def __init__( self,
record,
template=None,
forward_primer=None,
reverse_primer=None,
saltc=None,
forward_primer_concentration=None,
reverse_primer_concentration=None,
*args,
**kwargs):
#Dseqrecord.__init__(self,record,*args,**kwargs)
super(Amplicon, self).__init__(record, *args, **kwargs)
self.template = template
self.forward_primer = forward_primer
self.reverse_primer = reverse_primer
self.fwd_primer = self.forward_primer
self.rev_primer = self.reverse_primer
self.forward_primer_concentration = forward_primer_concentration
self.reverse_primer_concentration = reverse_primer_concentration
self.saltc = saltc
self.tmf = Tm_staluc(str(self.forward_primer.footprint),dnac=50, saltc=self.saltc)
self.tmr = Tm_staluc(str(self.reverse_primer.footprint),dnac=50, saltc=self.saltc)
self.tmf_dbd = tmbresluc(str(self.forward_primer.footprint),primerc=self.forward_primer_concentration)
self.tmr_dbd = tmbresluc(str(self.reverse_primer.footprint),primerc=self.reverse_primer_concentration)
def GC_TM_calc(tmp_seq, loc, GC_comb, disRC):
from Bio.Seq import Seq
from Bio.SeqUtils import GC
from Bio.SeqUtils.MeltingTemp import Tm_staluc
global TM_Min, TM_Max
[GC_Min, GC_Max] = GC_comb.split('-')
if disRC == 'False':
gc = GC(tmp_seq)
tm = Tm_staluc(tmp_seq, rna=0)
thermo = [round(gc, 2), round(tm, 2), tmp_seq]
elif disRC == 'True':
tmp_seqd = str(Seq(tmp_seq).reverse_complement())
gc = GC(tmp_seqd)
tm = Tm_staluc(tmp_seqd, rna=0)
thermo = [round(gc, 2), round(tm, 2), tmp_seq]
if (int(thermo[0]) >= int(GC_Min)) and (int(thermo[0]) <= int(GC_Max)):
if (int(thermo[1]) >= TM_Min) and (int(thermo[1]) <= TM_Max):
thermo.append('P')
return thermo
else:
thermo.append('F-Tm')
return thermo
else:
thermo.append('F-GC')
return thermo
def nearest_neighbour(self, sequence):
"""Calculate Tm with rule.
See http://www.basic.northwestern.edu/biotools/oligocalc.html"""
tm_nn = Tm_staluc(sequence,
dnac=self.primer_conc,
saltc=self.natrium_conc)
return round(tm_nn, 1)
def calGcTm(tmp_seq, loc):
from Bio.SeqUtils import GC
from Bio.SeqUtils.MeltingTemp import Tm_staluc
global TM_Min, TM_Max, bp_len
[GC_Min, GC_Max] = GC_limit.split('-')
gc = GC(tmp_seq)
tm = Tm_staluc(tmp_seq, rna=0)
thermo = [round(gc, 0), round(tm, 0), tmp_seq]
if (int(thermo[0]) >= int(GC_Min)) and (int(thermo[0]) <= int(GC_Max)):
if (int(thermo[1]) >= TM_Min) and (int(thermo[1]) <= TM_Max):
thermo.append('P')
return thermo
else:
thermo.append('F-Tm')
return thermo
else:
thermo.append('F-GC')
return thermo
def tm(self): return round(Tm_staluc(str(self.seq()), 50, 1000*float(self.cfragment.construct.settings.na_salt)),2)
def fullTm(self):
return Tm_staluc(self.bottomPrimer())
def bottomTm(self):
return Tm_staluc(self.rightHalf())
def topTm(self):
return Tm_staluc(self.leftHalf())