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#
# The MIT License
#
# Copyright (c) 2011 Seoul National University.
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# Contact: Hyeshik Chang <hyeshik@snu.ac.kr>
import unittest
import random
import gzip
import tabix
EXAMPLEFILE = '../example.gtf.gz'
def load_example_regions(path):
alldata = []
for line in gzip.GzipFile(EXAMPLEFILE):
fields = line.decode('ascii')[:-1].split('\t')
seqid = fields[0]
begin = int(fields[3])
end = int(fields[4])
alldata.append((seqid, begin, end, fields[:7]))
return alldata
def does_overlap(A, B, C, D):
return (A <= D <= B) or (C <= B <= D)
def sample_test_dataset(regions, ntests):
seqids = [seqid for seqid, _, _, _ in regions]
lowerbound = max(0, min(begin for _, begin, _, _ in regions) - 1000)
upperbound = max(end for _, _, end, _ in regions) + 1000
tests = []
for i in range(ntests):
seqid = random.choice(seqids)
low = random.randrange(lowerbound, upperbound)
high = random.randrange(low, upperbound)
# for 1-based both-end inclusive intervals
matches = [info for seq, begin, end, info in regions
if seqid == seq and does_overlap(begin, end, low, high)]
tests.append((seqid, low, high, matches))
return tests
def tbresult2excerpt(tbmatches):
return [fields[:7] for fields in tbmatches]
class TabixTest(unittest.TestCase):
regions = load_example_regions(EXAMPLEFILE)
testset = sample_test_dataset(regions, 500)
def setUp(self):
self.tb = tabix.Tabix(EXAMPLEFILE)
def testQuery(self):
for seqid, low, high, matches in self.testset:
tbresult = tbresult2excerpt(self.tb.query(seqid, low, high))
self.assertEqual(tbresult, matches)
def testQueryS(self):
for seqid, low, high, matches in self.testset:
tbresult = tbresult2excerpt(self.tb.querys('%s:%d-%d' %
(seqid, low, high)))
self.assertEqual(tbresult, matches)
if __name__ == '__main__':
unittest.main()
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