def dnaseq_read(self,newprotein=None,fileinput=None,variable='DNAseq',var2='dnaseqfile'):
"""Read in DNA Sequences and display them above the main sequence"""
self.data['newprotein']=newprotein
# If a file is provided use that, otherwise open the dialog
if fileinput == None:
dnaseqfile = self.open_file()
else:
dnaseqfile = fileinput
self.data[var2]=dnaseqfile
# Load the DNA sequence data
# - only simple file format supported at the moment
if self.data[var2]:
S=DNA_sequence.sequence()
seqfile=self.data[var2]
DNAseq=S.read_DNA_sequence(seqfile)
# Check the DNA sequence
ok,DNAseq=mutation.check_DNA(DNAseq)
if not ok:
# Give a warning
import tkMessageBox
tkMessageBox.showwarning("DNA sequence",
'DNA sequence contains invalid characters: %s' %DNAseq
,parent=self.master)
return
self.data[variable]=DNAseq
self.update_sequence_window()
# Activate/Deactivate buttons
self.projectChanged()
return dnaseqfile
def main():
#
# Parse the arguments
#
import sys, string
defaults = get_defaults()
#
args = string.join(sys.argv[1:])
args = string.split(args, '-')
for arg in args:
split = string.split(string.strip(arg))
if split == []:
continue
parm_name = split[0]
if not defaults.has_key(parm_name):
raise 'Unknown parameter: ', parm_name
#
# Deal with T/F
#
if len(split) == 1:
if defaults[parm_name][1] == 'T/F':
if defaults[parm_name][0]:
defaults[parm_name][0] = None
else:
defaults[parm_name][0] = 1
#
# Deal with all the other cases
#
elif len(split) == 2:
if defaults[parm_name][1] == 'number':
defaults[parm_name][0] = string.atof(split[1])
else:
defaults[parm_name][0] = split[1]
else:
raise 'Incorrect usage'
#
# Reformat
#
params = {}
for key in defaults.keys():
params[key] = defaults[key][0]
#
# Load the file and design the primer
#
if not params['seq']:
usage()
seq_file = params['seq']
new_AA = params['mutation'][-1]
AA_number = int(params['mutation'][1:-1])
S = DNA_sequence.sequence()
DNA_seq = S.readpir(seq_file)
Tm_desired = params['Tm']
find_restriction_site = 1
if params['no_restriction_site']:
find_restriction_site = None
#
# Do it!
#
import Protool
X = Protool.structureIO()
new_AA = X.threetoone[new_AA]
#
# Call the function for designing primers
#
new_enzymes, primers_results_dict, enzymes_that_already_cut, primer_starting_position, comb_on_Tm = exhaustive_research(
DNA_seq,
AA_number,
new_AA,
Tm_desired,
find_restriction_site,
enzyme_list=None)
megaprimer_dict = megaprimer(DNA_seq, Tm_desired=65)
return
def main():
#
# Parse the arguments
#
import sys,string
defaults=get_defaults()
#
args=string.join(sys.argv[1:])
args=string.split(args,'-')
for arg in args:
split=string.split(string.strip(arg))
if split==[]:
continue
parm_name=split[0]
if not defaults.has_key(parm_name):
raise 'Unknown parameter: ',parm_name
#
# Deal with T/F
#
if len(split)==1:
if defaults[parm_name][1]=='T/F':
if defaults[parm_name][0]:
defaults[parm_name][0]=None
else:
defaults[parm_name][0]=1
#
# Deal with all the other cases
#
elif len(split)==2:
if defaults[parm_name][1]=='number':
defaults[parm_name][0]=string.atof(split[1])
else:
defaults[parm_name][0]=split[1]
else:
raise 'Incorrect usage'
#
# Reformat
#
params={}
for key in defaults.keys():
params[key]=defaults[key][0]
#
# Load the file and design the primer
#
if not params['seq']:
usage()
seq_file=params['seq']
new_AA=params['mutation'][-1]
AA_number=int(params['mutation'][1:-1])
S=DNA_sequence.sequence()
DNA_seq=S.readpir(seq_file)
Tm_desired=params['Tm']
find_restriction_site=1
if params['no_restriction_site']:
find_restriction_site=None
#
# Do it!
#
import Protool
X=Protool.structureIO()
new_AA=X.threetoone[new_AA]
#
# Call the function for designing primers
#
new_enzymes, primers_results_dict, enzymes_that_already_cut, primer_starting_position,comb_on_Tm = exhaustive_research(DNA_seq,AA_number,new_AA,Tm_desired,find_restriction_site,enzyme_list=None)
megaprimer_dict = megaprimer (DNA_seq,Tm_desired=65)
return
