ final int i_a = target.indexOf( a );
+ return target.substring( i_a + a.length() ).trim();
+ }
+
+ final static String extractFromTo( final String target, final String a, final String b ) {
+ final int i_a = target.indexOf( a );
+ final int i_b = target.indexOf( b );
+ if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
+ throw new IllegalArgumentException( "attempt to extract from \"" + target + "\" between \"" + a
+ + "\" and \"" + b + "\"" );
+ }
+ return target.substring( i_a + a.length(), i_b ).trim();
+ }
+
+ final static String extractTo( final String target, final String b ) {
+ final int i_b = target.indexOf( b );
+ return target.substring( 0, i_b ).trim();
+ }
+
private static void addDataFromDbToNode( final boolean allow_to_set_taxonomic_data,
final int lines_to_return,
final SortedSet<String> not_found,
// Eat this, and move to next.
}
}
- else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
+ else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
if ( DEBUG ) {
- System.out.println( "embl: " + query );
+ System.out.println( "refseq: " + query );
}
try {
- db_entry = obtainEmblEntry( new Accession( query ), lines_to_return );
+ db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
}
catch ( final FileNotFoundException e ) {
// Eat this, and move to next.
}
}
- else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
+ else if ( acc.getSource().equals( Source.EMBL.toString() ) || acc.getSource().equals( Source.NCBI.toString() )
+ || acc.getSource().equals( Source.EMBL.toString() ) ) {
if ( DEBUG ) {
- System.out.println( "refseq: " + query );
+ System.out.println( acc.toString() );
+ }
+ try {
+ db_entry = obtainEmblEntry( acc, lines_to_return );
+ }
+ catch ( final FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
+ }
+ else if ( acc.getSource().equals( Source.GI.toString() ) ) {
+ if ( DEBUG ) {
+ System.out.println( "gi: " + query );
}
try {
db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
// Eat this exception.
}
}
+ if ( ( db_entry.getMolecularSequence() != null )
+ && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
+ && ( ALLOW_TO_OVERWRITE_MOL_SEQ || seq.getMolecularSequence().isEmpty() ) ) {
+ seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() );
+ seq.setMolecularSequenceAligned( false );
+ if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) {
+ seq.setType( "protein" );
+ }
+ else if ( db_entry.getMolecularSequence().getType() == TYPE.DNA ) {
+ seq.setType( "dna" );
+ }
+ else if ( db_entry.getMolecularSequence().getType() == TYPE.RNA ) {
+ seq.setType( "rna" );
+ }
+ }
if ( ( db_entry.getGoTerms() != null ) && !db_entry.getGoTerms().isEmpty() ) {
for( final GoTerm go : db_entry.getGoTerms() ) {
final Annotation ann = new Annotation( go.getGoId().getId() );
seq.addCrossReference( x );
}
}
+ if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) && !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+ seq.setLocation( "chr " + db_entry.getChromosome() + ", " + db_entry.getMap() );
+ }
+ else if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) ) {
+ seq.setLocation( "chr " + db_entry.getChromosome() );
+ }
+ else if ( !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+ seq.setLocation( db_entry.getMap() );
+ }
final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy();
if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
tax.setScientificName( db_entry.getTaxonomyScientificName() );
}
}
try {
- Thread.sleep( 10 );// Sleep for 10 ms
+ Thread.sleep( SLEEP );
}
catch ( final InterruptedException ie ) {
}
private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc
.getSource().equals( Source.UNIPROT.toString() ) )
&& ( acc.getSource().toString().equals( Source.EMBL.toString() ) ) && ( acc.getSource().toString()
- .equals( Source.REFSEQ.toString() ) ) ) ) );
+ .equals( Source.REFSEQ.toString() ) ) ) ) );
}
private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result ) throws IOException {
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