In order to convert files in ConKit, we need to use the ConKit I/O framework.
Note
ConKit I/O framework consists of three main functions that handle the relevant parsers: read(), write() and convert(). The latter effectively uses the former two but handles everything in one step.
1. Files can be read in ConKit’s internal hierarchies using simple Python code.
>>> import conkit.io
>>> msa = conkit.io.read('toxd/toxd.a3m', 'a3m')
2. Sequence hierarchies can also be written in a similarly easy format. Using the ``msa`` hierarchy we have created above:
>>> import conkit.io
>>> conkit.io.write('toxd/toxd.mfa', 'fasta', msa)
3. To convert file formats in single call, you can use the :func:`~conkit.io.convert` function.
>>> import conkit.io
>>> conkit.io.convert('toxd/toxd.a3m', 'a3m', 'toxd/toxd.mfa', 'fasta')
You can convert these files to many different other formats, for a full list check out the Table of available file formats.