adding retrieval of omim ids

andreasprlic · andreasprlic · commit 975788d6869a · 2014-01-29T10:19:30.000-08:00
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/parsers/genename/GeneName.java b/biojava3-genome/src/main/java/org/biojava3/genome/parsers/genename/GeneName.java
@@ -49,6 +49,7 @@ public class GeneName implements Serializable, Comparable<GeneName>{
 	String accessionNr;
 	String refseqIds;
 	String uniprot;
+	String omimId;
 	
 	public String getHgncId() {
 		return hgncId;
@@ -116,18 +117,27 @@ public String getUniprot() {
 	public void setUniprot(String uniprot) {
 		this.uniprot = uniprot;
 	}
-	@Override
-	public int compareTo(GeneName o) {
-		return hgncId.compareTo(o.getHgncId());
-	}
+	
+	
 	@Override
 	public String toString() {
 		return "GeneName [hgncId=" + hgncId + ", approvedSymbol="
 				+ approvedSymbol + ", approvedName=" + approvedName
 				+ ", status=" + status + ", previousSymbols=" + previousSymbols
 				+ ", previousNames=" + previousNames + ", synonyms=" + synonyms
 				+ ", chromosome=" + chromosome + ", accessionNr=" + accessionNr
-				+ ", refseqIds=" + refseqIds + ", uniprot=" + uniprot + "]";
+				+ ", refseqIds=" + refseqIds + ", uniprot=" + uniprot
+				+ ", omimId=" + omimId + "]";
+	}
+	public String getOmimId() {
+		return omimId;
+	}
+	public void setOmimId(String omimId) {
+		this.omimId = omimId;
+	}
+	@Override
+	public int compareTo(GeneName o) {
+		return hgncId.compareTo(o.getHgncId());
 	}
 	
 	
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/parsers/genename/GeneNamesParser.java b/biojava3-genome/src/main/java/org/biojava3/genome/parsers/genename/GeneNamesParser.java
@@ -29,6 +29,7 @@
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.biojava3.core.util.InputStreamProvider;
@@ -39,7 +40,7 @@
  *
  */
 public class GeneNamesParser {
-	public static final String DEFAULT_GENENAMES_URL = "http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_refseq_ids&col=md_prot_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag";
+	public static final String DEFAULT_GENENAMES_URL = "http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_prot_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag";
 
 	/** parses a file from the genenames website 
 	 *    
@@ -116,9 +117,9 @@ private static GeneName getGeneName(String line) {
 		
 		String[] s = line.split("\t");
 		
-		if ( s.length != 11) {
-			System.err.println("WARNING line does not contain 11 data items but " + s.length+"."  );
-			System.err.println(line);
+		if ( s.length != 12) {
+			System.err.println("WARNING line does not contain 12 data items but " + s.length+"."  );
+			System.err.println(line.replaceAll("\t", "|---|"));
 			return null;
 		}
 		GeneName gn = new GeneName();
@@ -132,9 +133,10 @@ private static GeneName getGeneName(String line) {
 		gn.setSynonyms(s[6]);
 		gn.setChromosome(s[7]);		
 		gn.setAccessionNr(s[8]);
-		gn.setRefseqIds(s[9]);
-		gn.setUniprot(s[10]);
-
+		gn.setOmimId(s[9]);
+		gn.setRefseqIds(s[10]);
+		gn.setUniprot(s[11]);
+		
 		
 		return gn;
 
