[3] | 1 | """ |
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| 2 | Tests for `bx.seq.qdna`. |
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| 3 | """ |
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| 4 | |
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| 5 | import unittest |
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| 6 | import sys |
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| 7 | import os.path |
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| 8 | import qdna |
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| 9 | |
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| 10 | test_qdna = "test_data/seq_tests/test.qdna" |
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| 11 | |
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| 12 | # Same sequence data as stored in test.qdna |
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| 13 | |
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| 14 | valid_seq = "C7wMwHQrMKqEtSREuUv5nsLinpTS8l7jXpbI7IipvCbHnhOdgx" \ |
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| 15 | + "5tzRgzYl4j85d:xSlvKPEKEIvZkfiX1YPkBi1Ibhfn9fTZd8gG" \ |
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| 16 | + "Wy284hJnwf93W4eHOjeRk7LuVYmH{UTYkYM:b4J4MruMq1ihhv" \ |
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| 17 | + "1Yl5W[xXEmi8[JuuLRgooBpy23PllMuUiIiKVIK5vzhjPPYp5Y" \ |
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| 18 | + "1eqPxo[e5I24KeCdTV94MZWNybUb:McC:1n4Jczk8JqnR4q1gY" \ |
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| 19 | + "HjLS4Bes3s5YvvWdKzS4VrFZy2erhd7YoWRoS[UK8JtSp1{Z1o" \ |
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| 20 | + "5:TpvN8mrmWrghiNw{S6nT8DSfF{1ff6kNGpI:FsZE2RgipTVO" \ |
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| 21 | + "mJN6vPm8MUgNYd7MDBEu37YOPzPjO1dr" |
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| 22 | |
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| 23 | valid_seq_len = len(valid_seq) |
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| 24 | |
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| 25 | class QDNATestCase(unittest.TestCase): |
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| 26 | |
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| 27 | def test_get(self): |
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| 28 | qdnafile = qdna.QdnaFile(file(test_qdna,"rb")) |
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| 29 | check_get(qdnafile, 0, valid_seq_len) |
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| 30 | check_get(qdnafile, 0, 40) |
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| 31 | check_get(qdnafile, valid_seq_len - 40, 40) |
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| 32 | |
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| 33 | def check_get(qdnafile, start, len): |
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| 34 | assert qdnafile.get(start, len) == valid_seq[start:start+len] |
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| 35 | |
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| 36 | test_classes = [ QDNATestCase ] |
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| 37 | suite = unittest.TestSuite( [ unittest.makeSuite( c ) for c in test_classes ] ) |
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