# ---------------------------------------------------------------------------- # Copyright (c) 2016-2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- import unittest import numpy as np import numpy.testing as npt from q2_demux._ecc import GolayDecoder golay = GolayDecoder() class ECCTests(unittest.TestCase): def test_golay_module1(self): """switch the last base, decode() should recover the original barcode """ sent = golay.encode([0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]) rec = sent[:-1] + 'C' # possible error here decoded, errors = golay.decode(rec) self.assertEqual(decoded, sent) self.assertLess(errors, 1.5) rec = sent[:-1] + 'T' # possible error here decoded, errors = golay.decode(rec) self.assertEqual(decoded, sent) self.assertLess(errors, 1.5) def test_golay_matches_old_code(self): """ decode should behave as micah's code did, i.e., same golay encoding """ original = 'GCATCGTCAACA' rec = 'GCATCGTCCACA' corr, nt_errs = golay.decode(rec) self.assertEqual(corr, original) self.assertEqual(nt_errs, 2) def test_decode_bits(self): """ decode_bits should have correct num_errs, even if corrected = None """ for bitvec in ten_bitvecs: corr, num_errs = golay.decode_bits(bitvec) if corr is None: self.assertEqual(num_errs, 4) else: self.assertEqual(((corr + bitvec) % 2).sum(), num_errs) def test_decode(self): """ decode should decode barcodes from tutorial""" barcodes = ['AGCACGAGCCTA', 'AACTCGTCGATG', 'ACAGACCACTCA', 'ACCAGCGACTAG', 'AGCAGCACTTGT', 'AACTGTGCGTAC', 'ACAGAGTCGGCT', 'ACCGCAGAGTCA', 'ACGGTGAGTGTC', ] for bc in barcodes: self.assertEqual(golay.decode(bc), (bc, 0)) for bc in barcodes: err_bc = 'C' + bc[1:] self.assertEqual(golay.decode(err_bc), (bc, 2)) def test_decode_length_check(self): """ decode should raise if a non 12nt sequence is provided""" with self.assertRaisesRegex(ValueError, "length 8nt.$"): golay.decode('ACGGTGAG') def test_decode_unrecognized_nt(self): self.assertEqual(golay.decode('XYZXYZXYZXYZ'), (None, 4)) def test_G_H(self): """generator and parity check matrices should be s.t. G dot H.T = zeros """ chkmtx = (np.dot(golay.DEFAULT_G, golay.DEFAULT_H.T) % 2) self.assertTrue((chkmtx == 0).all()) def test_another(self): """ decode_bits should fix""" def _make_12bits(): n = 12 res = np.zeros((2 ** n, n), dtype="int") for i in range(2 ** n): res[i] = tuple((0, 1)[i >> j & 1] for j in range(n - 1, -1, -1)) return res # all possible 12 bit messages all_12bits = _make_12bits() # test of decode_bits trans = np.dot(golay.DEFAULT_G.T, all_12bits[666]) % 2 err = ( 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0) rec = (trans + err) % 2 corr, num_errs = golay.decode_bits(rec) npt.assert_equal(corr, trans) npt.assert_equal(corr, np.mod(rec + err, 2)) self.assertEqual(num_errs, 2) def test_syndome_LUT(self): """default syndrome lookup table should have all syndromes as keys also tests other things""" syns = [] errvecs = golay._make_3bit_errors() for errvec in errvecs: syn = tuple(np.mod(np.dot(errvec, golay.DEFAULT_H.T), 2)) syns.append(syn) self.assertEqual(set(syns), set(golay.DEFAULT_SYNDROME_LUT.keys())) self.assertEqual(len(set(syns)), len(syns)) self.assertEqual(len(syns), len(errvecs)) self.assertEqual(len(errvecs), 2325) def test_make_3bit_errors(self): """ 3 bit errors should have all <= 3 bit errs, no >3 bit errors""" bitvecs = golay._make_3bit_errors() a = list([0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]) b = list([0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0]) self.assertTrue(a in map(list, bitvecs)) self.assertFalse(b in map(list, bitvecs)) def test_golay600_codes(self): """ all 600 codes should be left uncorrected, 0 errors""" for bc in golay600: corr, num_errs = golay.decode(bc) self.assertEqual(corr, bc) self.assertEqual(num_errs, 0) def test_golay600_2bit_errors(self): """ A->C, G->T errors should be 2 bit errors for all 600 barcodes """ for bc in golay600: if bc.count('A') == 0: continue # only check those with A's err_bc = bc.replace('A', 'C', 1) corr, num_errs = golay.decode(err_bc) self.assertEqual(corr, bc) self.assertEqual(num_errs, 2) for bc in golay600: if bc.count('G') == 0: continue # only check those with A's err_bc = bc.replace('G', 'T', 1) corr, num_errs = golay.decode(err_bc) self.assertEqual(corr, bc) self.assertEqual(num_errs, 2) def test_golay600_4bit_errors(self): """double A->C, G->T errors should be 2 bit errors for all 600 barcodes """ for bc in golay600: if bc.count('A') < 2: continue # only check those with A's err_bc = bc.replace('A', 'C', 2) corr, num_errs = golay.decode(err_bc) self.assertEqual(corr, None) self.assertEqual(num_errs, 4) for bc in golay600: if bc.count('T') < 2: continue # only check those with A's err_bc = bc.replace('T', 'G', 2) corr, num_errs = golay.decode(err_bc) self.assertEqual(corr, None) self.assertEqual(num_errs, 4) # random 24 bit vectors ten_bitvecs = np.array([ [0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0], [0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1], [0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1], [0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1], [1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1], [0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0], [0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0], [0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1], [0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1], [1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1]]) golay600_str = """ AACGCACGCTAG AACTCGTCGATG AACTGTGCGTAC AAGAGATGTCGA AAGCTGCAGTCG AATCAGTCTCGT AATCGTGACTCG ACACACTATGGC ACACATGTCTAC ACACGAGCCACA ACACGGTGTCTA ACACTAGATCCG ACACTGTTCATG ACAGACCACTCA ACAGAGTCGGCT ACAGCAGTGGTC ACAGCTAGCTTG ACAGTGCTTCAT ACAGTTGCGCGA ACATCACTTAGC ACATGATCGTTC ACATGTCACGTG ACATTCAGCGCA ACCACATACATC ACCAGACGATGC ACCAGCGACTAG ACCGCAGAGTCA ACCTCGATCAGA ACCTGTCTCTCT ACGACGTCTTAG ACGAGTGCTATC ACGATGCGACCA ACGCAACTGCTA ACGCGATACTGG ACGCGCAGATAC ACGCTATCTGGA ACGCTCATGGAT ACGGATCGTCAG ACGGTGAGTGTC ACGTACTCAGTG ACGTCTGTAGCA ACGTGAGAGAAT ACGTGCCGTAGA ACGTTAGCACAC ACTACAGCCTAT ACTACGTGTGGT ACTAGCTCCATA ACTATTGTCACG ACTCACGGTATG ACTCAGATACTC ACTCGATTCGAT ACTCGCACAGGA ACTCTTCTAGAG ACTGACAGCCAT ACTGATCCTAGT ACTGTACGCGTA ACTGTCGAAGCT ACTGTGACTTCA ACTTGTAGCAGC AGAACACGTCTC AGACCGTCAGAC AGACGTGCACTG AGACTGCGTACT AGAGAGCAAGTG AGAGCAAGAGCA AGAGTAGCTAAG AGAGTCCTGAGC AGATACACGCGC AGATCGGCTCGA AGATCTCTGCAT AGATGTTCTGCT AGCACACCTACA AGCACGAGCCTA AGCAGCACTTGT AGCAGTCGCGAT AGCATATGAGAG AGCCATACTGAC AGCGACTGTGCA AGCGAGCTATCT AGCGCTGATGTG AGCGTAGGTCGT AGCTATCCACGA AGCTCCATACAG AGCTCTCAGAGG AGCTGACTAGTC AGCTTGACAGCT AGGACGCACTGT AGGCTACACGAC AGGTGTGATCGC AGTACGCTCGAG AGTACTGCAGGC AGTAGTATCCTC AGTCACATCACT AGTCCATAGCTG AGTCTACTCTGA AGTCTCGCATAT AGTGAGAGAAGC AGTGCGATGCGT AGTGGATGCTCT AGTGTCACGGTG AGTGTTCGATCG AGTTAGTGCGTC AGTTCAGACGCT AGTTCTACGTCA ATAATCTCGTCG ATACACGTGGCG ATACAGAGCTCC ATACGTCTTCGA ATACTATTGCGC ATACTCACTCAG ATAGCTCCATAC ATAGGCGATCTC ATATCGCTACTG ATATGCCAGTGC ATCACGTAGCGG ATCACTAGTCAC ATCAGGCGTGTG ATCCGATCACAG ATCCTCAGTAGT ATCGATCTGTGG ATCGCGGACGAT ATCGCTCGAGGA ATCGTACAACTC ATCTACTACACG ATCTCTGGCATA ATCTGAGCTGGT ATCTGGTGCTAT ATCTTAGACTGC ATGACCATCGTG ATGACTCATTCG ATGAGACTCCAC ATGATCGAGAGA ATGCACTGGCGA ATGCAGCTCAGT ATGCCTGAGCAG ATGCGTAGTGCG ATGGATACGCTC ATGGCAGCTCTA ATGGCGTGCACA ATGGTCTACTAC ATGTACGGCGAC ATGTCACCGTGA ATGTGCACGACT ATGTGTCGACTT ATTATCGTGCAC ATTCTGTGAGCG CAACACGCACGA CAACTATCAGCT CAACTCATCGTA CAAGATCGACTC CAAGTGAGAGAG CACACGTGAGCA CACAGCTCGAAT CACAGTGGACGT CACATCTAACAC CACATTGTGAGC CACGACAGGCTA CACGGACTATAC CACGTCGATGGA CACGTGACATGT CACTACTGTTGA CACTCAACAGAC CACTCTGATTAG CACTGGTATATC CACTGTAGGACG CAGACATTGCGT CAGACTCGCAGA CAGAGGAGCTCT CAGATACACTTC CAGATCGGATCG CAGCACTAAGCG CAGCATGTGTTG CAGCGGTGACAT CAGCTAGAACGC CAGGTGCTACTA CAGTACGATCTT CAGTCACTAACG CAGTCGAAGCTG CAGTGATCCTAG CAGTGCATATGC CAGTGTCAGGAC CATACCAGTAGC CATAGACGTTCG CATAGCGAGTTC CATATACTCGCA CATATCGCAGTT CATCAGCGTGTA CATCATGAGGCT CATCGTATCAAC CATCTGTAGCGA CATGAGTGCTAC CATGCAGACTGT CATGGCTACACA CATGTAATGCTC CATGTCTCTCCG CATTCGATGACT CATTGTCTGTGA CCAGATGATCGT CCAGTGTATGCA CCATACATAGCT CCGACTGAGATG CCGATGTCAGAT CCTAGTACTGAT CCTCTCGTGATC CGAAGACTGCTG CGAATCGACACT CGACAGCTGACA CGACATGCTATT CGACTTATGTGT CGAGAGTTACGC CGAGCAGCACAT CGAGGCTCAGTA CGAGTCTAGTTG CGAGTTGTAGCG CGATAGATCTTC CGATATTCATCG CGATCGAGTGTT CGATGCACCAGA CGATGTCGTCAA CGCACATGTTAT CGCACTCTAGAA CGCAGACAGACT CGCAGCGGTATA CGCATGAGGATC CGCGATAGCAGT CGCGTAACTGTA CGCTAGAACGCA CGCTTATCGAGA CGGAGTGTCTAT CGGCGATGTACA CGTAAGTCTACT CGTACAGTTATC CGTACTAGACTG CGTAGAACGTGC CGTATCTGCGAA CGTATGCTGTAT CGTCAACGATGT CGTCACGACTAA CGTCAGACGGAT CGTCGATCTCTC CGTGACAATGTC CGTGATCTCTCC CGTGCATTATCA CGTGTACATCAG CGTGTGATCAGG CGTTACTAGAGC CGTTATGTACAC CGTTCGCATAGA CTAACGCAGTCA CTACACAAGCAC CTACATCTAAGC CTACGCGTCTCT CTACTACAGGTG CTACTGATATCG CTAGAACGCACT CTAGAGACTCTT CTAGCGAACATC CTAGGTCACTAG CTAGTCAGCTGA CTATAGTCGTGT CTATCAGTGTAC CTATCTAGCGAG CTATGCTTGATG CTCAATGACTCA CTCAGTATGCAG CTCATGTACAGT CTCCACATGAGA CTCCTACTGTCT CTCGAGAGTACG CTCGATTAGATC CTCGCACATATA CTCGTGGAGTAG CTCTCTACCTGT CTCTGAAGTCTA CTCTGCTAGCCT CTGAACGCTAGT CTGACACGACAG CTGAGATACGCG CTGAGCAGAGTC CTGCAGTACTTA CTGCTGCGAAGA CTGGACTCATAG CTGGAGCATGAC CTGGCTGTATGA CTGTATCGTATG CTGTCTCTCCTA CTGTGACATTGT CTGTGGATCGAT CTGTTCGTAGAG CTTAGCACATCA CTTGATGCGTAT CTTGTGTCGATA GAACATGATGAG GAACTGTATCTC GAAGAGTGATCA GAAGCTACTGTC GAAGTCTCGCAT GAATGATGAGTG GACACTCGAATC GACAGCGTTGAC GACAGGAGATAG GACAGTTACTGC GACATCGGCTAT GACCACTACGAT GACCGAGCTATG GACGAGTCAGTC GACGATATCGCG GACGCAGTAGCT GACGCTAGTTCA GACGTTGCACAG GACTAACGTCAC GACTAGACCAGC GACTCACTCAAT GACTCGAATCGT GACTGATCATCT GACTGCATCTTA GACTGTCATGCA GACTTCAGTGTG GAGAATACGTGA GAGACAGCTTGC GAGAGAATGATC GAGAGCTCTACG GAGATGCCGACT GAGCAGATGCCT GAGCATTCTCTA GAGCTGGCTGAT GAGGCTCATCAT GAGTAGCTCGTG GAGTATGCAGCC GAGTCTGAGTCT GAGTGAGTACAA GAGTGGTAGAGA GATACGTCCTGA GATAGCTGTCTT GATAGTGCCACT GATATGCGGCTG GATCAGAAGATG GATCCGACACTA GATCGCAGGTGT GATCGTCCAGAT GATCTATCCGAG GATCTCATAGGC GATCTTCAGTAC GATGATCGCCGA GATGCATGACGC GATGTCGTGTCA GATGTGAGCGCT GATTAGCACTCT GCAATAGCTGCT GCACATCGAGCA GCACGACAACAC GCACTCGTTAGA GCACTGAGACGT GCAGCACGTTGA GCAGCCGAGTAT GCAGGATAGATA GCAGGCAGTACT GCAGTATCACTG GCAGTTCATATC GCATAGTAGCCG GCATATAGTCTC GCATCGTCAACA GCATGTGCATGT GCATTGCGTGAG GCCACTGATAGT GCCAGAGTCGTA GCCTATACTACA GCGACTTGTGTA GCGAGATCCAGT GCGATATATCGC GCGGATGTGACT GCGTACAACTGT GCGTATCTTGAT GCGTTACACACA GCTAAGAGAGTA GCTAGATGCCAG GCTAGTCTGAAC GCTATCACGAGT GCTATTCGACAT GCTCAGTGCAGA GCTCGCTACTTC GCTGATGAGCTG GCTGCTGCAATA GCTGGTATCTGA GCTGTAGTATGC GCTGTGTAGGAC GCTTACATCGAG GCTTCATAGTGT GCTTGCGAGACA GGACGTCACAGT GGATCGCAGATC GGCAGTGTATCG GGCGACATGTAC GGCGTACTGATG GGCTATGACATC GGTATACGCAGC GGTCACTGACAG GGTCGTAGCGTA GGTGCGTGTATG GTACAAGAGTGA GTACGGCATACG GTACTCTAGACT GTAGACTGCGTG GTAGAGCTGTTC GTAGATGCTTCG GTAGCAACGTCT GTAGCGCGAGTT GTAGCTGACGCA GTAGTGTCTAGC GTATATCCGCAG GTATCCATGCGA GTATGACTGGCT GTATGCGCTGTA GTATGTTGCTCA GTCAACGCGATG GTCACGACTATT GTCATATCGTAC GTCATTCACGAG GTCCATAGCTAG GTCGACTCCTCT GTCGCTGTCTTC GTCGTAGCCAGA GTCGTGTGTCAA GTCTACACACAT GTCTATCGGAGT GTCTCATGTAGG GTCTCTCTACGC GTCTGACAGTTG GTCTGGATAGCG GTCTTCGTCGCT GTGACCTGATGT GTGACTGCGGAT GTGAGGTCGCTA GTGATAGTGCCG GTGCAATCGACG GTGCACATTATC GTGGCGATACAC GTGTACCTATCA GTGTCTACATTG GTGTGCTATCAG GTGTGTGTCAGG GTGTTGCAGCAT GTTAGAGCACTC GTTCGCGTATAG GTTGACGACAGC GTTGTATACTCG TAACAGTCGCTG TAACTCTGATGC TAAGCGCAGCAC TACACACATGGC TACACGATCTAC TACAGATGGCTC TACAGTCTCATG TACATCACCACA TACCGCTAGTAG TACGATGACCAC TACGCGCTGAGA TACGGTATGTCT TACGTGTACGTG TACTAATCTGCG TACTACATGGTC TACTGCGACAGT TACTGGACGCGA TACTTACTGCAG TACTTCGCTCGC TAGACTGTACTC TAGAGAGAGTGG TAGATAGCAGGA TAGATCCTCGAT TAGCACACCTAT TAGCATCGTGGT TAGCCTCTCTGC TAGCGACATCTG TAGCGGATCACG TAGCTCGTAACT TAGCTGAGTCCA TAGGTATCTCAC TAGTCGTCTAGT TAGTGCTGCGTA TAGTGTGCTTCA TAGTTGCGAGTC TATACGCGCATT TATCAGGTGTGC TATCGCGCGATA TATCTCGAACTG TATGCACCAGTG TATGCGAGGTCG TATGGCACACAC TATTCGTGTCAG TCAACAGCATCG TCAATCTAGCGT TCACAGATCCGA TCACGATTAGCG TCACTATGGTCA TCACTGGCAGTA TCACTTCTCGCT TCAGACAGACCG TCAGATCCGATG TCAGCCATGACA TCAGCTCAACTA TCAGGACTGTGT TCAGTACGAGGC TCAGTCGACGAG TCAGTGACGTAC TCATCGCGATAT TCATCTGACTGA TCATGGTACACT TCCACGTCGTCT TCCAGTGCGAGA TCCGTCGTCTGT TCCTAGCAGTGA TCCTCTGTCGAC TCCTGAGATACG TCGAATCACAGC TCGACTCCTCGT TCGAGACGCTTA TCGAGCGAATCT TCGAGGACTGCA TCGATACTTGTG TCGATGAACTCG TCGCATGAAGTC TCGCGTATTAGT TCGCTAGTGAGG TCGGCTACAGAG TCGTACGTCATA TCGTCGATAATC TCGTGATGTGAC TCGTGTCTATAG TCGTTCACATGA TCTACGGAGAGC TCTACTCGTAAG TCTAGCGTAGTG TCTAGTTAGTCG TCTCACTAGGTA TCTCCGCATGTC TCTCGTAATCAG TCTCTAGAGCAT TCTCTCCGTCGA TCTGAGTCTGAG TCTGCGTACTAA TCTGCTAGATGT TCTGTTGCTCTC TCTTAGACGACG TGAACGCTAGCT TGACATCAGCGG TGACCATATCGT TGACGCGATGCA TGACGGACATCT TGAGACGTGCTT TGAGAGAGCATA TGAGCACACACG TGAGCGATTCTG TGAGGATGATAG TGAGTCACTGGT TGAGTTCGCTAT TGATAGTGAGGA TGATCAGAAGAG TGATGCTAACTC TGATGTGTGACC TGCAGAGCTCAG TGCATTACGCAT TGCGCGAATACT TGCGTATAGTGC TGCGTCAGTTAG TGCGTGGTAGAC TGCTACCATGAG TGCTAGTCATAC TGCTATATCTGG TGCTCAGTATGT TGCTCGTAGGAT TGCTCTAGTGGA TGCTGTGAGCTA TGGATATGCGCT TGGCTCTACAGA TGGTCATCACTA TGTACACGGCGA TGTACCGATCAT TGTCAGTATTCG TGTCGCTGTAAT TGTCTTGATAGC TGTGACTCGTGA TGTGAGCACGGT TGTGCAAGCGAC TGTGCTGTGTAG TGTGGTACTACG TGTGTAGCGACT TGTGTGTGACTT TGTTATCGCACA TGTTGACACTAC TTACTGTGCGAT TTAGCGTCACGA TTATCACGTGCA TTATGCAGTCGT TTCATGACACTG TTCGATACTCGA TTGACAGTCACT TTGATGCTATGC TTGCGCATACTA TTGCGTCAGACA TTGTATGTGCGT """ golay600 = golay600_str.strip().split('\n') if __name__ == '__main__': unittest.main()