org.forester.ws.uniprot.SequenceDbWsTools Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of forester Show documentation
Show all versions of forester Show documentation
Applications and software libraries for evolutionary biology and comparative genomics research
// $Id:
// forester -- software libraries and applications
// for genomics and evolutionary biology research.
//
// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: www.phylosoft.org/forester
package org.forester.ws.uniprot;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.forester.phylogeny.data.Identifier;
import org.forester.util.ForesterUtil;
public final class SequenceDbWsTools {
private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true; //TODO turn off for final realease!
public enum Db {
UNKNOWN, UNIPROT;
}
public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/";
public final static String BASE_EMBL_DB_URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/";
public final static String EMBL_DBS_EMBL = "embl";
public final static String EMBL_DBS_REFSEQ_P = "refseqp";
public final static String EMBL_DBS_REFSEQ_N = "refseqn";
private final static String URL_ENC = "UTF-8";
// uniprot/expasy accession number format (6 chars):
// letter digit letter-or-digit letter-or-digit letter-or-digit digit
// ?: => no back-reference
// \A => begin of String
// \Z => end of String
private final static Pattern UNIPROT_AC_PATTERN = Pattern
.compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d[A-Z0-9]{3}\\d)(?:[^a-zA-Z0-9]|\\Z)" );
private final static boolean DEBUG = false;
private static String encode( final String str ) throws UnsupportedEncodingException {
return URLEncoder.encode( str.trim(), URL_ENC );
}
/**
* Returns null if no match.
*
* @param query
* @param db
* @return
*/
static public String parseUniProtAccessor( final String query ) {
final Matcher m = UNIPROT_AC_PATTERN.matcher( query );
if ( m.lookingAt() ) {
return m.group( 1 );
}
else {
return null;
}
}
public static List getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return )
throws IOException {
final List result = getTaxonomyStringFromCommonName( cn, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
}
return null;
}
public static List getTaxonomiesFromCommonNameStrict( final String cn,
final int max_taxonomies_return )
throws IOException {
final List taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List filtered_taxonomies = new ArrayList();
for( final UniProtTaxonomy taxonomy : taxonomies ) {
if ( taxonomy.getCommonName().equalsIgnoreCase( cn ) ) {
filtered_taxonomies.add( taxonomy );
}
}
return filtered_taxonomies;
}
return null;
}
public static List getTaxonomiesFromId( final String id, final int max_taxonomies_return )
throws IOException {
final List result = getTaxonomyStringFromId( id, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
}
return null;
}
public static List getTaxonomiesFromScientificName( final String sn,
final int max_taxonomies_return )
throws IOException {
// Hack! Craniata? ..
if ( sn.equals( "Drosophila" ) ) {
return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS );
}
else if ( sn.equals( "Xenopus" ) ) {
return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS );
}
// else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) {
// return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA );
// }
final List result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
}
return null;
}
/**
* Does not return "sub-types".
* For example, for "Mus musculus" only returns "Mus musculus"
* and not "Mus musculus", "Mus musculus bactrianus", ...
*
*/
public static List getTaxonomiesFromScientificNameStrict( final String sn,
final int max_taxonomies_return )
throws IOException {
final List taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List filtered_taxonomies = new ArrayList();
for( final UniProtTaxonomy taxonomy : taxonomies ) {
if ( taxonomy.getScientificName().equalsIgnoreCase( sn ) ) {
filtered_taxonomies.add( taxonomy );
}
}
return filtered_taxonomies;
}
return null;
}
public static List getTaxonomiesFromTaxonomyCode( final String code,
final int max_taxonomies_return )
throws IOException {
final String my_code = new String( code );
if ( ALLOW_TAXONOMY_CODE_HACKS ) {
final List l = resolveFakeTaxonomyCodes( max_taxonomies_return, my_code );
if ( l != null ) {
return l;
}
}
final List result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
}
return null;
}
private static List resolveFakeTaxonomyCodes( final int max_taxonomies_return, final String code )
throws IOException {
if ( code.equals( "CAP" ) ) {
return getTaxonomiesFromId( "283909", max_taxonomies_return );
}
else if ( code.equals( "FUGRU" ) ) {
return getTaxonomiesFromId( "31033", max_taxonomies_return );
}
else if ( code.equals( "GIALA" ) ) {
return getTaxonomiesFromId( "5741", max_taxonomies_return );
}
else if ( code.equals( "TRIVE" ) ) {
return getTaxonomiesFromId( "413071", max_taxonomies_return );
}
else if ( code.equals( "CAPOWC" ) ) {
return getTaxonomiesFromId( "192875", max_taxonomies_return );
}
else if ( code.equals( "SPHARC" ) ) {
return getTaxonomiesFromId( "667725", max_taxonomies_return );
}
else if ( code.equals( "THETRA" ) ) {
return getTaxonomiesFromId( "529818", max_taxonomies_return );
}
else if ( code.equals( "CHLVUL" ) ) {
return getTaxonomiesFromId( "574566", max_taxonomies_return );
}
else if ( code.equals( "CITCLE" ) ) {
return getTaxonomiesFromId( "85681", max_taxonomies_return );
}
else if ( code.equals( "MYCPOP" ) ) {
return getTaxonomiesFromId( "85929", max_taxonomies_return );
}
else if ( code.equals( "AGABB" ) ) {
return getTaxonomiesFromId( "597362", max_taxonomies_return );
}
else if ( code.equals( "BAUCOM" ) ) {
return getTaxonomiesFromId( "430998", max_taxonomies_return );
}
else if ( code.equals( "DICSQU" ) ) {
return getTaxonomiesFromId( "114155", max_taxonomies_return );
}
else if ( code.equals( "FOMPIN" ) ) {
return getTaxonomiesFromId( "40483", max_taxonomies_return );
}
else if ( code.equals( "HYDMA" ) ) {
return getTaxonomiesFromId( "6085", max_taxonomies_return );
}
else if ( code.equals( "MYCFI" ) ) {
return getTaxonomiesFromId( "83344", max_taxonomies_return );
}
else if ( code.equals( "OIDMAI" ) ) {
return getTaxonomiesFromId( "78148", max_taxonomies_return );
}
else if ( code.equals( "OSTRC" ) ) {
return getTaxonomiesFromId( "385169", max_taxonomies_return );
}
else if ( code.equals( "POSPL" ) ) {
return getTaxonomiesFromId( "104341", max_taxonomies_return );
}
else if ( code.equals( "SAICOM" ) ) {
return getTaxonomiesFromId( "5606", max_taxonomies_return );
}
else if ( code.equals( "SERLA" ) ) {
return getTaxonomiesFromId( "85982", max_taxonomies_return );
}
else if ( code.equals( "SPORO" ) ) {
return getTaxonomiesFromId( "40563", max_taxonomies_return );
}
else if ( code.equals( "ACRALC" ) ) {
return getTaxonomiesFromId( "398408", max_taxonomies_return );
}
else if ( code.equals( "THITER" ) ) {
return getTaxonomiesFromId( "35720", max_taxonomies_return );
}
else if ( code.equals( "MYCTHE" ) ) {
return getTaxonomiesFromId( "78579", max_taxonomies_return );
}
else if ( code.equals( "CONPUT" ) ) {
return getTaxonomiesFromId( "80637", max_taxonomies_return );
}
else if ( code.equals( "WOLCOC" ) ) {
return getTaxonomiesFromId( "81056", max_taxonomies_return );
}
else if ( code.equals( "CLAGRA" ) ) {
return getTaxonomiesFromId( "27339", max_taxonomies_return );
}
else if ( code.equals( "XANPAR" ) ) {
return getTaxonomiesFromId( "107463", max_taxonomies_return );
}
else if ( code.equals( "HYDPIN" ) ) {
return getTaxonomiesFromId( "388859", max_taxonomies_return );
}
else if ( code.equals( "SERLAC" ) ) {
return getTaxonomiesFromId( "85982", max_taxonomies_return );
}
else {
return null;
}
}
private static List getTaxonomyStringFromCommonName( final String cn, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=common%3a%22" + encode( cn ) + "%22&format=tab", max_lines_to_return );
}
private static List getTaxonomyStringFromId( final String id, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=id%3a%22" + encode( id ) + "%22&format=tab", max_lines_to_return );
}
private static List getTaxonomyStringFromScientificName( final String sn, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=scientific%3a%22" + encode( sn ) + "%22&format=tab", max_lines_to_return );
}
private static List getTaxonomyStringFromTaxonomyCode( final String code, final int max_lines_to_return )
throws IOException {
return queryUniprot( "taxonomy/?query=mnemonic%3a%22" + encode( code ) + "%22&format=tab", max_lines_to_return );
}
private static List uniProtTaxonomyToList( final UniProtTaxonomy tax ) {
final List l = new ArrayList();
l.add( tax );
return l;
}
private static List parseUniProtTaxonomy( final List result ) throws IOException {
final List taxonomies = new ArrayList();
for( final String line : result ) {
if ( ForesterUtil.isEmpty( line ) ) {
// Ignore empty lines.
}
else if ( line.startsWith( "Taxon" ) ) {
final String[] items = line.split( "\t" );
if ( !( items[ 1 ].equalsIgnoreCase( "Mnemonic" ) && items[ 2 ].equalsIgnoreCase( "Scientific name" )
&& items[ 3 ].equalsIgnoreCase( "Common name" ) && items[ 4 ].equalsIgnoreCase( "Synonym" )
&& items[ 5 ].equalsIgnoreCase( "Other Names" ) && items[ 6 ].equalsIgnoreCase( "Reviewed" )
&& items[ 7 ].equalsIgnoreCase( "Rank" ) && items[ 8 ].equalsIgnoreCase( "Lineage" ) ) ) {
throw new IOException( "Unreconized UniProt Taxonomy format: " + line );
}
}
else {
if ( line.split( "\t" ).length > 4 ) {
taxonomies.add( new UniProtTaxonomy( line ) );
}
}
}
return taxonomies;
}
public static List queryEmblDb( final Identifier id, final int max_lines_to_return ) throws IOException {
final StringBuilder url_sb = new StringBuilder();
url_sb.append( BASE_EMBL_DB_URL );
if ( ForesterUtil.isEmpty( id.getProvider() ) || id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
url_sb.append( SequenceDbWsTools.EMBL_DBS_EMBL );
url_sb.append( '/' );
}
else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) {
url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_P );
url_sb.append( '/' );
}
else {
url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N );
url_sb.append( '/' );
}
}
return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
}
public static List queryUniprot( final String query, final int max_lines_to_return ) throws IOException {
return queryDb( query, max_lines_to_return, BASE_UNIPROT_URL );
}
public static List queryDb( final String query, int max_lines_to_return, final String base_url )
throws IOException {
if ( ForesterUtil.isEmpty( query ) ) {
throw new IllegalArgumentException( "illegal attempt to use empty query " );
}
if ( max_lines_to_return < 1 ) {
max_lines_to_return = 1;
}
final URL url = new URL( base_url + query );
if ( DEBUG ) {
System.out.println( "url: " + url.toString() );
}
final URLConnection urlc = url.openConnection();
final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) );
String line;
final List result = new ArrayList();
while ( ( line = in.readLine() ) != null ) {
if ( DEBUG ) {
System.out.println( line );
}
result.add( line );
if ( result.size() > max_lines_to_return ) {
break;
}
}
in.close();
return result;
}
public static SequenceDatabaseEntry obtainUniProtEntry( final String query, final int max_lines_to_return )
throws IOException {
final List lines = queryUniprot( "uniprot/" + query + ".txt", max_lines_to_return );
return UniProtEntry.createInstanceFromPlainText( lines );
}
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl( final Identifier id, final int max_lines_to_return )
throws IOException {
final List lines = queryEmblDb( id, max_lines_to_return );
return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
}
public static SequenceDatabaseEntry obtainEmblEntry( final Identifier id, final int max_lines_to_return )
throws IOException {
final List lines = queryEmblDb( id, max_lines_to_return );
return EbiDbEntry.createInstanceFromPlainText( lines );
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy