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)