Source code for conkit.io.jones
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"""
Parser module specific to the "Jones" sequence file format
"""
__author__ = "Felix Simkovic"
__date__ = "13 Sep 2016"
__version__ = "0.1"
import os
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
[docs]class JonesParser(SequenceFileParser):
"""Parser class for Jones sequence files
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(JonesParser, 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:`SequenceFile <conkit.core.SequenceFile>`
"""
# Create a new sequence file instance
hierarchy = SequenceFile(f_id)
for i, line in enumerate(f_handle):
line = line.rstrip()
if not line:
continue
for a, c in enumerate(line):
if c.isalpha() or c == '-':
continue
else:
indicator = ['-'] * len(line)
indicator[a] = '^'
msg = "Unknown character in line {0}:{1}{1}{2}{1}{3}"
msg = msg.format(i+1, os.linesep, line, ''.join(indicator))
raise ValueError(msg)
sequence = line
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:`SequenceFile <conkit.core.SequenceFile>` or :obj:`Sequence <conkit.core.Sequence>`
"""
# Double check the type of hierarchy and reconstruct if necessary
sequence_file = self._reconstruct(hierarchy)
content = ""
for sequence_entry in sequence_file:
content += sequence_entry.seq + os.linesep
f_handle.write(content)