comparison mira.py @ 58:293ae67375e3 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 0f1bb5279a25edaf91444752f13e07c7c283a115

58:293ae67375e3

"""MiraAssemblyFormat class for the 'mira' format within Galaxy."""

from galaxy.datatypes.data import Text


class MiraAssemblyFormat(Text):
    """MIRA Assembly Format  data."""

    file_ext = "mira"

    def sniff(self, filename):
        """Determine if the file is a MIRA Assembly Format file.

        Note currently this only detects MIRA Assembly Format v2.0,
        as used in MIRA v3.9 and v4.0.

        It does not detect MIRA Assembly Format v1 as used in both
        MIRA v3.2 and v3.4.
        """
        h = open(filename)
        line = h.readline()
        if line.rstrip() != "@Version\t2\t0":
            h.close()
            return False
        line = h.readline()
        if line.rstrip() != "@Program\tMIRALIB":
            h.close()
            return False
        return True

    def merge(split_files, output_file):
        """Merge MIRA assembly files (not implemented).

        Merging multiple MIRA files is non-trivial and may not be possible...
        """
        if len(split_files) == 1:
            # For one file only, use base class method (move/copy)
            return Text.merge(split_files, output_file)
        if not split_files:
            raise ValueError("Given no MIRA, %r, to merge into %s"
                             % (split_files, output_file))
        raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
    merge = staticmethod(merge)

    def split(cls, input_datasets, subdir_generator_function, split_params):
        """Split a MIRA Assembly File (not implemented for now)."""
        if split_params is None:
            return None
        raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
    merge = staticmethod(merge)