2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.archaeopteryx.tools;
28 import java.io.IOException;
30 import java.net.URISyntaxException;
31 import java.util.Arrays;
32 import java.util.Enumeration;
33 import java.util.Hashtable;
34 import java.util.Vector;
36 import javax.swing.JApplet;
38 import org.forester.archaeopteryx.AptxUtil;
39 import org.forester.archaeopteryx.TreePanel;
40 import org.forester.phylogeny.PhylogenyNode;
41 import org.forester.phylogeny.data.Accession;
42 import org.forester.phylogeny.data.Identifier;
43 import org.forester.util.ForesterUtil;
44 import org.forester.util.SequenceIdParser;
45 import org.forester.ws.wabi.RestUtil;
47 public final class Blast {
49 final public static void openNcbiBlastWeb( final String query,
50 final boolean is_nucleic_acids,
53 //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
54 final StringBuilder uri_str = new StringBuilder();
55 uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=" );
56 if ( is_nucleic_acids ) {
57 uri_str.append( "Nucleotide" );
60 uri_str.append( "Proteins" );
62 uri_str.append( "&QUERY=" );
63 uri_str.append( query );
65 AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), applet != null, applet, "_aptx_blast" );
67 catch ( final IOException e ) {
68 AptxUtil.showErrorMessage( p, e.toString() );
71 catch ( final URISyntaxException e ) {
72 AptxUtil.showErrorMessage( p, e.toString() );
77 final public static String obtainQueryForBlast( final PhylogenyNode node ) {
79 if ( node.getNodeData().isHasSequence() ) {
80 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
81 query = node.getNodeData().getSequence().getMolecularSequence();
83 else if ( ( node.getNodeData().getSequence().getAccession() != null )
84 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
85 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
86 query = node.getNodeData().getSequence().getAccession().getSource() + "%7C";
88 query += node.getNodeData().getSequence().getAccession().getValue();
90 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
91 final Accession acc = AptxUtil.obtainSequenceAccessionFromName( node.getNodeData().getSequence()
94 query = acc.getSource() + "%7C" + acc.getValue();
98 else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
99 final Accession acc = AptxUtil.obtainSequenceAccessionFromName( node.getName() );
101 query = acc.getSource() + "%7C" + acc.getValue();
104 final Identifier id = SequenceIdParser.parse( node.getName() );
106 query = id.getValue();
113 final public static boolean isContainsQueryForBlast( final PhylogenyNode node ) {
114 return !ForesterUtil.isEmpty( obtainQueryForBlast( node ) );
117 final public void ddbjBlast( final String geneName ) {
118 // Retrieve accession number list which has specified gene name from searchByXMLPath of ARSA. Please click here for details of ARSA.
119 /*target: Sequence length is between 300bp and 1000bp.
121 Gene qualifire is same as specified gene name.*/
122 String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND "
123 + "/ENTRY/DDBJ/length<=1000) ";
124 queryPath += "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND ";
125 queryPath += "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='" + geneName + "'}})";
126 String query = "service=ARSA&method=searchByXMLPath&queryPath=" + queryPath
127 + "&returnPath=/ENTRY/DDBJ/primary-accession&offset=1&count=100";
129 String arsaResult = null;
131 arsaResult = RestUtil.getResult( query );
133 catch ( final IOException e ) {
134 // TODO Auto-generated catch block
137 final String[] arsaResultLines = arsaResult.split( "\n" );
139 final int arsaResultNum = Integer.parseInt( arsaResultLines[ 0 ].replaceAll( "hitscount =", "" ).trim() );
140 //If there is no hit, print a message and exit
141 if ( arsaResultNum == 0 ) {
142 System.out.println( "There is no entry for gene:" + geneName );
145 //Retrieve DNA sequence of top hit entry by using getFASTA_DDBJEntry of GetEntry.
146 //Retrieve DNA sequence of first fit.
147 final String repAccession = arsaResultLines[ 2 ];
148 query = "service=GetEntry&method=getFASTA_DDBJEntry&accession=" + repAccession;
149 String dnaSeq = null;
151 dnaSeq = RestUtil.getResult( query );
153 catch ( final IOException e ) {
154 // TODO Auto-generated catch block
157 System.out.println( "Retrieved DNA sequence is: " + dnaSeq );
158 //Execute blastn by using searchParam of Blast with step2's sequence. Specified option is -e 0.0001 -m 8 -b 50 -v 50. It means "Extract top 50 hit which E-value is more than 0.0001.". The reference databases are specified as follows. ddbjpri(primates) ddbjrod(rodents) ddbjmam(mammals) ddbjvrt(vertebrates ) ddbjinv(invertebrates).
159 //Execute blastn with step3's sequence
160 query = "service=Blast&method=searchParam&program=blastn&database=ddbjpri ddbjrod ddbjmam ddbjvrt "
161 + "ddbjinv&query=" + dnaSeq + "¶m=-m 8 -b 50 -v 50 -e 0.0001";
162 String blastResult = null;
164 blastResult = RestUtil.getResult( query );
166 catch ( final IOException e ) {
167 // TODO Auto-generated catch block
170 // Extract both accession number and similarity score from BLAST result.
171 // This step does not use Web API and extract the part of result or edit the result. Please click here to see the details of each column in the BLAST tab delimited format which is generated by -m 8 option.
172 final String blastResultLines[] = blastResult.split( "\n" );
173 final Vector<String[]> parsedBlastResult = new Vector<String[]>();
174 for( final String blastResultLine : blastResultLines ) {
175 final String cols[] = blastResultLine.split( "\t" );
176 final String accession = cols[ 1 ].substring( 0, cols[ 1 ].indexOf( "|" ) );
177 final String[] result = { accession, cols[ 2 ] };
178 parsedBlastResult.add( result );
180 // Retrieve species name by using searchByXMLPath of ARSA. If the plural subjects whose species
181 // name are same are in the result, the highest similarity score is used.
182 //Retrieve species from accession number.
183 final Hashtable<String, String> organismAccession = new Hashtable<String, String>();
184 for( int i = 0; i < parsedBlastResult.size(); i++ ) {
185 final String[] parsed = parsedBlastResult.elementAt( i );
186 query = "service=ARSA&method=searchByXMLPath&queryPath=/ENTRY/DDBJ/primary-accession=='" + parsed[ 0 ]
187 + "'&returnPath=/ENTRY/DDBJ/organism&offset=1&count=100";
188 String organism = null;
190 organism = RestUtil.getResult( query );
192 catch ( final IOException e ) {
193 // TODO Auto-generated catch block
196 final String[] organismLines = organism.split( "\n" );
197 organism = organismLines[ 2 ];
198 //If same organism name hits, use first hit.
199 if ( !organismAccession.containsKey( organism ) ) {
200 organismAccession.put( organism, parsed[ 0 ] + "\t" + parsed[ 1 ] );
205 System.out.println( "DDBJ entries: " + arsaResultNum );
206 System.out.println( "Representative accession: " + repAccession );
207 System.out.println( "Organism name\tDDBJ accession number\tSequence similarity" );
208 final String[] keys = new String[ organismAccession.size() ];
209 final Enumeration<String> enu = organismAccession.keys();
211 while ( enu.hasMoreElements() ) {
212 keys[ count ] = enu.nextElement();
216 for( final String key : keys ) {
217 System.out.println( key + "\t" + organismAccession.get( key ) );