biojava-tutorial/genomics/genenames.md at master

Parse Gene Name Information

The following code parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases.

    /** parses a file from the genenames website
	 *
	 * @param args
	 */
	public static void main(String[] args) {

		try {

			List<GeneName> geneNames = GeneNamesParser.getGeneNames();

			System.out.println("got " + geneNames.size() + " gene names");


			for ( GeneName g : geneNames){
				if ( g.getApprovedSymbol().equals("FOLH1"))
					System.out.println(g);
			}
			// and returns a list of beans that contains key-value pairs for each gene name

		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}

	}

If you have a local copy of this file, then you can just provide an input stream for it:

        URL url = new URL("file:///local/copy/of/file");

		InputStreamProvider prov = new InputStreamProvider();

		InputStream inStream = prov.getInputStream(url);

	    GeneNamesParser.getGeneNames(inStream);

Navigation: Home | Book 4: The Genomics Module | Chapter 2 : gene names information

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Parse Gene Name Information