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prepare_report_tests.py
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import unittest
from prepare_report import findSampleSheetEntry, parse_index_barcode_key_into_labels, sequence_labels, sequence_to_label
class TestPrepareReport(unittest.TestCase):
# CCTGCGA 1 I5
# TCGCAGG 1 I7
# GGTATCG:TTACAGT:AACGCTA:CCGTGAC Q2 13 14 15 16
# TACGTTC:ACGTAAG:CGTACCT:GTACGGA Q3 25 26 27 28
def test_simpleLookup(self):
full = 'CCTGCGA_TCGCAGG_GGTATCG:TTACAGT:AACGCTA:CCGTGAC_TACGTTC:ACGTAAG:CGTACCT:GTACGGA'
expectedLibraryID = 'testLibrary'
expectedPlateID = 'testPlate'
expectedExperiment = 'test1240kPlus'
keyMapping = {full: [expectedLibraryID, expectedPlateID, expectedExperiment]}
sampleSheetID, libraryID, plateID, experiment = findSampleSheetEntry(full, keyMapping)
self.assertEqual(full, sampleSheetID)
self.assertEqual(expectedLibraryID, libraryID)
self.assertEqual(expectedPlateID, plateID)
self.assertEqual(expectedExperiment, experiment)
def test_subsetLookup(self):
full = 'CCTGCGA_TCGCAGG_GGTATCG:TTACAGT:AACGCTA:CCGTGAC_TACGTTC:ACGTAAG:CGTACCT:GTACGGA'
singleBarcodes = 'CCTGCGA_TCGCAGG_CCGTGAC_ACGTAAG'
expectedLibraryID = 'testLibrary'
expectedPlateID = 'testPlate'
expectedExperiment = 'test1240kPlus'
keyMapping = dict()
keyMapping = {singleBarcodes: [expectedLibraryID, expectedPlateID, expectedExperiment]}
sampleSheetID, libraryID, plateID, experiment = findSampleSheetEntry(full, keyMapping)
self.assertEqual(singleBarcodes, sampleSheetID)
self.assertEqual(expectedLibraryID, libraryID)
self.assertEqual(expectedPlateID, plateID)
self.assertEqual(expectedExperiment, experiment)
def test_noMatch(self):
full = 'CCTGCGA_TCGCAGG_GGTATCG:TTACAGT:AACGCTA:CCGTGAC_TACGTTC:ACGTAAG:CGTACCT:GTACGGA'
expectedLibraryID = 'testLibrary'
expectedPlateID = 'testPlate'
expectedExperiment = 'test1240kPlus'
keyMapping = dict()
sampleSheetID, libraryID, plateID, experiment = findSampleSheetEntry(full, keyMapping)
self.assertEqual('', sampleSheetID)
self.assertEqual('', libraryID)
self.assertEqual('', plateID)
self.assertEqual('', experiment)
def test_multiple_matches(self):
full = 'CCTGCGA_TCGCAGG_GGTATCG:TTACAGT:AACGCTA:CCGTGAC_TACGTTC:ACGTAAG:CGTACCT:GTACGGA'
singleBarcodes1 = 'CCTGCGA_TCGCAGG_CCGTGAC_ACGTAAG'
singleBarcodes2 = 'CCTGCGA_TCGCAGG_CCGTGAC_GTACGGA'
keyMapping = dict()
keyMapping[singleBarcodes1] = ['test1a', 'test1b', 'test1c']
keyMapping[singleBarcodes2] = ['test2a', 'test2b', 'test2c']
MULTIPLE = 'MULTIPLE'
expectedLibraryID = MULTIPLE
expectedSampleSheetID = MULTIPLE
expectedPlateID = MULTIPLE
expectedExperiment = MULTIPLE
sampleSheetID, libraryID,plateID, experiment = findSampleSheetEntry(full, keyMapping)
self.assertEqual(expectedLibraryID, libraryID)
self.assertEqual(expectedSampleSheetID, sampleSheetID)
self.assertEqual(expectedPlateID, plateID)
self.assertEqual(expectedExperiment, experiment)
def test_barcode_labels(self):
barcode_filename = 'test/barcodes_q_only'
barcode_mapping = sequence_labels(barcode_filename)
# ATCGATT:CAGTCAA:GCTAGCC:TGACTGG Q1 1 2 3 4
self.assertEqual('Q1', barcode_mapping['ATCGATT:CAGTCAA:GCTAGCC:TGACTGG'])
self.assertEqual('1', barcode_mapping['ATCGATT'])
self.assertEqual('2', barcode_mapping['CAGTCAA'])
self.assertEqual('3', barcode_mapping['GCTAGCC'])
self.assertEqual('4', barcode_mapping['TGACTGG'])
# GGTCATT:TTAGCAA:AACTGCC:CCGATGG Q30 157 158 159 160
self.assertEqual('Q30', barcode_mapping['GGTCATT:TTAGCAA:AACTGCC:CCGATGG'])
self.assertEqual('157', barcode_mapping['GGTCATT'])
self.assertEqual('158', barcode_mapping['TTAGCAA'])
self.assertEqual('159', barcode_mapping['AACTGCC'])
self.assertEqual('160', barcode_mapping['CCGATGG'])
def test_i5_labels(self):
i5_filename = 'test/i5_Reich20170725'
i5_mapping = sequence_labels(i5_filename)
#GGACGCA 10
self.assertEqual('10', i5_mapping['GGACGCA'])
self.assertEqual('10', sequence_to_label('GGACGCA', i5_mapping))
#CGCCGTC 48
self.assertEqual('48', i5_mapping['CGCCGTC'])
self.assertEqual('48', sequence_to_label('CGCCGTC', i5_mapping))
not_in_set = 'AAAAAAA'
self.assertEqual(not_in_set, sequence_to_label(not_in_set, i5_mapping))
def test_i7_labels(self):
i7_filename = 'test/i7_Reich20170725'
i7_mapping = sequence_labels(i7_filename)
# TCGCAGG 1
self.assertEqual('1', i7_mapping['TCGCAGG'])
self.assertEqual('1', sequence_to_label('TCGCAGG', i7_mapping))
# CGAGATC 81
self.assertEqual('81', i7_mapping['CGAGATC'])
self.assertEqual('81', sequence_to_label('CGAGATC', i7_mapping))
# CCGTTGA 96
self.assertEqual('96', i7_mapping['CCGTTGA'])
self.assertEqual('96', sequence_to_label('CCGTTGA', i7_mapping))
def test_index_barcode_labeling(self):
barcode_filename = 'test/barcodes_q_only'
barcode_mapping = sequence_labels(barcode_filename)
i5_filename = 'test/i5_Reich20170725'
i5_mapping = sequence_labels(i5_filename)
i7_filename = 'test/i7_Reich20170725'
i7_mapping = sequence_labels(i7_filename)
key = 'GGACGCA_CGAGATC_ATCGATT:CAGTCAA:GCTAGCC:TGACTGG_GGTCATT:TTAGCAA:AACTGCC:CCGATGG'
i5, i7, p5, p7 = parse_index_barcode_key_into_labels(key, i5_mapping, i7_mapping, barcode_mapping)
self.assertEqual('10', i5)
self.assertEqual('81', i7)
self.assertEqual('Q1', p5)
self.assertEqual('Q30', p7)
def test_index_barcode_labeling_single_barcodes(self):
barcode_filename = 'test/barcodes_q_only'
barcode_mapping = sequence_labels(barcode_filename)
i5_filename = 'test/i5_Reich20170725'
i5_mapping = sequence_labels(i5_filename)
i7_filename = 'test/i7_Reich20170725'
i7_mapping = sequence_labels(i7_filename)
key = 'GGACGCA_CGAGATC_ATCGATT_TTAGCAA'
i5, i7, p5, p7 = parse_index_barcode_key_into_labels(key, i5_mapping, i7_mapping, barcode_mapping)
self.assertEqual('10', i5)
self.assertEqual('81', i7)
self.assertEqual('1', p5)
self.assertEqual('158', p7)
def test_index_barcode_labeling_not_in_set(self):
key = 'AAAAAAA_CCCCCCC_GGGGGGG_TTTTTTT'
i5, i7, p5, p7 = parse_index_barcode_key_into_labels(key, {}, {}, {})
self.assertEqual('AAAAAAA', i5)
self.assertEqual('CCCCCCC', i7)
self.assertEqual('GGGGGGG', p5)
self.assertEqual('TTTTTTT', p7)
def test_index_barcode_labeling_empty(self):
key = ''
i5, i7, p5, p7 = parse_index_barcode_key_into_labels(key, {}, {}, {})
self.assertEqual('', i5)
self.assertEqual('', i7)
self.assertEqual('', p5)
self.assertEqual('', p7)
def test_index_barcode_labeling_none(self):
i5, i7, p5, p7 = parse_index_barcode_key_into_labels(None, {}, {}, {})
self.assertEqual('', i5)
self.assertEqual('', i7)
self.assertEqual('', p5)
self.assertEqual('', p7)
if __name__ == '__main__':
unittest.main()