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import os
import random
import pyfastx
import pyfaidx
import unittest
join = os.path.join
data_dir = join(os.path.dirname(os.path.abspath(__file__)), 'data')
gzip_fasta = join(data_dir, 'test.fa.gz')
flat_fasta = join(data_dir, 'test.fa')
class SequenceTest(unittest.TestCase):
def setUp(self):
self.fastx = pyfastx.Fasta(gzip_fasta)
self.fasta = pyfastx.Fasta(flat_fasta)
self.faidx = pyfaidx.Fasta(flat_fasta, sequence_always_upper=True)
self.count = len(self.fastx)
def tearDown(self):
del self.fastx
del self.fasta
del self.faidx
if os.path.exists('{}.fxi'.format(gzip_fasta)):
os.remove('{}.fxi'.format(gzip_fasta))
if os.path.exists('{}.fxi'.format(flat_fasta)):
os.remove('{}.fxi'.format(flat_fasta))
if os.path.exists('{}.fai'.format(flat_fasta)):
os.remove('{}.fai'.format(flat_fasta))
def get_random_index(self):
return random.randint(0, self.count-1)
def test_seq_by_index(self):
#test get seq by index
idx = self.get_random_index()
expect = self.faidx[idx][:]
result = self.fastx[idx]
self.assertEqual(expect.name, result.name)
self.assertEqual(expect.seq, result.seq)
#test subseq
self.assertEqual(expect[0:10].seq, result[0:10].seq)
#test negative index
idx = (self.get_random_index() + 1) * -1
expect = self.faidx[self.count+idx][:]
result = self.fastx[idx]
self.assertEqual(expect.name, result.name)
self.assertEqual(expect.seq, result.seq)
def test_seq_by_key(self):
idx = self.get_random_index()
key = list(self.faidx.keys())[idx]
expect = self.faidx[key][:]
result = self.fastx[key]
self.assertEqual(expect.name, result.name)
self.assertEqual(expect.seq, result.seq)
def test_seq_reverse_complement(self):
idx = self.get_random_index()
expect = self.faidx[idx][:]
result = self.fastx[idx]
self.assertEqual(str(expect.reverse), result.reverse)
self.assertEqual(str(expect.complement), result.complement)
self.assertEqual(str(-expect), result.antisense)
def test_seq_raw(self):
idx = self.get_random_index()
seq = self.fastx[idx]
lines = []
with open(flat_fasta) as fh:
for line in fh:
if line.startswith('>{}'.format(seq.name)):
lines.append(line)
continue
if lines:
if line[0] == '>':
break
lines.append(line)
self.assertEqual(''.join(lines).replace('\n','\r\n'), seq.raw)
def test_seq_slice(self):
idx = self.get_random_index()
expect = str(self.faidx[idx])
result = self.fastx[idx]
flatseq = self.fasta[idx]
#test gzip subseq
self.assertEqual(expect[5:10], result[5:10].seq)
#test flat subseq
self.assertEqual(expect[5:10], flatseq[5:10].seq)
self.assertEqual(expect[20:], result[20:].seq)
#test two level slice
self.assertEqual(expect[10:100][:20], result[10:100][:20].seq)
#test sequence index
pos = random.randint(0, len(expect) - 1)
self.assertEqual(expect[pos], result[pos])
pos = random.randint(1, len(expect)) * -1
self.assertEqual(expect[pos], result[pos])
del flatseq
def test_seq_content(self):
idx = self.get_random_index()
result = self.fastx[idx]
expect = self.faidx[idx]
content = {'A': 0, 'C': 0, 'G': 0, 'T': 0}
content['A'] += expect[:].seq.count('A')
content['C'] += expect[:].seq.count('C')
content['G'] += expect[:].seq.count('G')
content['T'] += expect[:].seq.count('T')
expect_gc = (content['G']+content['C'])/sum(content.values())*100
self.assertEqual(result.composition, content)
self.assertEqual(round(result.gc_content, 3), round(expect_gc, 3))
#test gc skew
expect_skew = (content['G']-content['C'])/(content['G']+content['C'])
self.assertEqual(round(result.gc_skew, 3), round(expect_skew, 3))
def test_seq_iter(self):
idx = self.get_random_index()
fai_seq = self.faidx[idx]
fxi_seq = self.fastx[idx]
fas_seq = self.fasta[idx]
# test read seq line by line
flatsq = [line for line in fas_seq]
expect = [str(line) for line in fai_seq]
result = [line for line in fxi_seq]
self.assertEqual(expect, result)
self.assertEqual(expect, flatsq)
# test seq long name
self.assertEqual(fai_seq.long_name.strip(), fxi_seq.description)
# test seq str
self.assertEqual(str(fai_seq), str(fxi_seq))
# test seq contains
s, e = sorted(random.sample(range(1, len(fai_seq)), 2))
segment = str(fai_seq)[s-1:e]
self.assertTrue(segment in fxi_seq)
# test seq search
expect = str(fai_seq).index(segment) + 1
result = fxi_seq.search(segment)
self.assertEqual(expect, result)
def test_seq_repr(self):
s = self.fastx[0]
n = s.name
self.assertEqual(repr(s), "<Sequence> {} with length of {}".format(s.name, len(s)))
s = self.fastx[0][0:11]
self.assertEqual(repr(s), "<Sequence> {} from {} to {}".format(n, s.start, s.end))
#test name
self.assertEqual(s.name, "{}:{}-{}".format(n, s.start, s.end))
def test_full_compo(self):
idx = self.get_random_index()
fas = pyfastx.Fasta(flat_fasta, full_index=True)
self.assertEqual(self.fastx[idx].composition, fas[idx].composition)
def test_seq_exception(self):
with self.assertRaises(RuntimeError):
for line in self.fastx[0][10:20]:
print(line)
if __name__ == '__main__':
unittest.main()
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