def no_cutters(self, batch=CommOnly):
"""Returns the enzymes in a RestrictionBatch that do **not**
cut the sequence."""
ana = batch.search(self)
ncut = {
enz: sitelist
for (enz, sitelist) in ana.items() if not sitelist
}
return _RestrictionBatch(ncut)
def n_cutters(self, n=3, batch=CommOnly):
"""Returns the enzymes in a RestrictionBatch that cut the sequence
n times."""
ana = batch.search(self)
ncut = {
enz: sitelist
for (enz, sitelist) in ana.items() if len(sitelist) == n
}
return _RestrictionBatch(ncut)
from Bio.Restriction import AllEnzymes as _AllEnzymes
from Bio.Restriction import RestrictionBatch as _RestrictionBatch
import logging as _logging
import traceback as _traceback
_module_logger = _logging.getLogger("pydna."+__name__)
_text=""
try:
with open( _os.environ["pydna_enzymes"], encoding="utf-8") as _f:
_text = _f.read()
except FileNotFoundError:
_module_logger.warning("%s not found.", _os.environ["pydna_enzymes"])
except IsADirectoryError:
_module_logger.warning("%s is a directory.", _os.environ["pydna_enzymes"])
except IOError:
_module_logger.warning("%s found, but could not be read.", _os.environ["pydna_enzymes"])
except Exception as e:
_module_logger.warning(_traceback.format_exc())
myenzymes = _RestrictionBatch([e for e in _AllEnzymes if str(e).lower() in _text.lower()])
if __name__=="__main__":
cache = _os.getenv("pydna_cache")
_os.environ["pydna_cache"]="nocache"
import doctest
doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
_os.environ["pydna_cache"]=cache
