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| a | b/tests/test_barcodeFileParser.py | ||
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| 1 | #!/usr/bin/env python3 |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | import unittest |
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| 4 | import itertools |
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| 5 | import singlecellmultiomics.barcodeFileParser.barcodeFileParser as barcodeFileParser |
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| 6 | import pkg_resources |
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| 7 | |||
| 8 | """ |
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| 9 | These tests check if the barcode file parser is working correctly |
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| 10 | """ |
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| 11 | |||
| 12 | class TestBarcodeParser(unittest.TestCase): |
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| 13 | |||
| 14 | def test_insert(self): |
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| 15 | |||
| 16 | b = barcodeFileParser.BarcodeParser() |
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| 17 | |||
| 18 | b.addBarcode( |
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| 19 | barcodeFileAlias = 'test', |
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| 20 | barcode='AAA', |
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| 21 | index='TEST1') |
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| 22 | |||
| 23 | |||
| 24 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('AAA','test') |
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| 25 | self.assertEqual(index,'TEST1') |
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| 26 | self.assertEqual(barcode,'AAA') |
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| 27 | self.assertEqual(hd,0) |
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| 28 | |||
| 29 | def test_hamming_expansion(self): |
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| 30 | |||
| 31 | b = barcodeFileParser.BarcodeParser() |
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| 32 | b.addBarcode( barcodeFileAlias = 'test', barcode='AAA', index='TEST1') |
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| 33 | b.expand(1,'test') |
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| 34 | # Postive examples: |
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| 35 | for positive in ['AAT','CAA','AGA','TAA']: |
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| 36 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(positive,'test') |
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| 37 | self.assertEqual(index,'TEST1') |
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| 38 | self.assertEqual(barcode,'AAA') |
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| 39 | self.assertEqual(hd,1) |
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| 40 | |||
| 41 | #Negative examples |
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| 42 | for negative in ['TAT','CCA','GGA','TCA']: |
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| 43 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(negative,'test') |
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| 44 | self.assertNotEqual(barcode,'AAA') |
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| 45 | |||
| 46 | def test_hamming_expansion(self): |
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| 47 | |||
| 48 | b = barcodeFileParser.BarcodeParser() |
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| 49 | b.addBarcode( |
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| 50 | barcodeFileAlias = 'test', |
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| 51 | barcode='AAA', |
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| 52 | index='TEST1') |
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| 53 | b.addBarcode( |
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| 54 | barcodeFileAlias = 'test', |
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| 55 | barcode='AAT', |
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| 56 | index='TEST2') |
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| 57 | b.addBarcode( |
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| 58 | barcodeFileAlias = 'test', |
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| 59 | barcode='TTT', |
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| 60 | index='TEST3') |
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| 61 | |||
| 62 | b.expand(2,'test') |
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| 63 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('CTC','test') |
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| 64 | self.assertEqual(index,'TEST3') |
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| 65 | self.assertEqual(barcode,'TTT') |
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| 66 | self.assertEqual(hd,2) |
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| 67 | |||
| 68 | |||
| 69 | def test_hamming_expansion_collisions(self): |
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| 70 | |||
| 71 | b = barcodeFileParser.BarcodeParser() |
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| 72 | b.addBarcode( |
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| 73 | barcodeFileAlias = 'test', |
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| 74 | barcode='AAA', |
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| 75 | index='TEST1') |
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| 76 | b.addBarcode( |
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| 77 | barcodeFileAlias = 'test', |
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| 78 | barcode='AAT', |
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| 79 | index='TEST2') |
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| 80 | b.addBarcode( |
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| 81 | barcodeFileAlias = 'test', |
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| 82 | barcode='TTT', |
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| 83 | index='TEST3') |
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| 84 | |||
| 85 | b.expand(2,'test') |
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| 86 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('AAG','test') |
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| 87 | self.assertIsNone(index) |
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| 88 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('AAG','test') |
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| 89 | self.assertIsNone(index) |
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| 90 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('TCA','test') |
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| 91 | self.assertIsNone(index) |
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| 92 | |||
| 93 | |||
| 94 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('AAA','test') |
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| 95 | self.assertEqual(index,'TEST1') |
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| 96 | self.assertEqual(barcode,'AAA') |
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| 97 | self.assertEqual(hd,0) |
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| 98 | |||
| 99 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('TAA','test') |
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| 100 | self.assertEqual(index,'TEST1') |
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| 101 | self.assertEqual(barcode,'AAA') |
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| 102 | self.assertEqual(hd,1) |
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| 103 | |||
| 104 | |||
| 105 | def lazy_load_case(self, lazyloadsetting): |
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| 106 | b = barcodeFileParser.BarcodeParser(pkg_resources.resource_filename( |
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| 107 | 'singlecellmultiomics', |
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| 108 | 'modularDemultiplexer/barcodes/'), lazyLoad = lazyloadsetting,hammingDistanceExpansion=1) |
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| 109 | |||
| 110 | |||
| 111 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('GAATCTCG','celseq1') |
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| 112 | self.assertEqual(index,49) |
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| 113 | self.assertEqual(barcode,'GAATCTCG') |
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| 114 | self.assertEqual(hd,0) |
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| 115 | |||
| 116 | # Test lazy loading of hamming expansion: |
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| 117 | index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance('GTGCTATC','celseq1') |
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| 118 | self.assertEqual(index,95) |
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| 119 | self.assertEqual(barcode,'GTGCAATC') |
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| 120 | self.assertEqual(hd,1) |
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| 121 | |||
| 122 | |||
| 123 | def test_lazy_load(self): |
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| 124 | print('lazyLoad all:') |
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| 125 | self.lazy_load_case(lazyloadsetting='*') |
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| 126 | #print('lazyLoad single:') |
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| 127 | #self.lazy_load_case(lazyloadsetting=('celseq1',)) |
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| 128 | |||
| 129 | |||
| 130 | if __name__ == '__main__': |
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| 131 | unittest.main() |