def split(args):
hm_col_reader = csv.DictReader(args.columns)
hm_columns = map(lambda x: int(x['column']), hm_col_reader)
hm_columns = list(set(hm_columns))
seq_records = SeqIO.parse(args.alignment, 'fasta')
aln = Alignment(seq_records)
aln.split_hypermuts(hm_columns = hm_columns)
fn_base = path.join(args.out_dir, args.prefix)
hm_pos_handle = open(fn_base + '.pos.fasta', 'w')
hm_neg_handle = open(fn_base + '.neg.fasta', 'w')
AlignIO.write(aln.hm_pos_aln, hm_pos_handle, 'fasta')
AlignIO.write(aln.hm_neg_aln, hm_neg_handle, 'fasta')
for handle in [args.alignment, args.columns, hm_pos_handle, hm_neg_handle]:
handle.close()
def split(args):
hm_col_reader = csv.DictReader(args.columns)
hm_columns = map(lambda x: int(x['column']), hm_col_reader)
hm_columns = list(set(hm_columns))
seq_records = SeqIO.parse(args.alignment, 'fasta')
aln = Alignment(seq_records)
aln.split_hypermuts(hm_columns=hm_columns)
fn_base = path.join(args.out_dir, args.prefix)
hm_pos_handle = open(fn_base + '.pos.fasta', 'w')
hm_neg_handle = open(fn_base + '.neg.fasta', 'w')
AlignIO.write(aln.hm_pos_aln, hm_pos_handle, 'fasta')
AlignIO.write(aln.hm_neg_aln, hm_neg_handle, 'fasta')
for handle in [args.alignment, args.columns, hm_pos_handle, hm_neg_handle]:
handle.close()
class TestBasicSplit(unittest.TestCase):
def assertSeqsEqual(self, seq_record, string):
self.assertEqual(str(seq_record.seq), string)
def setUp(self):
aln_string = """
>seq1
GTCAGTCAGTCAGTCA
GTCAGTCAGTCAGTCA
>seq2
GTCAGTCAGTCAGTCA
GTCAGTCAGTCAGTCA
>seq3
ATCAATCAGTCAATCG
ATCAATCAGTCAATCG"""
self.seqs = helpers.parse_fasta_list(aln_string)
self.aln = Alignment(self.seqs)
def test_manual_split(self):
columns = [1, 2, 3, 5]
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 28)
self.assertEqual(pos.get_alignment_length(), 4)
self.assertEqual(neg[:, 0], "AAA")
self.assertEqual(neg[:, 11], "AAG")
self.assertSeqsEqual(neg[0, :], "ATCAGTCAGTCAGTCAGTCAGTCAGTCA")
self.assertEqual(pos[:, 1], "TTT")
def test_splitting_final_col(self):
columns = [3, 7, 32]
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 29)
self.assertEqual(pos.get_alignment_length(), 3)
self.assertEqual(neg[:, 0], "GGA")
self.assertEqual(neg[:, 12], "CCC")
self.assertSeqsEqual(neg[0, :], "GTAGTAGTCAGTCAGTCAGTCAGTCAGTC")
self.assertEqual(pos[:, 1], "CCC")
self.assertEqual(pos[:, 2], "AAG")
def test_splitting_on_no_hm(self):
columns = []
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 32)
self.assertEqual(pos.get_alignment_length(), 0)
self.assertEqual(neg[:, 0], "GGA")
self.assertSeqsEqual(neg[0, :], "GTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCA")
self.assertSeqsEqual(pos[0, :], "")
class TestBasicSplit(unittest.TestCase):
def assertSeqsEqual(self, seq_record, string):
self.assertEqual(str(seq_record.seq), string)
def setUp(self):
aln_string = """
>seq1
GTCAGTCAGTCAGTCA
GTCAGTCAGTCAGTCA
>seq2
GTCAGTCAGTCAGTCA
GTCAGTCAGTCAGTCA
>seq3
ATCAATCAGTCAATCG
ATCAATCAGTCAATCG"""
self.seqs = helpers.parse_fasta_list(aln_string)
self.aln = Alignment(self.seqs)
def test_manual_split(self):
columns = [1, 2, 3, 5]
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 28)
self.assertEqual(pos.get_alignment_length(), 4)
self.assertEqual(neg[:, 0], 'AAA')
self.assertEqual(neg[:, 11], 'AAG')
self.assertSeqsEqual(neg[0, :], 'ATCAGTCAGTCAGTCAGTCAGTCAGTCA')
self.assertEqual(pos[:, 1], 'TTT')
def test_splitting_final_col(self):
columns = [3, 7, 32]
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 29)
self.assertEqual(pos.get_alignment_length(), 3)
self.assertEqual(neg[:, 0], 'GGA')
self.assertEqual(neg[:, 12], 'CCC')
self.assertSeqsEqual(neg[0, :], 'GTAGTAGTCAGTCAGTCAGTCAGTCAGTC')
self.assertEqual(pos[:, 1], 'CCC')
self.assertEqual(pos[:, 2], 'AAG')
def test_splitting_on_no_hm(self):
columns = []
self.aln.split_hypermuts(hm_columns=columns)
neg, pos = self.aln.hm_neg_aln, self.aln.hm_pos_aln
self.assertEqual(neg.get_alignment_length(), 32)
self.assertEqual(pos.get_alignment_length(), 0)
self.assertEqual(neg[:, 0], 'GGA')
self.assertSeqsEqual(neg[0, :], 'GTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCA')
self.assertSeqsEqual(pos[0, :], '')
