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)