[3] | 1 | """ |
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| 2 | Tests for `bx.seqmapping`. |
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| 3 | """ |
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| 4 | |
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| 5 | import unittest |
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| 6 | import bx.seqmapping |
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| 7 | |
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| 8 | from numpy import array, allclose |
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| 9 | from StringIO import StringIO |
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| 10 | |
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| 11 | class CharMappingTests( unittest.TestCase ): |
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| 12 | def test_DNA( self ): |
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| 13 | assert( allclose( bx.seqmapping.DNA.translate( "ACGTacgt-?X" ), |
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| 14 | [ 0, 1, 2, 3, 0, 1, 2, 3, 4, -1, -1 ] ) ) |
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| 15 | def test_DNA_list( self ): |
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| 16 | assert( allclose( bx.seqmapping.DNA.translate_list( [ "ACGTA", "TGCAX" ] ), |
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| 17 | [ 0 + 3*6, 1 + 2*6, 2 + 1*6, 3 + 0*6, -1 ] ) ) |
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| 18 | def test_other( self ): |
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| 19 | m = bx.seqmapping.CharToIntArrayMapping() |
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| 20 | m.set_mapping( "A", 0 ) |
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| 21 | m.set_mapping( "B", 7 ) |
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| 22 | assert( allclose( m.translate( "ABCCBA" ), [ 0, 7, -1, -1, 7, 0 ] ) ) |
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| 23 | |
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| 24 | class IntMappingTests( unittest.TestCase ): |
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| 25 | def test_simple( self ): |
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| 26 | m = bx.seqmapping.IntToIntMapping( 4 ) |
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| 27 | m.set_mapping( 0, 0 ) |
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| 28 | m.set_mapping( 2, 0 ) |
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| 29 | m.set_mapping( 1, 1 ) |
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| 30 | m.set_mapping( 3, 1 ) |
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| 31 | assert( allclose( m.translate( array( [ 0, 1, 2, 3, 4 ], 'i' ) ), array( [ 0, 1, 0, 1, -1 ] ) ) ) |
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| 32 | |
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| 33 | eight_species_mapping = """TTTTTTTT 0 |
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| 34 | CCCCCCCC 4 |
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| 35 | AAAAAAAA 1 |
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| 36 | GGGGGGGG 5 |
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| 37 | AAAAA*AA 2 |
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| 38 | TTTTT*TT 0 |
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| 39 | GGGGG*GG 5 |
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| 40 | CCCCC*CC 4 |
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| 41 | GGGG*GGG 5 |
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| 42 | TTTT*TTT 2 |
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| 43 | GGGAAGGG 5 |
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| 44 | AAAA*AAA 2 |
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| 45 | TTTTT*T* 2 |
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| 46 | CCCCC*C* 4 |
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| 47 | CCCTTCCC 4 |
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| 48 | CCCC*CCC 4 |
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| 49 | TTTT**TT 2 |
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| 50 | AAAA**AA 2 |
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| 51 | AAAAA*A* 2 |
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| 52 | GGGGG*G* 5 |
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| 53 | AAAAAGAA 2 |
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| 54 | TTTTTCTT 2 |
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| 55 | GGGAA*GG 5 |
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| 56 | TTTT**T* 2 |
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| 57 | TTTCCTTT 0 |
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| 58 | AAAAAAA* 1 |
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| 59 | CCCTT*CC 3 |
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| 60 | TTTTTTT* 2 |
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| 61 | CC*CC*CC 3 |
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| 62 | AAAGGAAA 2 |
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| 63 | ------G- 2 |
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| 64 | """ |
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| 65 | |
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| 66 | rows = [ "AAATTGT-----ATGTCCATCCTTTAAAGGTCATTCCTTTAATGGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATCAAAC-----------------TTTCTTCCCTCCC-TACTTCAGTG", |
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| 67 | "AAATTGT-----ATGTCCATCCTTTAAAGGTCATTCCTTTAATGGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATCAAAC-----------------TTTCTTCCCTCCC-TACTTCAGTG", |
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| 68 | "AAATTTT-----ATGTCTATCCTTTAAAGGTCATTCCTCTAATAGTCTTTTCTGGACACCACTAGGGGTCAGAAGTAGTTCATTAAAC-----------------TTTCTTCCCTCCC-TACCTCAGTG", |
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| 69 | "AAACTGT-----ATCACCACCTTTTTAAGGTCATTTCTCTAATGATCCTGTT-GCATACCAGTAGGGGGCAGAAGTGTTCCGCTGATTTCCGCCCTCCTCCCCACCCCCCCACCCCCC-TTATTCAAAG", |
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| 70 | "*********************************************************************************************************************************", |
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| 71 | "-TATTAT-----ATGGCCATGTTCAAAAGGTTGTTTCTCTAATGATTCCTTC-TGATACCAGTAGGGGTCAGAAGTGGTCCATTGATT---------------------CTTTTCCTC-TGATTC-AAG", |
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| 72 | "AAATTGA--AAGATCTCACTCTTTGCCAGGTAGTCCATCTAAGGGTCACATATGGATACCAGCAGGGCCT-GAAGAAGCCCATTGAAT------------------------TTTCCC-ATCTTCAAGG", |
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| 73 | "AAATTCATGATAGTGTCACTCTTAAATAGATGATTC--------TTCACAT---GATGCCAGCAGGGGGC-AGAGCAGGCTGTGAAAT------------------------TTTCCCTTTCTTCAAAG" ] |
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| 74 | |
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| 75 | class AlignmentMappingTests( unittest.TestCase ): |
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| 76 | def test_largescale( self ): |
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| 77 | f = StringIO( eight_species_mapping ) |
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| 78 | n, m = bx.seqmapping.alignment_mapping_from_file( f ) |
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| 79 | t = bx.seqmapping.DNA.translate_list( rows ) |
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| 80 | i = m.translate( t ) |
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| 81 | |
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| 82 | |
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| 83 | test_classes = [ AlignmentMappingTests, CharMappingTests, IntMappingTests ] |
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| 84 | suite = unittest.TestSuite( [ unittest.makeSuite( c ) for c in test_classes ] ) |
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