def test_compute_n50_from_file(self):
"""
Test getting N50 from file
"""
with self.assertRaises(IOError):
get_fasta_readlengths('what.ever')
fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz')
self.assertEqual( 33586, compute_n50_from_file(fasta) )
def test_compute_n50_from_file(self):
"""
Test getting N50 from file
"""
with self.assertRaises(IOError):
get_fasta_readlengths('what.ever')
fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly',
'polished_assembly.fasta.gz')
self.assertEqual(33586, compute_n50_from_file(fasta))
def test_get_fasta_readlengths(self):
"""
Test getting num reads and total readlength
"""
with self.assertRaises(IOError):
get_fasta_readlengths('what.ever')
fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz')
l = get_fasta_readlengths(fasta)
self.assertEqual( 2, len(l) )
self.assertEqual( 47938, sum(l) )
def test_get_fasta_readlengths(self):
"""
Test getting num reads and total readlength
"""
with self.assertRaises(IOError):
get_fasta_readlengths('what.ever')
fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly',
'polished_assembly.fasta.gz')
l = get_fasta_readlengths(fasta)
self.assertEqual(2, len(l))
self.assertEqual(47938, sum(l))
def test_compute_n50_from_readlenths(self):
"""
Test getting N50 from length list
"""
fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz')
l = get_fasta_readlengths(fasta)
self.assertEqual( 33586, compute_n50(l) )
def test_compute_n50_from_readlenths(self):
"""
Test getting N50 from length list
"""
fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly',
'polished_assembly.fasta.gz')
l = get_fasta_readlengths(fasta)
self.assertEqual(33586, compute_n50(l))
def from_file(file_name):
# nreads, total = _compute_values(file_name)
read_lens = get_fasta_readlengths(file_name)
nreads = len(read_lens)
total = sum(read_lens)
return FastaContainer(nreads, total, file_name)