search

asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
Other
132 stars 28 forks source link

how to display the "--reldist" result? #16

Closed clouds-drift closed 1 year ago

clouds-drift commented 5 years ago

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

asntech commented 5 years ago

Apologies for the late response. Can you try by reinstalling pybedtools?