def setUp(self): ref_seq = helpers.parse_fasta(""" >all GGGGGGGGGTGTGTGTGT""") self.aln = Alignment(helpers.parse_fasta(""" >seq1 GGGGGGGGGTGTGTGTGT >seq2 AGAGAGAGGTGTGTGTGT >seq3 GGGGGGGGGTATATATAT """).values(), reference_sequence = ref_seq['all'])
def setUp(self): ref_seq = helpers.parse_fasta(""" >all GGGGGGGGGTGTGTGTGT""") self.aln = Alignment(helpers.parse_fasta(""" >seq1 GGGGGGGGGTGTGTGTGT >seq2 AGAGAGAGGTGTGTGTGT >seq3 GGGGGGGGGTATATATAT """).values(), reference_sequence=ref_seq['all'])
def setUp(self): ref_seq = Seq.Seq('GA' * 9 + 'GC' * 6 + 'GT' * 15) query_seq = 'AA' * 4 + 'GA' * 5 + 'AC' + 'GC' * 5 + 'GT' * 15 aln_string = '>seq1\n{0}'.format(query_seq) self.aln = Alignment(helpers.parse_fasta(aln_string).values(), reference_sequence=ref_seq) self.mutation_patterns = [mut_pattern.GA, mut_pattern.GM]
def main(): '''Main runner, to read data, compute and saves output.''' sequences = parse_fasta(os.path.join(os.path.dirname(__file__), 'data/rosalind_grph.txt')) adj_list = adjaceny_list(sequences, 3) with open(output_path(__file__), 'w') as output: output.write('\n'.join(adj_list))
def main(): '''Main runner, to read data, compute and saves output.''' sequences = parse_fasta(os.path.join(os.path.dirname(__file__), 'data/rosalind_gc.txt')) hi_gc = highest_gc(sequences) with open(output_path(__file__), 'w') as output: output.write(hi_gc['id'] + '\n') output.write(str(hi_gc['gc']))
def setUp(self): aln_string = """ >seq1 GTCAGTCAGTCAGTCACCCC >seq2 GTCAGTCAGTCAGTCACCCC >seq3 ATCAATCAGTCAATCACCCC """ self.seqs = helpers.parse_fasta(aln_string) self.aln = Alignment(self.seqs.values())
def setUp(self): aln_string = """ >seq1 GGTGACGCT >seq2 AGTAACGCT >seq3 GGTAACACT """ ref_seq = Seq.Seq('GGTGACGCT') self.aln = Alignment(helpers.parse_fasta(aln_string).values(), reference_sequence=ref_seq)
def main(): '''Main runner, to read data, compute and saves output.''' sequences = parse_fasta(os.path.join(os.path.dirname(__file__), 'data/rosalind_cons.txt')) matrix = profile_matrix(sequences) consensus = concensus_string(matrix) # add symbol labels to the profile matrix for printing labeled_matrix = ['A:','C:','G:','T:'] for i, row in enumerate(matrix): for col in row: labeled_matrix[i] += ' ' + str(col) with open(output_path(__file__), 'w') as output: output.write(consensus + '\n') output.write('\n'.join(labeled_matrix))
def test_with_reference_seqs(self): ref_seqs = helpers.parse_fasta(""" >cluster1 AAAAAAAAAAAAAAAAACCC >cluster2 CCTTGGCCGGTTGGCCGCCC """) aln_set = AlignmentSet(self.seqs, cluster_map=self.cluster_map, reference_sequences=ref_seqs) self.assertEqual(len(aln_set.clusters), 2) for result in aln_set.multiple_context_analysis([old_pattern]): hm_pos = result['call']['hm_pos'] if result['call']['sequence'] in ['seq2.{}'.format(i) for i in [1,2,3]]: self.assertTrue(hm_pos) else: self.assertFalse(hm_pos)
def setUp(self): aln_string = """ >seq1.1 GTCAGTCGGTCGGTCAGCCC >seq1.2 GTCAGTCGGTCGGTCAGCCC >seq1.3 AGCAATCAGGCAATCAGCCC >seq2.1 GGTTAACCGGTTAACCGCCC >seq2.2 GGTTAACCGGTTAACCGCCC >seq2.3 AATTAACCAATTAACCACCC """ self.cluster_map = {'cluster1': ['seq1.1', 'seq1.2', 'seq1.3'], 'cluster2': ['seq2.1', 'seq2.2', 'seq2.3']} self.seqs = helpers.parse_fasta(aln_string)
def test_with_reference_seqs(self): ref_seqs = helpers.parse_fasta(""" >cluster1 AAAAAAAAAAAAAAAAACCC >cluster2 CCTTGGCCGGTTGGCCGCCC """) aln_set = AlignmentSet(self.seqs, cluster_map=self.cluster_map, reference_sequences=ref_seqs) self.assertEqual(len(aln_set.clusters), 2) for result in aln_set.multiple_context_analysis([old_pattern]): hm_pos = result['call']['hm_pos'] if result['call']['sequence'] in [ 'seq2.{}'.format(i) for i in [1, 2, 3] ]: self.assertTrue(hm_pos) else: self.assertFalse(hm_pos)
def setUp(self): aln_string = """ >seq1.1 GTCAGTCGGTCGGTCAGCCC >seq1.2 GTCAGTCGGTCGGTCAGCCC >seq1.3 AGCAATCAGGCAATCAGCCC >seq2.1 GGTTAACCGGTTAACCGCCC >seq2.2 GGTTAACCGGTTAACCGCCC >seq2.3 AATTAACCAATTAACCACCC """ self.cluster_map = { 'cluster1': ['seq1.1', 'seq1.2', 'seq1.3'], 'cluster2': ['seq2.1', 'seq2.2', 'seq2.3'] } self.seqs = helpers.parse_fasta(aln_string)
def setUp(self): ref_seq = Seq.Seq('GA'*9 + 'GC'*6 + 'GT'*15) query_seq = 'AA'*4 + 'GA'*5 + 'AC' + 'GC'*5 + 'GT'*15 aln_string = '>seq1\n{0}'.format(query_seq) self.aln = Alignment(helpers.parse_fasta(aln_string).values(), reference_sequence=ref_seq) self.mutation_patterns=[mut_pattern.GA, mut_pattern.GM]