Source code for conkit.io.a2m

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"""
Parser module specific to HH-suite A2M sequence files

"""

__author__ = "Felix Simkovic"
__date__ = "30 Jul 2018"
__version__ = "1.0"

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


[docs]class A2mParser(SequenceFileParser):
    """Parser class for A2M sequence files

    """

    def __init__(self):
        super(A2mParser, self).__init__()

[docs]    def read(self, f_handle, f_id="a2m"):
        """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`

        """
        hierarchy = SequenceFile(f_id)
        for i, line in enumerate(f_handle):
            line = line.strip()
            if line:
                for j, char in enumerate(line):
                    if char.isalpha() or char == "-":
                        continue
                    indicator = ["-"] * len(line)
                    indicator[j] = "^"
                    msg = "Unknown character in line {0}:{1}{1}{2}{1}{3}"
                    msg = msg.format(i + 1, "\n", line, "".join(indicator))
                    raise ValueError(msg)
                sequence = Sequence("seq_{}".format(i), line)
                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` or :obj:`~conkit.core.sequence.Sequence`

        """
        sequence_file = self._reconstruct(hierarchy)
        content = ""
        for sequence_entry in sequence_file:
            content += sequence_entry.seq + "\n"
        f_handle.write(content)