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import os
import pyfaidx
import pyfastx
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')
gzip_fastq = join(data_dir, 'test.fq.gz')
flat_fasta = join(data_dir, 'test.fa')
flat_fastq = join(data_dir, 'test.fq')
class FastxTest(unittest.TestCase):
def setUp(self):
self.faidx = pyfaidx.Fasta(flat_fasta)
def tearDown(self):
del self.faidx
if os.path.exists('{}.fai'.format(flat_fasta)):
os.remove('{}.fai'.format(flat_fasta))
def test_fasta_iter(self):
for name, seq, comment in pyfastx.Fastx(gzip_fasta, comment=True):
s = self.faidx[name]
self.assertEqual(str(seq), seq)
self.assertEqual(' '.join(s.long_name.split()[1:]), comment)
def test_fasta_upper(self):
for name, seq in pyfastx.Fastx(flat_fasta, uppercase=True):
self.assertEqual(str(self.faidx[name]), seq)
def test_fastq_iter(self):
reads = {}
with open(flat_fastq) as fh:
for line in fh:
line = line.strip()
if line[0] == '@':
name = line.split()[0][1:]
comment = ' '.join(line.split()[1:])
reads[name] = [comment]
elif line == '+':
continue
else:
reads[name].append(line)
for name, seq, qual, comment in pyfastx.Fastx(gzip_fastq, "fastq", comment=True):
r = reads[name]
self.assertEqual(r[0], comment)
self.assertEqual(r[1], seq)
self.assertEqual(r[2], qual)
def test_fastx_repr(self):
fa = pyfastx.Fastx(gzip_fasta, "fasta")
self.assertEqual(repr(fa), "<Fastx> fasta {}".format(gzip_fasta))
fq = pyfastx.Fastx(gzip_fastq, "fastq")
self.assertEqual(repr(fq), "<Fastx> fastq {}".format(gzip_fastq))
def test_exception(self):
with self.assertRaises(FileExistsError):
_ = pyfastx.Fastx('test_file')
with self.assertRaises(RuntimeError):
_ = pyfastx.Fastx(gzip_fasta, format="fastx")
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