def test_remark_3(self):
sequence_file = SequenceFile("test")
sequence_file.remark = "Hello"
sequence_file.remark = "5"
sequence_file.remark = "World"
sequence_file.remark = "!"
self.assertEqual(["Hello", "5", "World", "!"], sequence_file.remark)
def test_remark_3(self):
sequence_file = SequenceFile('test')
sequence_file.remark = 'Hello'
sequence_file.remark = '5'
sequence_file.remark = 'World'
sequence_file.remark = '!'
self.assertEqual(['Hello', '5', 'World', '!'], sequence_file.remark)
def read(self, f_handle, f_id='a3m', remove_inserts=True):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
remove_inserts : bool, optional
Remove insert states [default: True]
Returns
-------
:obj:`~conkit.core.sequencefile.SequenceFile`
"""
sequence_file = SequenceFile(f_id)
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
sequence_file.remark = line[1:]
elif line.startswith('>'):
break
while True:
if not line.startswith('>'):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:]
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith('>'):
break
chunks.append(line)
line = f_handle.readline().rstrip()
seq_string = "".join(chunks)
if remove_inserts:
seq_string = self._remove_inserts(seq_string)
sequence_entry = Sequence(id, seq_string)
try:
sequence_file.add(sequence_entry)
except ValueError:
while True:
new_id = sequence_entry.id + "_{0}".format(
np.random.randint(0, 100000))
if new_id in sequence_file:
continue
else:
break
sequence_entry.id = new_id
sequence_file.add(sequence_entry)
if not line:
break
if not remove_inserts:
self._adjust_insert(sequence_file)
return sequence_file
def test_remark_5(self):
sequence_file = SequenceFile('test')
sequence_file.remark = 'hello'
sequence = Sequence('foo', 'GSMFTPK')
sequence.remark = 'bar'
sequence_file.add(sequence)
self.assertEqual(['hello'], sequence_file.remark)
self.assertEqual(['bar'], sequence_file[0].remark)
def test_remark_5(self):
sequence_file = SequenceFile("test")
sequence_file.remark = "hello"
sequence = Sequence("foo", "GSMFTPK")
sequence.remark = "bar"
sequence_file.add(sequence)
self.assertEqual(["hello"], sequence_file.remark)
self.assertEqual(["bar"], sequence_file[0].remark)
def read(self, f_handle, f_id='fasta'):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
Returns
-------
:obj:`SequenceFile <conkit.core.sequencefile.SequenceFile>`
"""
# Create a new sequence file instance
hierarchy = SequenceFile(f_id)
# Read any possible comments and store in file remarks
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
hierarchy.remark = line[1:]
elif line.startswith('>'):
break
# Read the sequence record(s) and store them
while True:
if not line.startswith('>'):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:] # Header without '>'
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith('>'):
break
chunks.append(line)
line = f_handle.readline().rstrip()
_seq_string = "".join(chunks) # Sequence from chunks
# Create the sequence record instance
sequence_entry = Sequence(id, _seq_string)
# Store the sequence in the file
hierarchy.add(sequence_entry)
if not line:
break
return hierarchy
def read(self, f_handle, f_id="fasta"):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
Returns
-------
:obj:`~conkit.core.sequencefile.SequenceFile`
Raises
------
:exc:`ValueError`
FASTA record needs to start with >
"""
hierarchy = SequenceFile(f_id)
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith("#"):
hierarchy.remark = line[1:]
elif line.startswith(">"):
break
while True:
if not line.startswith(">"):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:] # Header without '>'
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith(">"):
break
chunks.append(line)
line = f_handle.readline().rstrip()
_seq_string = "".join(chunks) # Sequence from chunks
sequence_entry = Sequence(id, _seq_string)
hierarchy.add(sequence_entry)
if not line:
break
return hierarchy
def test_remark_1(self):
sequence_file = SequenceFile('test')
sequence_file.remark = 'Hello'
self.assertEqual(['Hello'], sequence_file.remark)
def test_remark_1(self):
sequence_file = SequenceFile("test")
sequence_file.remark = "Hello"
self.assertEqual(["Hello"], sequence_file.remark)
def read(self, f_handle, f_id='a3m', remove_insert=True):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
remove_insert : bool, optional
Remove insert states [default: True]
Returns
-------
:obj:`SequenceFile <conkit.core.sequencefile.SequenceFile>`
"""
# Create a new sequence file instance
sequence_file = SequenceFile(f_id)
# Read any possible comments and store in file remarks
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
sequence_file.remark = line[1:]
elif line.startswith('>'):
break
# Read the sequence record(s) and store them
while True:
if not line.startswith('>'):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:] # Header without '>'
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith('>'):
break
chunks.append(line)
line = f_handle.readline().rstrip()
seq_string = "".join(chunks) # Sequence from chunks
# Remove insert states
if remove_insert:
seq_string = self._remove_insert(seq_string)
# Create the sequence record instance
sequence_entry = Sequence(id, seq_string)
# Store the sequence in the file
try:
sequence_file.add(sequence_entry)
except ValueError:
while True:
new_id = sequence_entry.id + "_{0}".format(
np.random.randint(0, 100000))
if new_id in sequence_file:
continue
else:
break
sequence_entry.id = new_id
sequence_file.add(sequence_entry)
if not line:
break
# Match the insert states of the sequence
if not remove_insert:
self._adjust_insert(sequence_file)
return sequence_file