how to display the "--reldist" result?
clouds-drift opened this issue · comments
I'm trying to use the "--reldist" calculation.
intervene pairwise --compute reldist --sort --test
Then it returns error:
Running Intervene with test data.
Performing a pairwise intersection analysis. Please wait...
Traceback (most recent call last):
File "/export/data2/anaconda2/bin/intervene", line 4, in
import('pkg_resources').run_script('intervene==0.6.4', 'intervene')
File "/export/data2/anaconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/export/data2/anaconda2/lib/python2.7/site-packages/pkg_resources/init.py", line 1527, in run_script
exec(code, namespace, namespace)
File "/export/data2/anaconda2/lib/python2.7/site-packages/intervene-0.6.4-py2.7.egg/EGG-INFO/scripts/intervene", line 606, in
main()
File "/export/data2/anaconda2/lib/python2.7/site-packages/intervene-0.6.4-py2.7.egg/EGG-INFO/scripts/intervene", line 426, in main
pairwise.pairwise_intersection(label_names, options)
File "/export/data2/anaconda2/lib/python2.7/site-packages/intervene-0.6.4-py2.7.egg/intervene/modules/pairwise/pairwise.py", line 412, in pairwise_intersection
matrix, bed_sizes = create_matrix(beds=options.input, bed_names=label_names, func=FUNC, verbose=False, sort_bed=options.sort, **kwoptions)
File "/export/data2/anaconda2/lib/python2.7/site-packages/intervene-0.6.4-py2.7.egg/intervene/modules/pairwise/pairwise.py", line 74, in create_matrix
matrix[bed_names[ia]][bed_names[ib]] = func(a, b, **kwoptions)
File "/export/data2/anaconda2/lib/python2.7/site-packages/intervene-0.6.4-py2.7.egg/intervene/modules/pairwise/pairwise.py", line 41, in reldist_of_a
return float(sum(a.reldist(b)['reldist'])) / max(len(a.reldist(b)['reldist']), 1)
File "/export/data2/anaconda2/lib/python2.7/site-packages/pybedtools/bedtool.py", line 349, in wrapped
return does_not_return_bedtool(stream, **kwargs)
File "/export/data2/anaconda2/lib/python2.7/site-packages/pybedtools/bedtool.py", line 69, in _reldist_output_handler
header = six.advance_iterator(iterable).split()
StopIteration
Apologies for the late response. Can you try by reinstalling pybedtools?