def output_primers(primers,names):
datum = ('name','sequence','len','Tm',r'%GC','ss-dG','BLAT')
header = "\n%-25s %-30s %-4s %-5s %-4s %-7s %-5s\n" % datum
sys.stdout.write(header)
lens = map(len,primers)
Tms = map(oligoTm.oligo_Tm,primers)
gcs = map(lambda p: seqtools.gc_content(p)*100,primers)
dGs = map(lambda p: unafold.hybrid_ss_min(p,NA='DNA',sodium=0.05),primers)
# trunc_primers = [p[-min(18,min(lens)):] for p in primers]
trunc_primers = primers # NO TRUNCATION
seqrecords = map(lambda t: seqtools.make_SeqRecord(*t),zip(names,trunc_primers))
# blat_hits = map(blat.search_sequence,seqrecords)
for datum in zip(names,primers,lens,Tms,gcs,dGs): #,blat_hits):
primer_string = "%-25s %-30s %-4i %-5.1f %-4.0f %-7.1f\n" % datum
sys.stdout.write(primer_string)
summary_data = lambda d: (np.mean(d),np.std(d),np.min(d),np.max(d))
sys.stdout.write('\nsummary:\n')
sys.stdout.write('num primers: %i\n' % len(primers))
sys.stdout.write('len mean: %5.1f std: %5.1f min: %5.1f max %5.1f\n' % summary_data(lens))
sys.stdout.write('Tm mean: %5.1f std: %5.1f min: %5.1f max %5.1f\n' % summary_data(Tms))
sys.stdout.write('%%GC mean: %5.1f std: %5.1f min: %5.1f max %5.1f\n' % summary_data(gcs))
sys.stdout.write('dGs mean: %5.1f std: %5.1f min: %5.1f max %5.1f\n' % summary_data(dGs))
def choose_PCR_primer(seq,target_Tm=62.):
candidates = generate_candidates(seq)
# filter for Tm
candidates = filter(lambda s: abs(oligoTm.oligoTm(s) - target_Tm) <= 2, candidates)
if len(candidates) == 0:
raise ValueError, "No primer candidates meet Tm cutoffs"
# filter for 0.4-0.6 GC content
candidates = filter(lambda s: abs(seqtools.gc_content(s) - 0.5) <= 0.1,candidates)
if len(candidates) == 0:
raise ValueError, "No primer candidates meet GC content cutoffs"
# rank on secondary structure minimization
candidates.sort(key=unafold.hybrid_ss_min)
return candidates[0]
def choose_PCR_primer(seq, target_Tm=62.):
candidates = generate_candidates(seq)
# filter for Tm
candidates = filter(lambda s: abs(oligoTm.oligoTm(s) - target_Tm) <= 2,
candidates)
if len(candidates) == 0:
raise ValueError, "No primer candidates meet Tm cutoffs"
# filter for 0.4-0.6 GC content
candidates = filter(lambda s: abs(seqtools.gc_content(s) - 0.5) <= 0.1,
candidates)
if len(candidates) == 0:
raise ValueError, "No primer candidates meet GC content cutoffs"
# rank on secondary structure minimization
candidates.sort(key=unafold.hybrid_ss_min)
return candidates[0]