I/O interface for file reading, writing and conversions
convert
(fname_in, format_in, fname_out, format_out, kwargs_in=None, kwargs_out=None)[source]¶Convert a file in format x to file in format y
Parameters: |
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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')
Note
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'))
read
(fname, format, f_id=’conkit’, **kwargs)[source]¶Parse a file handle to read into structure
Parameters: | |
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Returns: | The hierarchy instance of the requested file |
Return type: |
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, **kwargs)[source]¶Parse a file handle to read into structure
Parameters: |
|
---|
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)