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Source code for galaxy.datatypes.annotation

import logging
import tarfile

from galaxy.datatypes.binary import CompressedArchive
from galaxy.datatypes.data import (
    get_file_peek,
    Text,
)
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.sniff import (
    build_sniff_from_prefix,
    FilePrefix,
)
from galaxy.util import nice_size

log = logging.getLogger(__name__)


[docs]@build_sniff_from_prefix class SnapHmm(Text): file_ext = "snaphmm" edam_data = "data_1364"
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None: if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "SNAP HMM model" else: dataset.peek = "file does not exist" dataset.blurb = "file purged from disc"
[docs] def display_peek(self, dataset: DatasetProtocol) -> str: try: return dataset.peek except Exception: return f"SNAP HMM model ({nice_size(dataset.get_size())})"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool: """ SNAP model files start with zoeHMM """ return file_prefix.startswith("zoeHMM")
[docs]class Augustus(CompressedArchive): """ Class describing an Augustus prediction model """ file_ext = "augustus" edam_data = "data_0950" compressed = True
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None: if not dataset.dataset.purged: dataset.peek = "Augustus model" dataset.blurb = nice_size(dataset.get_size()) else: dataset.peek = "file does not exist" dataset.blurb = "file purged from disk"
[docs] def display_peek(self, dataset: DatasetProtocol) -> str: try: return dataset.peek except Exception: return f"Augustus model ({nice_size(dataset.get_size())})"
[docs] def sniff(self, filename: str) -> bool: """ Augustus archives always contain the same files """ if filename and tarfile.is_tarfile(filename): with tarfile.open(filename, "r") as temptar: for f in temptar: if not f.isfile(): continue if ( f.name.endswith("_exon_probs.pbl") or f.name.endswith("_igenic_probs.pbl") or f.name.endswith("_intron_probs.pbl") or f.name.endswith("_metapars.cfg") or f.name.endswith("_metapars.utr.cfg") or f.name.endswith("_parameters.cfg") or f.name.endswith("_parameters.cgp.cfg") or f.name.endswith("_utr_probs.pbl") or f.name.endswith("_weightmatrix.txt") ): return True else: return False return False