def sites_outside_snp(target_seq, snp_pos, allele_pos_end):
sites_outside = []
pe_len = len(pe.clean_recognition_sequence)
pe_seq = expand_sequence(pe.clean_recognition_sequence.lower())
# seq_before_snp = snp.ex_wt_sequence[:snp.snp_pos - pe_len]
# seq_after_snp = snp.ex_wt_sequence[snp.snp_pos + snp.wt_allele_len:]
for i in range(0, len(target_seq) - pe_len):
try:
if i in range(snp_pos - pe_len, allele_pos_end):
raise fexceps.DigestError
for ii in range(0, pe_len):
if not can_recognize(target_seq[i+ii], pe_seq[ii]):
raise fexceps.DigestError
sites_outside.append(i)
except fexceps.DigestError:
pass
if not pe.clean_recognition_sequence == \
reverse_complement(pe.clean_recognition_sequence):
pe_seq_rc = expand_sequence(reverse_complement(pe.clean_recognition_sequence.lower()))
for i in range(0, len(target_seq) - pe_len):
try:
if i in range(snp_pos - pe_len, allele_pos_end):
raise fexceps.DigestError
for ii in range(0, pe_len):
if not can_recognize(target_seq[i+ii], pe_seq_rc[ii]):
raise fexceps.DigestError
sites_outside.append(i)
except fexceps.DigestError:
pass
return sites_outside
def pe_can_determine_snp(pe:PrototypeEnzyme,
snp:Snp,
max_num_of_mismatches):
pe_len = len(pe.clean_recognition_sequence)
pe_seq = expand_sequence(pe.clean_recognition_sequence.lower())
wt_sites = gen_mask(pe_len,
pe_seq,
snp.ex_wt_sequence,
snp.snp_pos,
snp.wt_pos_end,
snp.wt_allele_len,
)
mut_sites = gen_mask(pe_len,
pe_seq,
snp.ex_mut_sequence,
snp.snp_pos,
snp.mut_pos_end,
snp.mut_allele_len,
)
if not pe.clean_recognition_sequence == \
reverse_complement(pe.clean_recognition_sequence):
pe_seq_rc = expand_sequence(reverse_complement(pe.clean_recognition_sequence.lower()))
wt_sites = wt_sites + gen_mask(pe_len,
pe_seq_rc,
snp.ex_wt_sequence,
snp.snp_pos,
snp.wt_pos_end,
snp.wt_allele_len,
)
mut_sites = mut_sites + gen_mask(pe_len,
pe_seq_rc,
snp.ex_mut_sequence,
snp.snp_pos,
snp.mut_pos_end,
snp.mut_allele_len,
)
wt_filtered = []
for wt_site in wt_sites:
try:
for mut_site in mut_sites:
wt_site = test_intercept(wt_site, mut_site)
wt_filtered.append(wt_site)
except fexceps.SitesCollisionError:
pass
mut_filtered = []
for mut_site in mut_sites:
try:
for wt_site in wt_sites:
mut_site = test_intercept(mut_site, wt_site)
mut_filtered.append(mut_site)
except fexceps.SitesCollisionError:
pass
return (wt_filtered, mut_filtered)