BioJava contains a parser the refFlat.txt.gz from the UCSC genome browser that contains a mapping of gene names to chromosome positions.
try {
List<GeneChromosomePosition> genePositions= GeneChromosomePositionParser.getChromosomeMappings();
System.out.println("got " + genePositions.size() + " gene positions") ;
for (GeneChromosomePosition pos : genePositions){
if ( pos.getGeneName().equals("FOLH1")) {
System.out.println(pos);
break;
}
}
} catch(Exception e){
e.printStackTrace();
}If a local copy of the file is available, it can be provide via this:
URL url = new URL("file://local/copy/of/file");
InputStreamProvider prov = new InputStreamProvider();
InputStream inStream = prov.getInputStream(url);
GeneChromosomePositionParser.getChromosomeMappings(inStream);
Navigation: Home | Book 4: The Genomics Module | Chapter 3 : chromosomal positions