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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.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): 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): try: return dataset.peek except Exception: return f"SNAP HMM model ({nice_size(dataset.get_size())})"
[docs] def sniff_prefix(self, file_prefix: FilePrefix): """ 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): 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): try: return dataset.peek except Exception: return f"Augustus model ({nice_size(dataset.get_size())})"
[docs] def sniff(self, filename): """ 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