Source code for conkit.io.clustal

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"""
Parser module specific to CLUSTAL sequence files
"""

__author__ = "Felix Simkovic"
__date__ = "30 Jul 2018"
__version__ = "0.1"

import collections

from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile


[docs]class ClustalParser(SequenceFileParser):
    """Parser class for CLUSTAL sequence files
    """

    def __init__(self):
        super(ClustalParser, self).__init__()

[docs]    def read(self, f_handle, f_id="fasta"):
        """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.SequenceFile`

        Raises
        ------
        :exc:`TypeError`
           Incorrect file format

        """
        header = f_handle.readline().rstrip()
        if header[:7].upper() != "CLUSTAL":
            raise TypeError("Incorrect file format")
        cache = collections.OrderedDict()
        for line in f_handle:
            line = line.strip()
            line_set = set(line)
            if not line or any(char in line_set for char in ["*", ":", "."]):
                continue
            else:
                parts = line.strip().split()
                id_, chunk = parts[:2]
                if id_ in cache:
                    cache[id_] += chunk
                else:
                    cache[id_] = chunk

        hierarchy = SequenceFile(f_id)
        while len(cache) > 0:
            id_, seq = cache.popitem(last=False)  # FIFO
            sequence = Sequence(id_, seq)
            hierarchy.add(sequence)

        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.SequenceFile`, :obj:`~conkit.core.sequence.Sequence`

        """
        hierarchy = self._reconstruct(hierarchy)
        chunker = []
        longest = 0
        for sequence in hierarchy:
            this = [sequence.id]
            if len(sequence.id) > longest:
                longest = len(sequence.id)
            for i in range(0, sequence.seq_len, 60):
                this += [sequence.seq[i : i + 60]]
            chunker += [this]
        content = "CLUSTAL FORMAT written with ConKit\n\n"
        linetemplate = "%-{}s\t%s\n".format(longest)
        while len(chunker) > 0:
            entry = chunker.pop(0)
            content += linetemplate % (entry[0], entry[1])
            entry.pop(1)
            if len(entry) > 1:
                chunker.append(entry)
        f_handle.write(content)