def select_size(self,size = None):
""" Select which reagent type """
# local namespace
all_sizes = self.settings['all_sizes']
default_size = self.settings['default_size']
# determine whether default size is used
if size == None:
print 'Using default enzyme size ({})...'.format(default_size)
size = default_size
# reassign based on product selection
assert size in all_sizes, "selected size not found in enzyme info!"
# find location of info
index = all_sizes.index(size)
# pull values
self.settings['size'] = size
self.settings['concentration'] = self.settings['all_concentrations'][index]
self.settings['units_per_ml'] = self.settings['all_units_per_ml'][index]
self.settings['cost'] = self.settings['all_costs'][index]
# update object attributes
obj_update(self)
def __init__(self, *args, **kwargs):
""" Restriction enzyme input """
self.database_folder = './database/sequences/'
# digestion settings
self.settings = {
'name': None,
'author': None,
'description': None,
'sequence': None,
'codon_set': None,
'elements': None,
'concentration': None,
'form': None,
'tags': None,
'origin': None, # what experiments produced fragment
'source': None, # what website, author, etc
'url': None, # background information
'break_5': None, # 5' backbone breaks
'break_3': None # 3' backbone breaks
}
# update settings
for arg in args:
self.settings.update(arg)
self.settings.update(kwargs)
# update object attributes with internal settings
obj_update(self)
def __init__(self,*args,**kwargs):
""" Restriction enzyme input """
default_name = 'XhoI'
database_fname = './database/restriction_enzymes.xlsx'
# digestion settings
self.settings = {
'name':None,
'sequence':None,
'source':None,
'size':None,
'site_type':None,
'site_location':None,
'default_size':None,
# current product info
'concentration':None,
'units_per_ml':None,
'cost':None,
# available product info
'all_sizes':None,
'all_concentrations':None,
'all_units_per_ml':None,
'all_costs':None,
'active_temperature':None,
'inactive_temperature':None,
'inactive_time':None,
'url':None
}
# update settings
for arg in args: self.settings.update(arg)
self.settings.update(kwargs)
# TODO: consider taking out
# set enzyme to default if no name is passed
if self.settings['name'] == None:
print 'No enzyme specified, using {}...'.format(default_name)
self.settings['name'] = default_name
# database request, update settings
database = request_xlsx(self.settings['name'],database_fname)
dict_update(self.settings,database) # dicts are mutably updated
# update object attributes
obj_update(self)
def load(self, name=None):
# set sequence to default if no name is passed
if self.settings['name'] == None and name == None:
print 'No sequence name specified, exiting...'
return None
elif name == None:
print 'Using {} as sequence name...'.format(self.settings['name'])
name = self.settings['name']
# build fname to call
fname = self.database_folder + name + '.txt'
# sequence file, update settings
database = _load_sequence_file(fname)
dict_update(self.settings, database) # dicts are mutably updated
obj_update(self)
def __init__(self,*args,**kwargs):
""" Digest input """
# digestion settings
settings = {
'sequence':None,
'enzyme':None
}
# update settings
for arg in args: settings.update(arg)
settings.update(kwargs)
# use defaults if input and enzymes not selected
if settings['sequence'] == None:
settings['sequence'] = 'XhoI-Plasmid'
if settings['enzyme'] == None:
settings['enzyme'] = 'XhoI'
# check database for sequences
if isinstance(settings['sequence'],str):
sequence = Sequence(name=settings['sequence'])
sequence.load()
elif isinstance(settings['sequence'],object):
sequence = settings['sequence']
else:
raise TypeError('Unknpwn sequence type passed to function <{}>!'.format(
type(settings['sequence'])))
# check database for enzyme
# TODO: add compatibility for multiple enzyme reaction
if isinstance(settings['enzyme'],str):
enzyme = RestrictionEnzyme(name=settings['enzyme'])
elif isinstance(settings['enzyme'],object):
enzyme = settings['enzyme']
else:
raise TypeError('Unknpwn enzyme type passed to function <{}>!'.format(
type(settings['enzyme'])))
enzyme.select_size()
enzyme_name = enzyme.name
enzyme_volume = (1./enzyme.units_per_ml,'mL')
enzyme_temp = (enzyme.active_temperature,'C')
# TODO: break sequence at site
# reagent listing
mix_settings = {
'reagents':
{
enzyme_name:enzyme_volume,
'NEBuffer':(10,'X'),
},
'filler':'dH2O',
'total':(50,'uL'),
'temperature':(-4,'C')
}
incubate_settings = {
'preparation':'Gently mix by flicking.',
'temperature':enzyme_temp,
'time':(1,'hour'),
'movement':'stationary'
}
# sinc
self.protocols = [Mix(mix_settings),
Incubate(incubate_settings)]
# Output cut sequence object (breaks in backbone)
cut_sequence = deepcopy(sequence) # copies the sequence
breaks = _cut(cut_sequence,enzyme) # add backbone breaks
obj_update(cut_sequence,breaks) # add breaks to sequence
cut_sequence.add_origin('digest with {}'.format(enzyme.name)) # add origin
self.output = cut_sequence