2 // FORESTER -- software libraries and applications
\r
3 // for evolutionary biology research and applications.
\r
5 // Copyright (C) 2008-2009 Christian M. Zmasek
\r
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
\r
7 // Copyright (C) 2000-2001 Washington University School of Medicine
\r
8 // and Howard Hughes Medical Institute
\r
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
\r
10 // All rights reserved
\r
12 // This library is free software; you can redistribute it and/or
\r
13 // modify it under the terms of the GNU Lesser General Public
\r
14 // License as published by the Free Software Foundation; either
\r
15 // version 2.1 of the License, or (at your option) any later version.
\r
17 // This library is distributed in the hope that it will be useful,
\r
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
\r
20 // Lesser General Public License for more details.
\r
22 // You should have received a copy of the GNU Lesser General Public
\r
23 // License along with this library; if not, write to the Free Software
\r
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
26 // Contact: phylosoft @ gmail . com
\r
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
\r
29 package org.forester.util;
\r
31 import java.util.regex.Matcher;
\r
32 import java.util.regex.Pattern;
\r
34 import org.forester.phylogeny.PhylogenyNode;
\r
35 import org.forester.phylogeny.data.Accession;
\r
36 import org.forester.phylogeny.data.Accession.Source;
\r
37 import org.forester.phylogeny.data.Sequence;
\r
39 public final class SequenceAccessionTools {
\r
41 // gb_ADF31344_1_segmented_worms_
\r
43 // gb_EHB07727_1_rodents_
\r
44 // dbj_BAF37827_1_turtles_
\r
45 // emb_CAA73223_1_primates_
\r
46 // lcl_91970_unknown_
\r
47 // mites|ref_XP_002434188_1
\r
48 // ref_XP_002434188_1_mites___ticks_
\r
49 // ref_NP_001121530_1_frogs___toads_
\r
50 //The format for GenBank Accession numbers are:
\r
51 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
\r
52 //Protein: 3 letters + 5 numerals
\r
53 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
\r
54 public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern
\r
55 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
\r
56 public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern
\r
57 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
\r
58 public final static Pattern GENBANK_PROT_PATTERN = Pattern
\r
59 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
\r
60 public final static Pattern GI_PATTERN = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );
\r
61 public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern
\r
62 .compile( "(?:\\b|_)([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
\r
63 public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern
\r
64 .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
\r
65 public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern
\r
66 .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|_)" );
\r
67 public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );
\r
68 // RefSeq accession numbers can be distinguished from GenBank accessions
\r
69 // by their distinct prefix format of 2 characters followed by an
\r
70 // underscore character ('_'). For example, a RefSeq protein accession is NP_015325.
\r
71 private final static Pattern REFSEQ_PATTERN = Pattern
\r
72 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );
\r
74 private SequenceAccessionTools() {
\r
75 // Hiding the constructor.
\r
78 public final static boolean isProteinDbQuery( final String query ) {
\r
79 final String r1 = parseRefSeqAccessorFromString( query );
\r
80 if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {
\r
83 final String r2 = parseUniProtAccessorFromString( query );
\r
84 if ( !ForesterUtil.isEmpty( r2 ) ) {
\r
87 return GENBANK_PROT_PATTERN.matcher( query ).lookingAt();
\r
90 public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) {
\r
91 String a = obtainUniProtAccessorFromDataFields( n );
\r
92 if ( !ForesterUtil.isEmpty( a ) ) {
\r
93 return new Accession( a, Source.UNIPROT );
\r
95 a = obtainGenbankAccessorFromDataFields( n );
\r
96 if ( !ForesterUtil.isEmpty( a ) ) {
\r
97 return new Accession( a, Source.NCBI );
\r
99 a = obtainRefSeqAccessorFromDataFields( n );
\r
100 if ( !ForesterUtil.isEmpty( a ) ) {
\r
101 return new Accession( a, Source.REFSEQ );
\r
103 a = obtainGiNumberFromDataFields( n );
\r
104 if ( !ForesterUtil.isEmpty( a ) ) {
\r
105 return new Accession( a, Source.GI );
\r
110 public final static Accession obtainFromSeqAccession( final PhylogenyNode n ) {
\r
111 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
\r
112 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getSource() )
\r
113 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
114 final String source = n.getNodeData().getSequence().getAccession().getSource().toLowerCase();
\r
115 final String value = n.getNodeData().getSequence().getAccession().getValue();
\r
116 if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source
\r
117 .equals( "sp" ) ) ) {
\r
118 return new Accession( value, Source.UNIPROT );
\r
120 else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) {
\r
121 return new Accession( value, Source.EMBL );
\r
123 else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) {
\r
124 return new Accession( value, Source.NCBI );
\r
126 else if ( source.equals( "refseq" ) ) {
\r
127 return new Accession( value, Source.REFSEQ );
\r
129 else if ( source.equals( "gi" ) ) {
\r
130 return new Accession( value, Source.GI );
\r
136 public final static String obtainGenbankAccessorFromDataFields( final PhylogenyNode n ) {
\r
138 if ( n.getNodeData().isHasSequence() ) {
\r
139 final Sequence seq = n.getNodeData().getSequence();
\r
140 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
\r
141 a = parseGenbankAccessorFromString( seq.getSymbol() );
\r
143 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
\r
144 a = parseGenbankAccessorFromString( seq.getGeneName() );
\r
146 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
\r
147 a = parseGenbankAccessorFromString( seq.getName() );
\r
149 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
\r
150 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
\r
151 a = parseGenbankAccessorFromString( seq.getAccession().getValue() );
\r
154 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
155 a = parseGenbankAccessorFromString( n.getName() );
\r
160 public final static String obtainGiNumberFromDataFields( final PhylogenyNode n ) {
\r
162 if ( n.getNodeData().isHasSequence() ) {
\r
163 final Sequence seq = n.getNodeData().getSequence();
\r
164 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
\r
165 a = parseGInumberFromString( seq.getName() );
\r
167 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
\r
168 a = parseGInumberFromString( seq.getGeneName() );
\r
170 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
\r
171 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
\r
172 a = parseGInumberFromString( seq.getAccession().getValue() );
\r
175 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
176 a = parseGInumberFromString( n.getName() );
\r
181 public final static String obtainRefSeqAccessorFromDataFields( final PhylogenyNode n ) {
\r
183 if ( n.getNodeData().isHasSequence() ) {
\r
184 final Sequence seq = n.getNodeData().getSequence();
\r
185 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
\r
186 a = parseRefSeqAccessorFromString( seq.getSymbol() );
\r
188 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
\r
189 a = parseRefSeqAccessorFromString( seq.getGeneName() );
\r
191 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
\r
192 a = parseRefSeqAccessorFromString( seq.getName() );
\r
194 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
\r
195 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
\r
196 a = parseRefSeqAccessorFromString( seq.getAccession().getValue() );
\r
199 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
200 a = parseRefSeqAccessorFromString( n.getName() );
\r
205 public final static String obtainUniProtAccessorFromDataFields( final PhylogenyNode n ) {
\r
207 if ( n.getNodeData().isHasSequence() ) {
\r
208 final Sequence seq = n.getNodeData().getSequence();
\r
209 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
\r
210 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getSymbol() );
\r
212 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
\r
213 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getName() );
\r
215 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
\r
216 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getGeneName() );
\r
218 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
\r
219 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
\r
220 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getAccession().getValue() );
\r
223 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
224 a = SequenceAccessionTools.parseUniProtAccessorFromString( n.getName() );
\r
229 public final static Accession parseAccessorFromString( final String s ) {
\r
230 if ( !ForesterUtil.isEmpty( s ) ) {
\r
231 String v = parseUniProtAccessorFromString( s );
\r
232 if ( !ForesterUtil.isEmpty( v ) ) {
\r
233 return new Accession( v, Source.UNIPROT );
\r
235 v = parseGenbankAccessorFromString( s );
\r
236 if ( !ForesterUtil.isEmpty( v ) ) {
\r
237 return new Accession( v, Source.NCBI );
\r
239 v = parseRefSeqAccessorFromString( s );
\r
240 if ( !ForesterUtil.isEmpty( v ) ) {
\r
241 return new Accession( v, Source.REFSEQ );
\r
243 v = parseGInumberFromString( s );
\r
244 if ( !ForesterUtil.isEmpty( v ) ) {
\r
245 return new Accession( v, Source.GI );
\r
247 v = parseEnsemlAccessorFromString( s );
\r
248 if ( !ForesterUtil.isEmpty( v ) ) {
\r
249 return new Accession( v, Source.ENSEMBL );
\r
255 public final static String parseGenbankAccessorFromString( final String s ) {
\r
256 Matcher m = GENBANK_NUC_PATTERN_1.matcher( s );
\r
257 if ( m.lookingAt() ) {
\r
258 return m.group( 1 );
\r
261 m = GENBANK_NUC_PATTERN_2.matcher( s );
\r
262 if ( m.lookingAt() ) {
\r
263 return m.group( 1 );
\r
266 m = GENBANK_PROT_PATTERN.matcher( s );
\r
267 if ( m.lookingAt() ) {
\r
268 return m.group( 1 );
\r
277 public final static String parseGenbankProteinAccessorFromString( final String s ) {
\r
278 final Matcher m = GENBANK_PROT_PATTERN.matcher( s );
\r
279 if ( m.lookingAt() ) {
\r
280 return m.group( 1 );
\r
287 public final static String parseGInumberFromString( final String s ) {
\r
288 final Matcher m = GI_PATTERN.matcher( s );
\r
290 return m.group( 1 );
\r
295 public final static String parseEnsemlAccessorFromString( final String s ) {
\r
296 final Matcher m = ENSEMBL_PATTERN.matcher( s );
\r
298 return m.group( 1 );
\r
303 public final static String parseRefSeqAccessorFromString( final String s ) {
\r
304 final Matcher m = REFSEQ_PATTERN.matcher( s );
\r
305 if ( m.lookingAt() ) {
\r
306 return m.group( 1 );
\r
311 public final static String parseUniProtAccessorFromString( final String s ) {
\r
312 Matcher m = UNIPROT_KB_PATTERN_1.matcher( s );
\r
314 return m.group( 1 );
\r
316 m = UNIPROT_KB_PATTERN_2.matcher( s );
\r
320 m = UNIPROT_KB_PATTERN_0.matcher( s );
\r
322 return m.group( 1 );
\r