Source code for conkit.io.JonesIO
"""
Parser module specific to the "Jones" sequence file format
"""
__author__ = "Felix Simkovic"
__date__ = "13 Sep 2016"
__version__ = 0.1
from conkit.core import Sequence
from conkit.core import SequenceFile
from conkit.io._ParserIO import _SequenceFileParser
import os
import re
SEQ_RECORD = re.compile(r'^([A-Z0-9~-]+)$')
[docs]class JonesIO(_SequenceFileParser):
"""Parser class for Jones sequence files
Description
-----------
This format is a "new" definition of sequence-only records.
It assumes that there are no comments, headers or any other
data in the file.
The only information present are sequences, whereby one sequence
is represented in a single line!
"""
def __init__(self):
super(JonesIO, self).__init__()
[docs] def read(self, f_handle, f_id='jones'):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
Returns
-------
:obj:`conkit.core.SequenceFile`
"""
# Create a new sequence file instance
hierarchy = SequenceFile(f_id)
for i, line in enumerate(f_handle):
if not line:
continue
if not SEQ_RECORD.match(line):
raise ValueError('Unknown entry in line {0}: {1}'.format(i+1, line))
sequence = SEQ_RECORD.match(line).group(1)
sequence_entry = Sequence('seq_{i}'.format(i=i), sequence)
hierarchy.add(sequence_entry)
return hierarchy
[docs] def write(self, f_handle, hierarchy):
"""Write a sequence file instance to to file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`conkit.core.SequenceFile` or :obj:`conkit.core.Sequence`
"""
# Double check the type of hierarchy and reconstruct if necessary
sequence_file = self._reconstruct(hierarchy)
for sequence_entry in sequence_file:
f_handle.write(sequence_entry.seq + os.linesep)
return