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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