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;
29 import java.util.Arrays;
30 import java.util.Enumeration;
31 import java.util.Hashtable;
32 import java.util.Vector;
34 import org.forester.ws.wabi.RestUtil;
41 public void go( final String geneName ) {
42 // Retrieve accession number list which has specified gene name from searchByXMLPath of ARSA. Please click here for details of ARSA.
43 /*target: Sequence length is between 300bp and 1000bp.
45 Gene qualifire is same as specified gene name.*/
46 String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND "
47 + "/ENTRY/DDBJ/length<=1000) ";
48 queryPath += "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND ";
49 queryPath += "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='" + geneName + "'}})";
50 String query = "service=ARSA&method=searchByXMLPath&queryPath=" + queryPath
51 + "&returnPath=/ENTRY/DDBJ/primary-accession&offset=1&count=100";
53 String arsaResult = null;
55 arsaResult = RestUtil.getResult( query );
57 catch ( final IOException e ) {
58 // TODO Auto-generated catch block
61 final String[] arsaResultLines = arsaResult.split( "\n" );
63 final int arsaResultNum = Integer.parseInt( arsaResultLines[ 0 ].replaceAll( "hitscount =", "" ).trim() );
64 //If there is no hit, print a message and exit
65 if ( arsaResultNum == 0 ) {
66 System.out.println( "There is no entry for gene:" + geneName );
69 //Retrieve DNA sequence of top hit entry by using getFASTA_DDBJEntry of GetEntry.
70 //Retrieve DNA sequence of first fit.
71 final String repAccession = arsaResultLines[ 2 ];
72 query = "service=GetEntry&method=getFASTA_DDBJEntry&accession=" + repAccession;
75 dnaSeq = RestUtil.getResult( query );
77 catch ( final IOException e ) {
78 // TODO Auto-generated catch block
81 System.out.println( "Retrieved DNA sequence is: " + dnaSeq );
82 //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).
83 //Execute blastn with step3's sequence
84 query = "service=Blast&method=searchParam&program=blastn&database=ddbjpri ddbjrod ddbjmam ddbjvrt "
85 + "ddbjinv&query=" + dnaSeq + "¶m=-m 8 -b 50 -v 50 -e 0.0001";
86 String blastResult = null;
88 blastResult = RestUtil.getResult( query );
90 catch ( final IOException e ) {
91 // TODO Auto-generated catch block
94 // Extract both accession number and similarity score from BLAST result.
95 // 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.
96 final String blastResultLines[] = blastResult.split( "\n" );
97 final Vector<String[]> parsedBlastResult = new Vector<String[]>();
98 for( final String blastResultLine : blastResultLines ) {
99 final String cols[] = blastResultLine.split( "\t" );
100 final String accession = cols[ 1 ].substring( 0, cols[ 1 ].indexOf( "|" ) );
101 final String[] result = { accession, cols[ 2 ] };
102 parsedBlastResult.add( result );
104 // Retrieve species name by using searchByXMLPath of ARSA. If the plural subjects whose species
105 // name are same are in the result, the highest similarity score is used.
106 //Retrieve species from accession number.
107 final Hashtable<String, String> organismAccession = new Hashtable<String, String>();
108 for( int i = 0; i < parsedBlastResult.size(); i++ ) {
109 final String[] parsed = parsedBlastResult.elementAt( i );
110 query = "service=ARSA&method=searchByXMLPath&queryPath=/ENTRY/DDBJ/primary-accession=='" + parsed[ 0 ]
111 + "'&returnPath=/ENTRY/DDBJ/organism&offset=1&count=100";
112 String organism = null;
114 organism = RestUtil.getResult( query );
116 catch ( final IOException e ) {
117 // TODO Auto-generated catch block
120 final String[] organismLines = organism.split( "\n" );
121 organism = organismLines[ 2 ];
122 //If same organism name hits, use first hit.
123 if ( !organismAccession.containsKey( organism ) ) {
124 organismAccession.put( organism, parsed[ 0 ] + "\t" + parsed[ 1 ] );
129 System.out.println( "DDBJ entries: " + arsaResultNum );
130 System.out.println( "Representative accession: " + repAccession );
131 System.out.println( "Organism name\tDDBJ accession number\tSequence similarity" );
132 final String[] keys = new String[ organismAccession.size() ];
133 final Enumeration<String> enu = organismAccession.keys();
135 while ( enu.hasMoreElements() ) {
136 keys[ count ] = enu.nextElement();
140 for( final String key : keys ) {
141 System.out.println( key + "\t" + organismAccession.get( key ) );