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#!/usr/bin/env python
"""
Test for running many random intersections in parallel. Use this for making
sure the open file bug (#38) doesn't return. Not part of the standard test
suite because of the amount of time it takes to run....
Stored here because it's a test, but .py extension removed so nosetests doesn't
find it.
"""
import pybedtools
import sys
import os
prog = sys.argv[0]
usage = """
Tries to create the open file bug by performing 10k iterations.
To test BedTool.randomstats:
%(prog)s randomstats
To test BedTool.naive_jaccard:
%(prog)s jaccard
""" % locals()
if not os.path.exists('TEMP'):
os.makedirs('TEMP')
if len(sys.argv) < 2:
print(usage)
sys.exit(1)
pybedtools.set_tempdir('TEMP')
gfn = pybedtools.chromsizes_to_file({'chr1': (0, 1000)})
a = pybedtools.example_bedtool('a.bed').set_chromsizes({'chr1': (1, 1000)})
b = pybedtools.example_bedtool('b.bed')
if sys.argv[1] == 'randomstats':
results = a.randomstats(b, 100000, report_iterations=True, processes=8,
intersect_kwargs={'sorted': True})
elif sys.argv[1] == 'newrandomstats':
results = a.randomstats(b, 100000, processes=8,
new=True, genome_fn=gfn,
intersect_kwargs={'sorted': True})
elif sys.argv[1] == 'jaccard':
results = a.random_jaccard(other=b, iterations=10000, genome_fn=gfn,
processes=8, shuffle_kwargs=dict(chrom=True),
)
else:
print(usage)
sys.exit(1)
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