# ----------------------------------------------------------------------------- # Copyright (c) 2015, The Deblur Development Team. # # Distributed under the terms of the BSD 3-clause License. # # The full license is in the file LICENSE, distributed with this software. # ----------------------------------------------------------------------------- from unittest import TestCase, main from io import StringIO from os.path import join, dirname, abspath import skbio import numpy as np from deblur.sequence import Sequence from deblur.workflow import sequence_generator from deblur.deblurring import get_sequences, deblur, get_default_error_profile class DeblurringTests(TestCase): def setUp(self): self.seqs = [("151_9240;size=170;", "---tagggcaagactccatggt-----"), ("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"), ("151_64278;size=200;", "---tactagcaagattcctggt-----"), ("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"), ("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"), ("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"), ("151_41690;size=157;", "---agg-gcgagattcctagtgg----"), ("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"), ("151_527;size=964;", "---acggaggatgatgcgcggt-----"), ("151_5777;size=305;", "---ggagtgcaagattccaggt-----")] self.test_data_dir = join(dirname(abspath(__file__)), 'data') def test_get_default_error_profile(self): goodprofile = [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] self.assertEqual(goodprofile, get_default_error_profile()) def test_get_sequences_error_real_length(self): seqs = [("151_9240;size=170;", "----tagggcaagactccatg-----"), ("151_6640;size=1068;", "--acggaggcga-atgcgtggt----"), ("151_64278;size=200;", "---tactagcaagattcctgg-----")] with self.assertRaises(ValueError): get_sequences(seqs) def test_get_sequences_error_length(self): seqs = [("151_9240;size=170;", "----tagggcaagactccatg----"), ("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"), ("151_64278;size=200;", "---tactagcaagattcctgg-----")] with self.assertRaises(ValueError): get_sequences(seqs) def test_get_sequences_empty_file(self): gen = skbio.read(join(self.test_data_dir, 'seqs_empty.fasta'), format='fasta') self.assertEqual(get_sequences(gen), None) def test_get_sequences_error_empty(self): self.assertIsNone(get_sequences([])) def test_deblur_noseqs(self): """If no sequences supplied, need to return None """ res = deblur([]) self.assertEqual(res, None) def test_get_sequences(self): exp_seqs = [ Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"), Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"), Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"), Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"), Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"), Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"), Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"), Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"), Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"), Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----")] obs_seqs = get_sequences(self.seqs) self.assertEqual(obs_seqs, exp_seqs) def test_deblur_toy_example(self): seqs_f = StringIO(TEST_SEQS_1) obs = deblur(sequence_generator(seqs_f)) exp = [ Sequence("E.Coli;size=1000;", "tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt" "ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg" "gcaagcttgagtctcgtagaggggggcagaattccag")] self.assertEqual(obs, exp) def test_deblur(self): seqs_f = StringIO(TEST_SEQS_2) obs = deblur(sequence_generator(seqs_f)) exp = [ Sequence("E.Coli-999;size=720;", "tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt" "ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg" "gcaagcttgagtctcgtagaggggggcagaattccag")] self.assertEqual(obs, exp) def test_deblur_indel(self): """Test if also removes indel sequences """ seqs_f = StringIO(TEST_SEQS_2) # add the MSA for the indel seqs = sequence_generator(seqs_f) newseqs = [] for chead, cseq in seqs: tseq = cseq[:10] + '-' + cseq[10:] newseqs.append((chead, tseq)) # now add a sequence with an A insertion at the expected freq. # (30 < 0.02 * (720 / 0.47) where 0.47 is the mod_factor) so should # be removed cseq = newseqs[0][1] tseq = cseq[:10] + 'A' + cseq[11:-1] + '-' chead = '>indel1-read;size=30;' newseqs.append((chead, tseq)) # and add a sequence with an A insertion but at higher freq. (not # expected by indel upper bound - (31 > 0.02 * (720 / 0.47) so should # not be removed) cseq = newseqs[0][1] tseq = cseq[:10] + 'A' + cseq[11:-1] + '-' chead = '>indel2-read;size=31;' newseqs.append((chead, tseq)) obs = deblur(newseqs) # remove the '-' (same as in launch_workflow) for s in obs: s.sequence = s.sequence.replace('-', '') # the expected output exp = [ Sequence("E.Coli-999;size=720;", "tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt" "ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg" "gcaagcttgagtctcgtagaggggggcagaattccag")] # make sure we get 2 sequences as output - the original and the # indel2 (too many reads for the expected indel probabilty) self.assertEqual(len(obs), 2) # and that it is the correct sequence self.assertEqual(obs[0].sequence, exp[0].sequence) self.assertEqual(obs[1].label, '>indel2-read;size=31;') def test_deblur_with_non_default_error_profile(self): error_dist = [1, 0.05, 0.000005, 0.000005, 0.000005, 0.000005, 0.0000025, 0.0000025, 0.0000025, 0.0000025, 0.0000025, 0.0000005, 0.0000005, 0.0000005, 0.0000005] seqs_f = StringIO(TEST_SEQS_2) obs = deblur(sequence_generator(seqs_f), error_dist=error_dist) exp = [ Sequence("E.Coli-999;size=720;", "tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt" "ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg" "gcaagcttgagtctcgtagaggggggcagaattccag")] self.assertEqual(obs, exp) error_dist = np.array( [1, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005]) seqs_f = StringIO(TEST_SEQS_2) obs = deblur(sequence_generator(seqs_f), error_dist=error_dist) exp = [ Sequence("E.Coli-999;size=720;", "tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt" "ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg" "gcaagcttgagtctcgtagaggggggcagaattccag")] self.assertEqual(obs, exp) TEST_SEQS_1 = """>E.Coli;size=1000; tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgt taagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagctt gagtctcgtagaggggggcagaattccag >Error;size=3; aacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgt taagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagctt gagtctcgtagaggggggcagaattccag """ TEST_SEQS_2 = """>E.Coli-999;size=720; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-781;size=5; TGCGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-987;size=4; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGGCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-861;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCATGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-791;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACACAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-832;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGATTTCCAG >E.Coli-476;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAAGCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-633;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CTGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-894;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCAAG >E.Coli-702;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAAATCCAG >E.Coli-986;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGACGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-991;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGGTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-975;size=3; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGTCAGAATTCCAG >E.Coli-670;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTCGAGGGGGGCAGAATTCCAG >E.Coli-709;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGCGGCAGAATTCCAG >E.Coli-640;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCCCGTAGAGGGGGGCAGAATTCCAG >E.Coli-831;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAC >E.Coli-663;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTATCGTAGAGGGGGGCAGAATTCCAG >E.Coli-645;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCCTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-799;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTTCAG >E.Coli-807;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGATTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-795;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCGTCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-785;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGAGGGCAGAATTCCAG >E.Coli-743;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGGATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-737;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATTTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-749;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTGCAG >E.Coli-818;size=2; TCCGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-636;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGAAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-235;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCACAATTCCAG >E.Coli-228;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGATTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-311;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTTGAGGGGGGCAGAATTCCAG >E.Coli-393;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATATGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-336;size=2; TACGGAGGGTGCAAGAGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-190;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTGTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-66;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGCCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-198;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAAGGGGGCAGAATTCCAG >E.Coli-225;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCTAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-216;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGGAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-555;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCGGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-538;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGTCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-561;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CAGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-615;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAAACC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-604;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGAGGGGCAGAATTCCAG >E.Coli-498;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC TCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-455;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGCCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-507;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTACATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-519;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGAAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-511;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCTG >E.Coli-983;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGTGGGGGGCAGAATTCCAG >E.Coli-968;size=2; TACGGAGGGTGGAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-997;size=2; TACGGAGGGTGCAAGCCTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-1000;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCTCGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-883;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCACCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-911;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGGACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-963;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACCGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-941;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATGCTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-932;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGGAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-915;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCGACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-917;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACAGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG >E.Coli-838;size=2; TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGACAGAATTCCAG >E.Coli-851;size=2; TACGGAGGGTGCATGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG """ if __name__ == '__main__': main()