def get_opt_cloningprimer_pair(seq):
oligo_calc = primer3.thermoanalysis.ThermoAnalysis(mv_conc=20, dv_conc=1.5, dntp_conc=0.8, dna_conc=50, max_nn_length=60)
# Change if you have personal condition for PCR
## mv_conc : The millimolar (mM) concentration of monovalent salt cations (usually KCl) in the PCR.
## dv_conc : The millimolar concentration of divalent salt cations (usually MgCl^(2+)) in the PCR.
## dntp_conc : The millimolar concentration of the sum of all deoxyribonucleotide triphosphates.
## dna_conc : A value to use as nanomolar (nM) concentration of each annealing oligo over the course the PCR.
## max_nn_length : longest seq length for primer Tm analysis
primerF_list = []
primerR_list = []
for i in range(16,25):
primerF = seq[0:i]
#primerR = kang.rev_comp(seq[-i-3:-3]) # stop codon excluded
primerR = kang.rev_comp(seq[-i:]) # stop codon included
if 45 <= oligo_calc.calcTm(primerF) <= 63:
primerF_list.append(primerF)
else:
pass
#print (primerF, oligo_calc.calcTm(primerF) )
if 45 <= oligo_calc.calcTm(primerR) <= 63:
primerR_list.append(primerR)
primerF_list_Tm = [oligo_calc.calcTm(x) for x in primerF_list]
primerR_list_Tm = [oligo_calc.calcTm(x) for x in primerR_list]
return primerF_list,primerR_list,primerF_list_Tm,primerR_list_Tm
def get_opt_cloningprimer_pair(seq):
oligo_calc = primer3.thermoanalysis.ThermoAnalysis(mv_conc=20, dv_conc=1.5, dntp_conc=0.8, dna_conc=50, max_nn_length=60)
# Change if you have personal condition for PCR
## mv_conc : The millimolar (mM) concentration of monovalent salt cations (usually KCl) in the PCR.
## dv_conc : The millimolar concentration of divalent salt cations (usually MgCl^(2+)) in the PCR.
## dntp_conc : The millimolar concentration of the sum of all deoxyribonucleotide triphosphates.
## dna_conc : A value to use as nanomolar (nM) concentration of each annealing oligo over the course the PCR.
## max_nn_length : longest seq length for primer Tm analysis
primerF_list = []
primerR_list = []
for i in range(16,25):
primerF = seq[0:i]
#primerR = kang.rev_comp(seq[-i-3:-3]) # stop codon excluded
primerR = kang.rev_comp(seq[-i:]) # stop codon included
if 56 <= oligo_calc.calcTm(primerF) <= 63:
primerF_list.append(primerF)
else:
pass
#print (primerF, oligo_calc.calcTm(primerF) )
if 56 <= oligo_calc.calcTm(primerR) <= 63:
primerR_list.append(primerR)
primerF_list_Tm = [oligo_calc.calcTm(x) for x in primerF_list]
primerR_list_Tm = [oligo_calc.calcTm(x) for x in primerR_list]
comp_tm = []
for i,tmF in enumerate(primerF_list_Tm):
for j,tmR in enumerate(primerR_list_Tm):
if abs(tmF-tmR) <= 3:
comp_tm.append([i,j,tmF,tmR])
comp_tm.sort(key=lambda x : x[2]+x[3])
try:
ixF,ixR = comp_tm[0][0],comp_tm[0][1]
return primerF_list[ixF],primerF_list_Tm[ixF],primerR_list[ixR],primerR_list_Tm[ixR]
except IndexError:
return None,None,None,None
cT = dicT2cls[strTN]
cT.strCDS_list.append([int(strL1), int(strL2)])
except KeyError:
print('!!')
exit()
Outfile = open(file_fa + '.cds.fa', 'w')
for TN in dicT2cls:
cT = dicT2cls[TN]
cds_locs = cT.strCDS_list
cds_locs.sort(key=lambda x: x[0])
#cdsseq_pre = ''
start_loc = cds_locs[0]
intL1, intL2 = start_loc
#cdsseq_pre = dicHD2seq[cT.strChr][intL1-1-1000:intL1-1]
cdsseq_pre = ''
for cds_loc in cds_locs:
intL1, intL2 = cds_loc
cdsseq_pre += dicHD2seq[cT.strChr][intL1 - 1:intL2]
end_loc = cds_locs[-1]
intL1, intL2 = end_loc
#cdsseq_pre += dicHD2seq[cT.strChr][intL2:intL2+1000]
if cT.strSTRD == '+':
print('>' + cT.strTN, file=Outfile)
print(cdsseq_pre, file=Outfile)
elif cT.strSTRD == '-':
print('>' + cT.strTN, file=Outfile)
print(kang.rev_comp(cdsseq_pre), file=Outfile)
except KeyError:
print('!!')
exit()
Outfile = open(file_fa+'.cds.fa','w')
for TN in dicT2cls:
cT = dicT2cls[TN]
cds_locs = cT.strCDS_list
cds_locs.sort(key = lambda x : x[0])
#cdsseq_pre = ''
start_loc = cds_locs[0]
intL1, intL2 = start_loc
#cdsseq_pre = dicHD2seq[cT.strChr][intL1-1-1000:intL1-1]
cdsseq_pre = ''
for cds_loc in cds_locs:
intL1, intL2 = cds_loc
cdsseq_pre += dicHD2seq[cT.strChr][intL1-1:intL2]
end_loc = cds_locs[-1]
intL1, intL2 = end_loc
#cdsseq_pre += dicHD2seq[cT.strChr][intL2:intL2+1000]
if cT.strSTRD == '+':
print('>'+cT.strTN,file=Outfile)
print(cdsseq_pre,file=Outfile)
elif cT.strSTRD == '-':
print('>'+cT.strTN,file=Outfile)
print(kang.rev_comp(cdsseq_pre),file=Outfile)
zip([x.split('=')[0] for x in strInfo_list],
[x.split('=')[1] for x in strInfo_list]))
try:
genename = dicID2mRNA[dicInfo['Parent']]
except KeyError:
print(line)
print(dicInfo['Parent'])
exit()
for strLoc, strM, strU, strDi in indexed_list:
if intL1 <= int(strLoc) <= intL2:
intLoc = int(strLoc)
if sys.argv[2] == 'CG':
if strDi == '+':
context = dicHD2seq[strC][intLoc - 1 - 2:intLoc + 3]
else:
context = kang.rev_comp(dicHD2seq[strC][intLoc - 1 -
3:intLoc + 2])
else:
if strDi == '+':
context = dicHD2seq[strC][intLoc - 1 - 2:intLoc + 4]
else:
context = kang.rev_comp(dicHD2seq[strC][intLoc - 1 -
4:intLoc + 2])
if len(context) == dkmer[sys.argv[2]]:
print('>' + strC + '_' + strLoc, file=Outfile_kmer)
print(context, file=Outfile_kmer)
else:
pass
try:
dicGN2count[genename][1] += int(strU)
dicGN2count[genename][0] += int(strM)
except KeyError:
list_cds_seq_snp.append(cds_seq_snp)
if strand == '+':
list_cds_seq_snp_pep = []
for cds_seq_snp in list_cds_seq_snp:
cds_seq_snp_pep = kang.translation(cds_seq_snp)
list_cds_seq_snp_pep.append(cds_seq_snp_pep)
if len(set(list_cds_seq_snp_pep)) > 1: # ... .. .. .... ... 1. ...
pass
else:
continue
else:
list_cds_seq_snp_pep = []
for cds_seq_snp in list_cds_seq_snp:
cds_seq_snp_pep = kang.translation(kang.rev_comp(cds_seq_snp))
list_cds_seq_snp_pep.append(cds_seq_snp_pep)
if len(set(list_cds_seq_snp_pep)) > 1: # ... .. .. .... ... 1. ...
pass
else:
continue
print('#',
genename,
strand,
dic_annot[genename],
file=Outfile_nonsynalign)
print('# pep_seq', file=Outfile_nonsynalign)
pos_pepvar_array = seq_comp(list_vcf_label, list_cds_seq_snp_pep,
Outfile_nonsynalign)
if line[0] == '#' or line.strip() == '':
continue
cell = line.strip().split('\t')
strLG = cell[0]
print(cell)
strSC = cell[1].replace('*', '')
if 'SS' in strSC:
strSC = strSC.replace('SS', 'SuperScaf_')
else:
strSC = strSC.replace('s', 'scaffold_')
LGIncludedSC.append(strSC)
strD = cell[2]
if strD == 'F':
strSeq = dicHD2Seq[strSC]
elif strD == 'R':
strSeq = kang.rev_comp(dicHD2Seq[strSC])
else:
strSeq = dicHD2Seq[strSC]
try:
dicLG2Seq[strLG] += 'N' * 500 + strSeq
except KeyError:
dicLG2Seq[strLG] = strSeq
for strLG in dicLG2Seq:
print('>' + strLG, file=Outfile_chr)
print(dicLG2Seq[strLG], file=Outfile_chr)
for strHD in dicHD2Seq:
if strHD in LGIncludedSC:
continue
print('>' + strHD, file=Outfile_scaff)
print(dicHD2Seq[strHD], file=Outfile_scaff)
if strand == '+':
list_cds_seq_snp_pep = []
for cds_seq_snp in list_cds_seq_snp:
cds_seq_snp_pep = kang.translation(cds_seq_snp)
list_cds_seq_snp_pep.append(cds_seq_snp_pep)
if len(set(list_cds_seq_snp_pep)) > 1: # ... .. .. .... ... 1. ...
pass
else: continue
else:
list_cds_seq_snp_pep = []
for cds_seq_snp in list_cds_seq_snp:
cds_seq_snp_pep = kang.translation(kang.rev_comp(cds_seq_snp))
list_cds_seq_snp_pep.append(cds_seq_snp_pep)
if len(set(list_cds_seq_snp_pep)) > 1: # ... .. .. .... ... 1. ...
pass
else: continue
print ('#',genename,strand,dic_annot[genename],file=Outfile_nonsynalign)
print ('# pep_seq',file=Outfile_nonsynalign)
pos_pepvar_array = seq_comp(list_vcf_label,list_cds_seq_snp_pep,Outfile_nonsynalign)
print ('# cds_seq',file=Outfile_nonsynalign)
if strand == '+':
pos_snp_array = seq_comp(list_vcf_label,list_cds_seq_snp,Outfile_nonsynalign)
else:
pos_snp_array = seq_comp(list_vcf_label,[kang.rev_comp(x) for x in list_cds_seq_snp],Outfile_nonsynalign)
for n,pos_snp in enumerate(pos_snp_array):
for line in open(file_joo):
if line[0] == '#' or line.strip() == '':
continue
cell = line.strip().split('\t')
strLG = cell[0]
print(cell)
strSC = cell[1].replace('*','')
if 'SS' in strSC:
strSC = strSC.replace('SS','SuperScaf_')
else : strSC = strSC.replace('s','scaffold_')
LGIncludedSC.append(strSC)
strD = cell[2]
if strD == 'F':
strSeq = dicHD2Seq[strSC]
elif strD == 'R':
strSeq = kang.rev_comp(dicHD2Seq[strSC])
else : strSeq = dicHD2Seq[strSC]
try:
dicLG2Seq[strLG] += 'N'*500+strSeq
except KeyError:
dicLG2Seq[strLG] = strSeq
for strLG in dicLG2Seq:
print('>'+strLG,file=Outfile_chr)
print(dicLG2Seq[strLG],file=Outfile_chr)
for strHD in dicHD2Seq:
if strHD in LGIncludedSC:
continue
print('>'+strHD,file=Outfile_scaff)
print(dicHD2Seq[strHD],file=Outfile_scaff)
for line in open(file_in):
cell = line.strip().split('\t')
strLink = 'SuperScaf_%d' % i
i += 1
seq = ''
for ecell in cell:
strSC = ecell.split(',')[0].replace('s', 'scaffold_') # scaffold name
if strSC in done:
print(strSC)
print('!!!')
exit()
done.append(strSC)
strOrt = ecell.split(',')[1][0] # Orientation F or R
if strOrt == 'F':
if seq == '':
seq += dicHD2seq[strSC]
else:
seq += 'N' * 500 + dicHD2seq[strSC]
else:
if seq == '':
seq += dicHD2seq[strSC]
else:
seq += 'N' * 500 + kang.rev_comp(dicHD2seq[strSC])
print('>' + strLink, file=Outfile)
print(seq, file=Outfile)
for strHD in dicHD2seq:
if strHD in done:
continue
print('>' + strHD, file=Outfile)
print(dicHD2seq[strHD], file=Outfile)
seq = ''
for ecell in cell:
strSC = ecell.split(',')[0].replace('s','scaffold_') # scaffold name
if strSC in done:
print(strSC)
print('!!!')
exit()
done.append(strSC)
strOrt = ecell.split(',')[1][0] # Orientation F or R
if strOrt == 'F':
if seq == '':
seq += dicHD2seq[strSC]
else:
seq += 'N'*500 + dicHD2seq[strSC]
else :
if seq == '':
seq += dicHD2seq[strSC]
else:
seq += 'N'*500 + kang.rev_comp(dicHD2seq[strSC])
print('>'+strLink,file=Outfile)
print(seq,file=Outfile)
for strHD in dicHD2seq:
if strHD in done:
continue
print('>'+strHD,file=Outfile)
print(dicHD2seq[strHD],file=Outfile)
