I/O interface for file reading, writing and conversions
convert
(fname_in, format_in, fname_out, format_out)[source]¶Convert a file in format x to file in format y
Parameters: | fname_in : filehandle, filename format_in : str
fname_out : filehandle, filename format_out : str
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Notes
A3M format comes by default WITHOUT insert states, these are removed. To obtain
an alignment WITH insert states, use format a3m-inserts
.
>>> from conkit import io
>>> with open('example.out', 'r') as f_in, open('example.rr', 'w') as f_out:
... io.convert(f_in, 'pconsc3', f_out, 'casprr'))
Examples
>>> from conkit import io
>>> with open('example.a3m', 'r') as f_in, open('example.fas', 'w') as f_out:
... io.convert(f_in, 'a3m', f_out, 'fasta')
read
(f_in, format, f_id='conkit')[source]¶Parse a file handle to read into structure
Parameters: | f_in
format : str
f_id : str
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Returns: | hierarchy
|
Examples
>>> from conkit import io
>>> with open('example.a3m', 'r') as f_in:
... hierarchy = io.read(f_in, 'a3m')
>>> from conkit import io
>>> with open('example.mat', 'r') as f_in:
... hierarchy = io.read(f_in, 'ccmpred')
write
(fname, format, hierarchy)[source]¶Parse a file handle to read into structure
Parameters: | fname : filehandle, filename format : str
hierarchy
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Examples
>>> 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)
>>> 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)