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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"))
# This has two names, depending on Python version
if not hasattr(unittest.TestCase, 'assertRaisesRegex'):
setattr(unittest.TestCase, 'assertRaisesRegex',
unittest.TestCase.assertRaisesRegexp)
class StreamTest(unittest.TestCase):
def setUp(self):
self.gff_file = op.join(datadir, "U89959_sas.gff3")
self.ins = gt.GFF3InStream(self.gff_file)
def test_pull(self):
add_introns_stream = gt.AddIntronsStream(self.ins)
fi = gt.FeatureIndexMemory()
gt.FeatureStream(add_introns_stream, fi).pull()
self.assertTrue('1877523' in fi.get_seqids())
def test_checker(self):
tc = gt.extended.TypeCheckerBuiltin()
self.ins.set_type_checker(tc)
self.ins.pull()
def test_checker_fail(self):
tc = gt.extended.TypeCheckerBuiltin()
gff_file = op.join(datadir, "unknowntype.gff3")
ins = gt.GFF3InStream(gff_file)
ins.set_type_checker(tc)
self.assertRaisesRegex(
gt.core.error.GTError,
'GenomeTools error: type "something" on line 3',
ins.pull)
def test_tidy_fail(self):
gff_file = op.join(datadir, "missing_gff3_header.gff3")
ins = gt.GFF3InStream(gff_file)
self.assertRaisesRegex(
gt.core.error.GTError,
'does not begin with "##gff-version" or "##gff-version"',
ins.pull)
def test_tidy_succ(self):
gff_file = op.join(datadir, "missing_gff3_header.gff3")
ins = gt.GFF3InStream(gff_file)
ins.enable_tidy_mode()
fi = gt.FeatureIndexMemory()
gt.FeatureStream(ins, fi).pull()
self.assertTrue('ctg123' in fi.get_seqids())
class TestDuplicateStream(unittest.TestCase):
def setUp(self):
self.gff_file = op.join(datadir, "addintrons.gff3")
self.ins = gt.GFF3InStream(self.gff_file)
def test_dup(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.DuplicateFeatureStream(self.ins, "intron", "exon"),
fi).pull()
f = fi.get_features_for_seqid('ctg123')
dfi = gt.FeatureNodeIteratorDepthFirst(f[0])
f = dfi.next()
types = set([])
while f:
types.update([f.type])
f = dfi.next()
self.assertTrue('intron' in types, types)
class TestMergeStream(unittest.TestCase):
def setUp(self):
self.gff_file = op.join(datadir, "mergefeat.gff3")
self.ins = gt.GFF3InStream(self.gff_file)
def test_merge(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.MergeFeatureStream(self.ins), fi).pull()
f = fi.get_features_for_seqid('seq1')
self.assertEqual(len(f), 1)
dfi = gt.FeatureNodeIteratorDirect(f[0])
sub = dfi.next()
self.assertEqual(None, dfi.next())
self.assertEqual(sub.start, 1000)
self.assertEqual(sub.end, 10000)
class TestInterFeat(unittest.TestCase):
def setUp(self):
self.gff_file = op.join(datadir, "addintrons.gff3")
self.ins = gt.GFF3InStream(self.gff_file)
def test_inter(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.InterFeatureStream(self.ins, "exon", "intron"),
fi).pull()
f = fi.get_features_for_seqid('ctg123')
dfi = gt.FeatureNodeIteratorDepthFirst(f[0])
f = dfi.next()
types = set([])
while f:
types.update([f.type])
f = dfi.next()
self.assertTrue('intron' in types, types)
class TestCustomExample(unittest.TestCase):
def setUp(self):
self.gff_file = op.join(datadir, "eden.gff3")
self.ins = gt.GFF3InStream(self.gff_file)
def test_inter(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.CustomStreamExample(self.ins),
fi).pull()
f = fi.get_features_for_seqid('ctg123')
dfi = gt.FeatureNodeIteratorDepthFirst(f[0])
f = dfi.next()
types = set([])
while f:
types.update([f.type])
f = dfi.next()
self.assertTrue('bar' in types, types)
if __name__ == "__main__":
unittest.main()
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