def test_open_f_handle_4(self):
fname = self.tempfile()
with _iotools.open_f_handle(fname, "w") as fhandle:
self.assertEqual("w", fhandle.mode)
fhandle.write("hello world!")
with _iotools.open_f_handle(fname, "r") as fhandle:
self.assertEqual("r", fhandle.mode)
self.assertEqual("hello world!", fhandle.read().strip())
def test_open_f_handle_3(self):
fname = self.tempfile()
with _iotools.open_f_handle(fname, "w") as fhandle:
self.assertEqual("w", fhandle.mode)
f_in_handle = _iotools.open_f_handle(fname, "w")
with _iotools.open_f_handle(f_in_handle, "w") as fhandle:
self.assertEqual("w", fhandle.mode)
f_in_handle.close()
def test_open_f_handle_4(self):
fname = _iotools.create_tmp_f()
with _iotools.open_f_handle(fname, 'write') as fhandle:
self.assertEqual('w', fhandle.mode)
fhandle.write("hello world!")
with _iotools.open_f_handle(fname, 'read') as fhandle:
self.assertEqual('r', fhandle.mode)
self.assertEqual("hello world!", fhandle.read().strip())
os.unlink(fname)
def test_open_f_handle_3(self):
fname = _iotools.create_tmp_f()
with _iotools.open_f_handle(fname, 'write') as fhandle:
self.assertEqual('w', fhandle.mode)
f_in_handle = _iotools.open_f_handle(fname, 'write')
with _iotools.open_f_handle(f_in_handle, 'write') as fhandle:
self.assertEqual('w', fhandle.mode)
f_in_handle.close()
os.unlink(fname)
def read(fname, format, f_id="conkit", **kwargs):
"""Parse a file handle to read into structure
Parameters
----------
fname : filehandle, filename
A file path or open file handle
format : str
File format of handle
f_id : str
Identifier for the returned file
Returns
-------
hierarchy
The hierarchy instance of the requested file
Examples
--------
1) Read a Multiple Sequence Alignment file into a ConKit hierarchy:
>>> from conkit import io
>>> with open('example.a3m', 'r') as f_in:
... hierarchy = io.read(f_in, 'a3m')
2) Read a contact prediction file into a conkit hierarchy:
>>> from conkit import io
>>> with open('example.mat', 'r') as f_in:
... hierarchy = io.read(f_in, 'ccmpred')
"""
if format in PARSER_CACHE:
parser_in = PARSER_CACHE.import_class(format)()
else:
raise ValueError("Unrecognised format: {}".format(format))
kwargs.update({"f_id": f_id})
if format == "a3m-inserts":
kwargs["remove_inserts"] = False
if format in BINARY_FILE_FORMATS:
mode = "rb"
else:
mode = "r"
with open_f_handle(fname, mode) as f_in:
hierarchy = parser_in.read(f_in, **kwargs)
return hierarchy
def write(fname, format, hierarchy, **kwargs):
"""Parse a file handle to read into structure
Parameters
----------
fname : filehandle, filename
A file path or open file handle
format : str
File format of handle
hierarchy
ConKit hierarchy to write
Examples
--------
1) Write a ConKit hierarchy into a Multiple Sequence Alignment file:
>>> from conkit import io
>>> with open('example.fas', 'r') as f_in, open('example.a3m', 'w') as f_out:
... hierarchy = io.read(f_in, 'fasta')
... io.write(f_out, 'a3m', hierarchy)
2) Write a ConKit hierarchy into a contact prediction file:
>>> from conkit import io
>>> with open('example.txt', 'r') as f_in, open('example.rr', 'w') as f_out:
... hierarchy = io.read(f_in, 'psicov')
... io.write(f_out, 'casprr', hierarchy)
"""
if format in PARSER_CACHE:
parser_out = PARSER_CACHE.import_class(format)()
else:
raise ValueError("Unrecognised format: {}".format(format))
if format in ["flib", "pconsc", "pconsc2", "saint2"]:
kwargs["write_header_footer"] = False
with open_f_handle(fname, "w") as f_out:
parser_out.write(f_out, hierarchy, **kwargs)
def test_open_f_handle_6(self):
fname = _iotools.create_tmp_f()
with self.assertRaises(ValueError):
_iotools.open_f_handle(fname, 'foo')
with self.assertRaises(ValueError):
_iotools.open_f_handle(fname, 'bar')
def test_open_f_handle_5(self):
with self.assertRaises(TypeError):
_iotools.open_f_handle(1, 'read')
with self.assertRaises(TypeError):
_iotools.open_f_handle(1.0, 'write')
def test_open_f_handle_6(self):
fname = self.tempfile()
with self.assertRaises(ValueError):
_iotools.open_f_handle(fname, "foo")
with self.assertRaises(ValueError):
_iotools.open_f_handle(fname, "bar")
def test_open_f_handle_5(self):
with self.assertRaises(TypeError):
_iotools.open_f_handle(1, "r")
with self.assertRaises(TypeError):
_iotools.open_f_handle(1.0, "w")