biojava-tutorial/genomics/karyotype.md at master

Parsing a karyotype file from the UCSC genome browser

Karyotype information for the human genome can be read from UCSC's cytoBand.txt.gz file.

        CytobandParser me = new CytobandParser();
		try {
			SortedSet<Cytoband> cytobands = me.getAllCytobands(new URL(http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz));
			SortedSet<StainType> types = new TreeSet<StainType>();
			for (Cytoband c : cytobands){
				System.out.println(c);
				if ( ! types.contains(c.getType()))
					types.add(c.getType());
			}
			System.out.println(types);
		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}

If a local copy of the file is available you can specify it in the following way:

SortedSet<Cytoband> cytobands = me.getAllCytobands(new URL("file://path/to/local/copy/"));

Navigation: Home | Book 4: The Genomics Module | Chapter 5 : karyotype (cytoband)

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Parsing a karyotype file from the UCSC genome browser