Isochore processing can't handle missing chromosome annotations

[rdalbanus]

Hi, Andreas,

I think I figured how to make the isochores files work, but now I'm running into another issue. If my sample doesn't have a chromosome annotation that is present in the isochore file, the software crashes:

Traceback (most recent call last):
  File "/lab/sw/ve/pl2/bin/gat-run.py", line 4, in <module>
    __import__('pkg_resources').run_script('gat==1.3.5', 'gat-run.py')
  File "/lab/sw/ve/pl2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 738, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/lab/sw/ve/pl2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1499, in run_script
    exec(code, namespace, namespace)
  File "/lab/sw/ve/pl2/lib/python2.7/site-packages/gat-1.3.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/gat-run.py", line 317, in <module>
    sys.exit(main(sys.argv))
  File "/lab/sw/ve/pl2/lib/python2.7/site-packages/gat-1.3.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/gat-run.py", line 295, in main
    annotator_results = fromSegments(options, args)
  File "/lab/sw/ve/pl2/lib/python2.7/site-packages/gat-1.3.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/gat-run.py", line 86, in fromSegments
    segments, annotations, workspaces, isochores = IO.buildSegments(options)
  File "/lab/sw/ve/pl2/lib/python2.7/site-packages/gat-1.3.5-py2.7-linux-x86_64.egg/gat/IO.py", line 180, in buildSegments
    isochores.intersect(workspaces["collapsed"])
  File "gat/Engine.pyx", line 3061, in gat.Engine.IntervalCollection.intersect (gat/Engine.c:44811)
  File "gat/Engine.pyx", line 2797, in gat.Engine.IntervalDictionary.__delitem__ (gat/Engine.c:37344)
KeyError: 'chrX'

In this case, it's complaining that chrX is in the isochores file, but not in the input files. For this particular analysis, I was using an input where I removed the sex chromosomes. In order to solve this problem, I had to make a new isochore file without the sex chromosomes. Same thing happened in another female sample, when it gave the KeyError for chrY.

Ideally, we should use the same full isochore file for each input, and GAT decides internally which chromosome annotations to use.

Best,
Ricardo

Update: I was just looking at some previous logs and found the same error, even though I wasn't using isochores. Seems like this issue is caused by the chromosomes annotations not being present int the workspace as well.

[AndreasHeger]

Thanks, @rdalbanus , I have fixed this.