From 32b66090883b7ca47347fef19152d84bd02c0b9d Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Thu, 7 Jun 2012 06:36:03 +0000 Subject: [PATCH] phylotastic hackathon at NESCENT 120606 --- .../org/forester/analysis/TaxonomyDataManager.java | 10 +++--- .../tools/AncestralTaxonomyInferrer.java | 4 +-- .../archaeopteryx/tools/SequenceDataRetriver.java | 36 ++++++++++++------- .../org/forester/phylogeny/data/Identifier.java | 2 +- forester/java/src/org/forester/test/Test.java | 38 ++++++++++---------- .../src/org/forester/util/SequenceIdParser.java | 8 ++--- .../src/org/forester/ws/uniprot/EbiDbEntry.java | 16 +++++++-- .../forester/ws/uniprot/SequenceDatabaseEntry.java | 2 ++ ...{UniProtWsTools.java => SequenceDbWsTools.java} | 22 ++++++------ .../src/org/forester/ws/uniprot/UniProtEntry.java | 5 +++ 10 files changed, 83 insertions(+), 60 deletions(-) rename forester/java/src/org/forester/ws/uniprot/{UniProtWsTools.java => SequenceDbWsTools.java} (96%) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index 019df24..99c1de1 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -48,7 +48,7 @@ import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.ForesterUtil; import org.forester.ws.uniprot.UniProtTaxonomy; -import org.forester.ws.uniprot.UniProtWsTools; +import org.forester.ws.uniprot.SequenceDbWsTools; public final class TaxonomyDataManager extends RunnableProcess { @@ -176,19 +176,19 @@ public final class TaxonomyDataManager extends RunnableProcess { } private final static List getTaxonomiesFromCommonName( final String query ) throws IOException { - return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN ); + return SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN ); } private final static List getTaxonomiesFromId( final String query ) throws IOException { - return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN ); + return SequenceDbWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN ); } private final static List getTaxonomiesFromScientificName( final String query ) throws IOException { - return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN ); + return SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN ); } private final static List getTaxonomiesFromTaxonomyCode( final String query ) throws IOException { - return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN ); + return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN ); } static final boolean isHasAppropriateId( final Taxonomy tax ) { diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java index a42d1ec..ec8ba76 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java @@ -34,7 +34,7 @@ import org.forester.analysis.AncestralTaxonomyInferenceException; import org.forester.archaeopteryx.MainFrameApplication; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.Phylogeny; -import org.forester.ws.uniprot.UniProtWsTools; +import org.forester.ws.uniprot.SequenceDbWsTools; public class AncestralTaxonomyInferrer extends RunnableProcess { @@ -49,7 +49,7 @@ public class AncestralTaxonomyInferrer extends RunnableProcess { } public static String getBaseUrl() { - return UniProtWsTools.BASE_UNIPROT_URL; + return SequenceDbWsTools.BASE_UNIPROT_URL; } private void inferTaxonomies() { diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java index 507d28c..d389aec 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java @@ -25,7 +25,6 @@ package org.forester.archaeopteryx.tools; -import java.io.FileNotFoundException; import java.io.IOException; import java.net.UnknownHostException; import java.util.SortedSet; @@ -45,7 +44,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.ForesterUtil; import org.forester.util.SequenceIdParser; import org.forester.ws.uniprot.SequenceDatabaseEntry; -import org.forester.ws.uniprot.UniProtWsTools; +import org.forester.ws.uniprot.SequenceDbWsTools; public final class SequenceDataRetriver extends RunnableProcess { @@ -55,7 +54,7 @@ public final class SequenceDataRetriver extends RunnableProcess { private final static boolean DEBUG = true; private enum Db { - UNIPROT, EMBL, NCBI, NONE; + UNIPROT, EMBL, NCBI, NONE, REFSEQ; } public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) { @@ -170,11 +169,18 @@ public final class SequenceDataRetriver extends RunnableProcess { db = Db.EMBL; } else if ( !ForesterUtil.isEmpty( node.getName() ) ) { - if ( ( query = UniProtWsTools.parseUniProtAccessor( node.getName() ) ) != null ) { + if ( ( query = SequenceDbWsTools.parseUniProtAccessor( node.getName() ) ) != null ) { db = Db.UNIPROT; } else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) { - db = Db.NCBI; + + if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) { + db = Db.NCBI; + } + else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) { + db = Db.REFSEQ; + } + } } SequenceDatabaseEntry db_entry = null; @@ -183,25 +189,23 @@ public final class SequenceDataRetriver extends RunnableProcess { if ( DEBUG ) { System.out.println( "uniprot: " + query ); } - - db_entry = UniProtWsTools.obtainUniProtEntry( query, 200 ); - + db_entry = SequenceDbWsTools.obtainUniProtEntry( query, 200 ); } if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) { if ( DEBUG ) { System.out.println( "embl: " + query ); } - - db_entry = UniProtWsTools.obtainEmblEntry( query, 200 ); - + db_entry = SequenceDbWsTools.obtainEmblEntry( new Identifier( query ), 200 ); if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) { db = Db.EMBL; } } } + else if ( ( db == Db.REFSEQ ) && ( id != null ) ) { + db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, 200 ); + } else if ( ( db == Db.NCBI ) && ( id != null ) ) { - System.out.println( "db == Db.NCBI && id != null" ); - db_entry = UniProtWsTools.obtainrefSeqentryFromEmbl( id, 200 ); + db_entry = SequenceDbWsTools.obtainEmblEntry( id, 200 ); } if ( ( db_entry != null ) && !db_entry.isEmpty() ) { if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) { @@ -212,6 +216,12 @@ public final class SequenceDataRetriver extends RunnableProcess { else if ( db == Db.UNIPROT ) { type = "uniprot"; } + else if ( db == Db.NCBI ) { + type = "ncbi"; + } + else if ( db == Db.REFSEQ ) { + type = "refseq"; + } seq.setAccession( new Accession( db_entry.getAccession(), type ) ); } if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) { diff --git a/forester/java/src/org/forester/phylogeny/data/Identifier.java b/forester/java/src/org/forester/phylogeny/data/Identifier.java index 555743e..d3b4437 100644 --- a/forester/java/src/org/forester/phylogeny/data/Identifier.java +++ b/forester/java/src/org/forester/phylogeny/data/Identifier.java @@ -34,7 +34,7 @@ import org.forester.util.ForesterUtil; public final class Identifier implements PhylogenyData { - final public static String NCBI = "ncbi"; + final public static String NCBI = "ncbi"; final public static String REFSEQ = "refseq"; final private String _value; diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index cdad772..5704870 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -107,7 +107,7 @@ import org.forester.util.SequenceIdParser; import org.forester.ws.uniprot.DatabaseTools; import org.forester.ws.uniprot.SequenceDatabaseEntry; import org.forester.ws.uniprot.UniProtTaxonomy; -import org.forester.ws.uniprot.UniProtWsTools; +import org.forester.ws.uniprot.SequenceDbWsTools; import org.forester.ws.wabi.TxSearch; import org.forester.ws.wabi.TxSearch.RANKS; import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS; @@ -7850,7 +7850,7 @@ public final class Test { private static boolean testUniprotTaxonomySearch() { try { - List results = UniProtWsTools + List results = SequenceDbWsTools .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 ); if ( results.size() != 1 ) { return false; @@ -7871,7 +7871,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); if ( results.size() != 1 ) { return false; } @@ -7891,7 +7891,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 ); if ( results.size() != 1 ) { return false; } @@ -7911,7 +7911,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); if ( results.size() != 1 ) { return false; } @@ -8002,47 +8002,47 @@ public final class Test { } private static boolean testUniprotEntryRetrieval() { - if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { return false; } try { - final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 ); + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); if ( !entry.getAccession().equals( "P12345" ) ) { return false; } diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java index 767a310..d75a6dd 100644 --- a/forester/java/src/org/forester/util/SequenceIdParser.java +++ b/forester/java/src/org/forester/util/SequenceIdParser.java @@ -32,7 +32,6 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; import org.forester.phylogeny.data.Identifier; -import org.forester.ws.uniprot.DatabaseTools; public final class SequenceIdParser { @@ -65,11 +64,7 @@ public final class SequenceIdParser { private final static Pattern REFSEQ_PATTERN = Pattern .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" ); - - private final static boolean DEBUG = true; - - - + /** * Returns null if no match. @@ -78,6 +73,7 @@ public final class SequenceIdParser { public final static Identifier parse( final String s ) { String v = parseGenbankAccessor( s ); if ( !ForesterUtil.isEmpty( v ) ) { + return new Identifier( v, Identifier.NCBI ); } v = parseRefSeqAccessor( s ); diff --git a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java index 735d68f..c840dff 100644 --- a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java +++ b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java @@ -37,6 +37,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { private String _os; private String _tax_id; private String _symbol; + private String _provider; private EbiDbEntry() { } @@ -47,10 +48,10 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { } - public static SequenceDatabaseEntry createInstanceForRefSeq( final List lines ) { + public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List lines ) { final EbiDbEntry e = new EbiDbEntry(); for( final String line : lines ) { - System.out.println( "-" + line ); + // System.out.println( "-" + line ); if ( line.startsWith( "ACCESSION" ) ) { e.setPA( DatabaseTools.extract( line, "ACCESSION" ) ); } @@ -83,7 +84,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { public static SequenceDatabaseEntry createInstanceFromPlainText( final List lines ) { final EbiDbEntry e = new EbiDbEntry(); for( final String line : lines ) { - System.out.println( "->" + line ); + if ( line.startsWith( "PA" ) ) { e.setPA( DatabaseTools.extract( line, "PA" ) ); } @@ -175,4 +176,13 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) ); } + + @Override + public String getProvider() { + return _provider; + } + + public void setProvider( final String provider ) { + _provider = provider; + } } diff --git a/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java b/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java index 9089737..a98c004 100644 --- a/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java +++ b/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java @@ -30,6 +30,8 @@ public interface SequenceDatabaseEntry { public boolean isEmpty(); public String getAccession(); + + public String getProvider(); public String getSequenceName(); diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java b/forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java similarity index 96% rename from forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java rename to forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java index 65bea2d..83f3c6f 100644 --- a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java +++ b/forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java @@ -40,7 +40,7 @@ import java.util.regex.Pattern; import org.forester.phylogeny.data.Identifier; import org.forester.util.ForesterUtil; -public final class UniProtWsTools { +public final class SequenceDbWsTools { private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true; //TODO turn off for final realease! @@ -333,19 +333,19 @@ public final class UniProtWsTools { url_sb.append( BASE_EMBL_DB_URL ); if ( ForesterUtil.isEmpty( id.getProvider() ) || id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) { - url_sb.append( '/'); - url_sb.append( UniProtWsTools.EMBL_DBS_EMBL ); + + url_sb.append( SequenceDbWsTools.EMBL_DBS_EMBL ); url_sb.append( '/'); } else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) { if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) { - url_sb.append( '/'); - url_sb.append( UniProtWsTools.EMBL_DBS_REFSEQ_P ); + + url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_P ); url_sb.append( '/'); } else { - url_sb.append( '/'); - url_sb.append( UniProtWsTools.EMBL_DBS_REFSEQ_N ); + + url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N ); url_sb.append( '/'); } } @@ -391,15 +391,15 @@ public final class UniProtWsTools { return UniProtEntry.createInstanceFromPlainText( lines ); } - public static SequenceDatabaseEntry obtainrefSeqentryFromEmbl( final Identifier id, final int max_lines_to_return ) + public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Identifier id, final int max_lines_to_return ) throws IOException { final List lines = queryEmblDb( id, max_lines_to_return ); - return EbiDbEntry.createInstanceForRefSeq( lines ); + return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines ); } - public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return ) + public static SequenceDatabaseEntry obtainEmblEntry( final Identifier id, final int max_lines_to_return ) throws IOException { - final List lines = queryEmblDb( new Identifier( query ), max_lines_to_return ); + final List lines = queryEmblDb( id , max_lines_to_return ); return EbiDbEntry.createInstanceFromPlainText( lines ); } } diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java index cd5d541..d5056e6 100644 --- a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java +++ b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java @@ -139,4 +139,9 @@ public final class UniProtEntry implements SequenceDatabaseEntry { && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) ); } + + @Override + public String getProvider() { + return "uniprot"; + } } -- 1.7.10.2