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#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import gt
import os
op = os.path
datadir = op.abspath(op.join(op.dirname(__file__), "..", "..",
"testdata"))
"""
###
1877523 gth gene 25221 26100 1 + . ID=gene12;Target=8690053 1 521 +
1877523 gth exon 25221 25310 1 + . Parent=gene12
1877523 gth five_prime_cis_splice_site 25311 25312 0.993 + . Parent=gene12
1877523 gth three_prime_cis_splice_site 25508 25509 0.439 + . Parent=gene12
1877523 gth exon 25510 25626 1 + . Parent=gene12
1877523 gth five_prime_cis_splice_site 25627 25628 0.998 + . Parent=gene12
1877523 gth three_prime_cis_splice_site 25711 25712 0.996 + . Parent=gene12
1877523 gth exon 25713 25841 1 + . Parent=gene12
1877523 gth five_prime_cis_splice_site 25842 25843 0.63 + . Parent=gene12
1877523 gth three_prime_cis_splice_site 25914 25915 0.926 + . Parent=gene12
1877523 gth exon 25916 26100 1 + . Parent=gene12
###
"""
class FeatureNodeIteratorTest(unittest.TestCase):
def setUp(self):
fi = gt.FeatureIndexMemory()
self.gff_file = op.join(datadir, "U89959_sas.gff3")
fi.add_gff3file(self.gff_file)
self.fi = fi
self.feature = fi.get_features_for_range(25000, 26000, '1877523')[0]
def test_depth_first(self):
dfi = gt.FeatureNodeIteratorDepthFirst(self.feature)
found = dfi.next()
self.assertEqual(found.get_attribute("ID"), "gene12")
self.assertEqual(found.type, "gene")
found = dfi.next()
self.assertEqual(found.type, 'exon')
found = dfi.next()
self.assertEqual(found.type, 'five_prime_cis_splice_site')
found = dfi.next()
found = dfi.next()
self.assertEqual(found.type, 'exon')
def test_direct(self):
di = gt.FeatureNodeIteratorDirect(self.feature)
found = di.next()
types = {}
while found:
types[found.type] = 1
found = di.next()
#self.assertTrue('gene' in types)
self.assertTrue('exon' in types)
self.assertTrue('five_prime_cis_splice_site' in types)
self.assertTrue('three_prime_cis_splice_site' in types)
self.assertEqual(found, None)
if __name__ == "__main__":
unittest.main()
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