def _fwdStrand():
fwd_hamming_distances = seqstr.rollingHammingDistance(primer_str,
genome_rc_str)
fwd_hd_thresh = np.percentile(fwd_hamming_distances, hamming_percentile)
fwd_primer_footprint = (-(primer_idx+primer_length), (-primer_idx))
fwd_hamming_distances[fwd_primer_footprint[0]: \
fwd_primer_footprint[1]] = primer_length
fwd_hotspots, = np.where((fwd_hamming_distances < fwd_hd_thresh))
highest_tm_idx = None
highest_tm = -100
for idx in fwd_hotspots:
tm = primer3.calcHeterodimerTm(
primer_str, genome_str[-(idx+primer_length):-idx],
**params['thermo_params'])
if tm > highest_tm:
highest_tm_idx = idx
highest_tm = tm
strand_results.put((highest_tm, highest_tm_idx, 1))
def _revStrand():
rev_hamming_distances = seqstr.rollingHammingDistance(primer_str,
genome_str)
rev_hd_thresh = np.percentile(rev_hamming_distances, hamming_percentile)
rev_primer_footprint = ((primer_idx), (primer_idx+primer_length))
rev_hamming_distances[rev_primer_footprint[0]: \
rev_primer_footprint[1]] = primer_length
rev_hotspots, = np.where((rev_hamming_distances < rev_hd_thresh))
highest_tm_idx = None
highest_tm = -100
for idx in rev_hotspots:
tm = primer3.calcHeterodimerTm(
primer_str, genome_rc_str[idx:idx+primer_length],
**params['thermo_params'])
if tm > highest_tm:
highest_tm_idx = idx
highest_tm = tm
strand_results.put((highest_tm, highest_tm_idx, 0))
def _revStrand():
rev_hamming_distances = seqstr.rollingHammingDistance(primer_str[12:],
genome_str)
rev_hd_thresh = np.percentile(rev_hamming_distances, hamming_percentile)
rev_primer_footprint = ((primer_idx), (primer_idx+primer_length))
rev_hamming_distances[rev_primer_footprint[0]: \
rev_primer_footprint[1]] = primer_length
rev_hotspots, = np.where((rev_hamming_distances < rev_hd_thresh))
highest_dg_idx = None
highest_dg = -100
for idx in rev_hotspots:
dg = primer3.calcEndStability(
primer_str, genome_rc_str[idx:idx+primer_length],
**params['thermo_params']).dg
if dg > highest_dg:
highest_dg_idx = idx
highest_dg = dg
strand_results.put((highest_dg, highest_dg_idx, 0))
def _fwdStrand():
fwd_hamming_distances = seqstr.rollingHammingDistance(primer_str[12:],
genome_rc_str)
fwd_hd_thresh = np.percentile(fwd_hamming_distances, hamming_percentile)
fwd_primer_footprint = (-(primer_idx+primer_length), (-primer_idx))
fwd_hamming_distances[fwd_primer_footprint[0]: \
fwd_primer_footprint[1]] = primer_length
fwd_hotspots, = np.where((fwd_hamming_distances < fwd_hd_thresh))
highest_dg_idx = None
highest_dg = -100
for idx in fwd_hotspots:
dg = primer3.calcEndStability(
primer_str, genome_str[-(idx+primer_length):-idx],
**params['thermo_params']).dg
if dg > highest_dg:
highest_dg_idx = idx
highest_dg = dg
sys.stdout.flush()
strand_results.put((highest_dg, highest_dg_idx, 1))