X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FSequenceAccessionTools.java;h=aaa42aa182dc9bd8b5deb4137a19d04f66508386;hb=0b49b8e750b34d28a5989facdd8a7959870de996;hp=c65fbc5039f423b5da06a77dbe6ffdfdc0cc0992;hpb=397137f4f105810096dc6034ccc1e1013ed11644;p=jalview.git diff --git a/forester/java/src/org/forester/util/SequenceAccessionTools.java b/forester/java/src/org/forester/util/SequenceAccessionTools.java index c65fbc5..aaa42aa 100644 --- a/forester/java/src/org/forester/util/SequenceAccessionTools.java +++ b/forester/java/src/org/forester/util/SequenceAccessionTools.java @@ -33,40 +33,38 @@ import java.util.regex.Pattern; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Accession; +import org.forester.phylogeny.data.Accession.Source; import org.forester.phylogeny.data.Sequence; public final class SequenceAccessionTools { - // gb_ADF31344_1_segmented_worms_ - // gb_AAA96518_1 - // gb_EHB07727_1_rodents_ - // dbj_BAF37827_1_turtles_ - // emb_CAA73223_1_primates_ - // lcl_91970_unknown_ - // mites|ref_XP_002434188_1 - // ref_XP_002434188_1_mites___ticks_ - // ref_NP_001121530_1_frogs___toads_ //The format for GenBank Accession numbers are: //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals //Protein: 3 letters + 5 numerals //http://www.ncbi.nlm.nih.gov/Sequin/acc.html - public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); - public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); - public final static Pattern GENBANK_PROT_PATTERN = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); - public final static Pattern GI_PATTERN = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" ); - public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "\\b([A-Z][0-9][A-Z0-9]{3}[0-9])\\b" ); - public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern - .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" ); - public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern - .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" ); - // RefSeq accession numbers can be distinguished from GenBank accessions + public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + public final static Pattern GENBANK_PROT_PATTERN = Pattern + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + public final static Pattern GI_PATTERN = Pattern + .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" ); + public final static String UNIPROT_KB_BASE_PATTERN_STR = "((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))"; + public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "(?:\\b|_)" + + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); + public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]" + + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); + public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern + .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|" + + UNIPROT_KB_BASE_PATTERN_STR + + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" ); + public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" ); + // RefSeq accession numbers can be distinguished from GenBank accessions // by their distinct prefix format of 2 characters followed by an - // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. - private final static Pattern REFSEQ_PATTERN = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" ); + // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. + private final static Pattern REFSEQ_PATTERN = Pattern + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" ); private SequenceAccessionTools() { // Hiding the constructor. @@ -87,19 +85,19 @@ public final class SequenceAccessionTools { public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) { String a = obtainUniProtAccessorFromDataFields( n ); if ( !ForesterUtil.isEmpty( a ) ) { - return new Accession( a, Accession.UNIPROT ); + return new Accession( a, Source.UNIPROT ); } a = obtainGenbankAccessorFromDataFields( n ); if ( !ForesterUtil.isEmpty( a ) ) { - return new Accession( a, Accession.NCBI ); + return new Accession( a, Source.NCBI ); } a = obtainRefSeqAccessorFromDataFields( n ); if ( !ForesterUtil.isEmpty( a ) ) { - return new Accession( a, Accession.REFSEQ ); + return new Accession( a, Source.REFSEQ ); } a = obtainGiNumberFromDataFields( n ); if ( !ForesterUtil.isEmpty( a ) ) { - return new Accession( a, Accession.GI ); + return new Accession( a, Source.GI ); } return null; } @@ -112,19 +110,19 @@ public final class SequenceAccessionTools { final String value = n.getNodeData().getSequence().getAccession().getValue(); if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source .equals( "sp" ) ) ) { - return new Accession( value, Accession.UNIPROT ); + return new Accession( value, Source.UNIPROT ); } else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) { - return new Accession( value, Accession.EMBL ); + return new Accession( value, Source.EMBL ); } else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) { - return new Accession( value, Accession.NCBI ); + return new Accession( value, Source.NCBI ); } else if ( source.equals( "refseq" ) ) { - return new Accession( value, Accession.REFSEQ ); + return new Accession( value, Source.REFSEQ ); } else if ( source.equals( "gi" ) ) { - return new Accession( value, Accession.GI ); + return new Accession( value, Source.GI ); } } return null; @@ -227,19 +225,23 @@ public final class SequenceAccessionTools { if ( !ForesterUtil.isEmpty( s ) ) { String v = parseUniProtAccessorFromString( s ); if ( !ForesterUtil.isEmpty( v ) ) { - return new Accession( v, Accession.UNIPROT ); + return new Accession( v, Source.UNIPROT ); } v = parseGenbankAccessorFromString( s ); if ( !ForesterUtil.isEmpty( v ) ) { - return new Accession( v, Accession.NCBI ); + return new Accession( v, Source.NCBI ); } v = parseRefSeqAccessorFromString( s ); if ( !ForesterUtil.isEmpty( v ) ) { - return new Accession( v, Accession.REFSEQ ); + return new Accession( v, Source.REFSEQ ); } v = parseGInumberFromString( s ); if ( !ForesterUtil.isEmpty( v ) ) { - return new Accession( v, Accession.GI ); + return new Accession( v, Source.GI ); + } + v = parseEnsemlAccessorFromString( s ); + if ( !ForesterUtil.isEmpty( v ) ) { + return new Accession( v, Source.ENSEMBL ); } } return null; @@ -285,6 +287,14 @@ public final class SequenceAccessionTools { return null; } + public final static String parseEnsemlAccessorFromString( final String s ) { + final Matcher m = ENSEMBL_PATTERN.matcher( s ); + if ( m.find() ) { + return m.group( 1 ); + } + return null; + } + public final static String parseRefSeqAccessorFromString( final String s ) { final Matcher m = REFSEQ_PATTERN.matcher( s ); if ( m.lookingAt() ) { @@ -294,11 +304,7 @@ public final class SequenceAccessionTools { } public final static String parseUniProtAccessorFromString( final String s ) { - Matcher m = UNIPROT_KB_PATTERN_0.matcher( s ); - if ( m.find() ) { - return m.group( 1 ); - } - m = UNIPROT_KB_PATTERN_1.matcher( s ); + Matcher m = UNIPROT_KB_PATTERN_1.matcher( s ); if ( m.find() ) { return m.group( 1 ); } @@ -306,6 +312,10 @@ public final class SequenceAccessionTools { if ( m.find() ) { return m.group(); } + m = UNIPROT_KB_PATTERN_0.matcher( s ); + if ( m.find() ) { + return m.group( 1 ); + } return null; } }