// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx.tools;
-
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.swing.JApplet;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.TreePanel;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.util.ForesterUtil;
-import org.forester.ws.wabi.RestUtil;
-
-public class Blast {
-
- final static Pattern identifier_pattern_1 = Pattern.compile ("^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})\\s*$");
- final static Pattern identifier_pattern_2 = Pattern.compile ("^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})[|,; ].*$");
-
- public Blast() {
- }
-
+import org.forester.util.SequenceAccessionTools;
- public static void NcbiBlastWeb( String query, JApplet applet, TreePanel p ) {
+public final class Blast {
- //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
-
-
- StringBuilder uri_str = new StringBuilder();
- uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=Proteins&QUERY=" );
+ final public static void openNcbiBlastWeb( final String query,
+ final boolean is_nucleic_acids,
+
+ final TreePanel p ) {
+ //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
+ final StringBuilder uri_str = new StringBuilder();
+ uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=" );
+ if ( is_nucleic_acids ) {
+ uri_str.append( "Nucleotide" );
+ }
+ else {
+ uri_str.append( "Proteins" );
+ }
+ uri_str.append( "&QUERY=" );
uri_str.append( query );
try {
-
- AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), applet != null, applet, "_aptx_blast" );
+ AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), "_aptx_blast" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( p, e.toString() );
AptxUtil.showErrorMessage( p, e.toString() );
e.printStackTrace();
}
-
}
- public static String obtainQueryForBlast( final PhylogenyNode node ) {
+
+ final public static String obtainQueryForBlast( final PhylogenyNode node ) {
String query = "";
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- query = node.getNodeData().getSequence().getMolecularSequence();
- }
- else if ( node.getNodeData().getSequence().getAccession() != null && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- query = node.getNodeData().getSequence().getAccession().getSource() + "%7C";
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ query = node.getNodeData().getSequence().getMolecularSequence();
}
- query += node.getNodeData().getSequence().getAccession().getValue();
- }
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
- String name = node.getNodeData().getSequence().getName();
- final Matcher matcher1 = identifier_pattern_1.matcher( name );
- final Matcher matcher2 = identifier_pattern_2.matcher( name );
- String group1 = "";
- String group2 = "";
-
- if ( matcher1.matches() ) {
- group1 = matcher1.group( 1 );
- group2 = matcher1.group( 2 );
- System.out.println( "1 1=" + group1 );
-
- System.out.println( "1 2=" + group2 );
+ if ( ForesterUtil.isEmpty( query ) && ( node.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+ .getAccession().getValue() );
+ if ( id != null ) {
+ query = id.getValue();
+ }
}
- if ( matcher2.matches() ) {
- group1 = matcher2.group( 1 );
- group2 = matcher2.group( 2 );
- System.out.println( "2 1=" + group1 );
-
- System.out.println( "2 2=" + group2 );
+ if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+ .getName() );
+ if ( id != null ) {
+ query = id.getValue();
+ }
}
- if (!ForesterUtil.isEmpty( group1 ) && !ForesterUtil.isEmpty( group2 )) {
- query = group1 + "%7C" + group2;
+ if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+ .getSymbol() );
+ if ( id != null ) {
+ query = id.getValue();
+ }
+ }
+ if ( ForesterUtil.isEmpty( query )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+ .getGeneName() );
+ if ( id != null ) {
+ query = id.getValue();
+ }
+ }
+ }
+ if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getName() );
+ if ( id != null ) {
+ query = id.getValue();
}
-
}
-
-
- System.out.println( query );
-
return query;
}
-
- public void ddbjBlast( final String geneName ) {
- // Retrieve accession number list which has specified gene name from searchByXMLPath of ARSA. Please click here for details of ARSA.
- /*target: Sequence length is between 300bp and 1000bp.
- Feature key is CDS.
- Gene qualifire is same as specified gene name.*/
- String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND "
- + "/ENTRY/DDBJ/length<=1000) ";
- queryPath += "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND ";
- queryPath += "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='" + geneName + "'}})";
- String query = "service=ARSA&method=searchByXMLPath&queryPath=" + queryPath
- + "&returnPath=/ENTRY/DDBJ/primary-accession&offset=1&count=100";
- //Execute ARSA
- String arsaResult = null;
- try {
- arsaResult = RestUtil.getResult( query );
- }
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- final String[] arsaResultLines = arsaResult.split( "\n" );
- //Get hit count
- final int arsaResultNum = Integer.parseInt( arsaResultLines[ 0 ].replaceAll( "hitscount =", "" ).trim() );
- //If there is no hit, print a message and exit
- if ( arsaResultNum == 0 ) {
- System.out.println( "There is no entry for gene:" + geneName );
- return;
- }
- //Retrieve DNA sequence of top hit entry by using getFASTA_DDBJEntry of GetEntry.
- //Retrieve DNA sequence of first fit.
- final String repAccession = arsaResultLines[ 2 ];
- query = "service=GetEntry&method=getFASTA_DDBJEntry&accession=" + repAccession;
- String dnaSeq = null;
- try {
- dnaSeq = RestUtil.getResult( query );
- }
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- System.out.println( "Retrieved DNA sequence is: " + dnaSeq );
- //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).
- //Execute blastn with step3's sequence
- query = "service=Blast&method=searchParam&program=blastn&database=ddbjpri ddbjrod ddbjmam ddbjvrt "
- + "ddbjinv&query=" + dnaSeq + "¶m=-m 8 -b 50 -v 50 -e 0.0001";
- String blastResult = null;
- try {
- blastResult = RestUtil.getResult( query );
- }
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- // Extract both accession number and similarity score from BLAST result.
- // 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.
- final String blastResultLines[] = blastResult.split( "\n" );
- final Vector<String[]> parsedBlastResult = new Vector<String[]>();
- for( final String blastResultLine : blastResultLines ) {
- final String cols[] = blastResultLine.split( "\t" );
- final String accession = cols[ 1 ].substring( 0, cols[ 1 ].indexOf( "|" ) );
- final String[] result = { accession, cols[ 2 ] };
- parsedBlastResult.add( result );
- }
- // Retrieve species name by using searchByXMLPath of ARSA. If the plural subjects whose species
- // name are same are in the result, the highest similarity score is used.
- //Retrieve species from accession number.
- final Hashtable<String, String> organismAccession = new Hashtable<String, String>();
- for( int i = 0; i < parsedBlastResult.size(); i++ ) {
- final String[] parsed = parsedBlastResult.elementAt( i );
- query = "service=ARSA&method=searchByXMLPath&queryPath=/ENTRY/DDBJ/primary-accession=='" + parsed[ 0 ]
- + "'&returnPath=/ENTRY/DDBJ/organism&offset=1&count=100";
- String organism = null;
- try {
- organism = RestUtil.getResult( query );
- }
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- final String[] organismLines = organism.split( "\n" );
- organism = organismLines[ 2 ];
- //If same organism name hits, use first hit.
- if ( !organismAccession.containsKey( organism ) ) {
- organismAccession.put( organism, parsed[ 0 ] + "\t" + parsed[ 1 ] );
- }
- }
- // Print result.
- // Print Result
- System.out.println( "DDBJ entries: " + arsaResultNum );
- System.out.println( "Representative accession: " + repAccession );
- System.out.println( "Organism name\tDDBJ accession number\tSequence similarity" );
- final String[] keys = new String[ organismAccession.size() ];
- final Enumeration<String> enu = organismAccession.keys();
- int count = 0;
- while ( enu.hasMoreElements() ) {
- keys[ count ] = enu.nextElement();
- ++count;
- }
- Arrays.sort( keys );
- for( final String key : keys ) {
- System.out.println( key + "\t" + organismAccession.get( key ) );
- }
+ final public static boolean isContainsQueryForBlast( final PhylogenyNode node ) {
+ return !ForesterUtil.isEmpty( obtainQueryForBlast( node ) );
}
}
git://source.jalview.org / jalview.git / blobdiff