def _update_ORF_frame(self, i, nuc, j, frame, d_vars):
d_vars["codon"][j] = d_vars["codon"][j] + nuc
if len(d_vars["codon"][j]) == 3:
# test for start forward (if none already found)
is_start = d_vars["codon"][j] in self._codons_start
if is_start & np.isnan(d_vars["pos_ATG_f"][j]):
d_vars["pos_ATG_f"][j] = i - 2
# test for stop forward
is_stop = d_vars["codon"][j] in self._codons_stop
if is_stop:
d_vars["end_f"][j] = i
# test is length of CDS or ORF found is enough to be in output
if self._type_filter == "CDS":
len_to_filter = d_vars["end_f"][j] - d_vars["pos_ATG_f"][
j] # len_CDS
else:
len_to_filter = d_vars["end_f"][j] - d_vars["begin_f"][
j] # len_ORF
if len_to_filter > self._threshold:
len_ORF = d_vars["end_f"][j] - d_vars["begin_f"][j]
len_CDS = d_vars["end_f"][j] - d_vars["pos_ATG_f"][j]
self._ORF_pos.append([d_vars["begin_f"][j],d_vars["end_f"][j],\
frame+1, d_vars["pos_ATG_f"][j], len_ORF, len_CDS])
d_vars["begin_f"][j] = i + 1
d_vars["pos_ATG_f"][j] = np.nan
# test for start reverse
is_start_rev = d_vars["codon"][j] in self._codons_start_rev
if is_start_rev:
d_vars["pos_ATG_r"][j] = i
# test for stop reverse
is_stop_rev = d_vars["codon"][j] in self._codons_stop_rev
if is_stop_rev:
d_vars["end_r"][j] = i - 3
# test is length of CDS or ORF found is enough to be in output
if self._type_filter == "CDS":
len_to_filter = d_vars["pos_ATG_r"][j] - d_vars["begin_r"][
j] # len_CDS
else:
len_to_filter = d_vars["end_r"][j] - d_vars["begin_r"][
j] # len_ORF
if len_to_filter > self._threshold:
len_ORF = d_vars["end_r"][j] - d_vars["begin_r"][j]
len_CDS = d_vars["pos_ATG_r"][j] - d_vars["begin_r"][j]
self._ORF_pos.append([d_vars["begin_r"][j],d_vars["end_r"][j],\
-(frame+1), d_vars["pos_ATG_r"][j], len_ORF, len_CDS])
d_vars["begin_r"][j] = i - 3 + 1
d_vars["pos_ATG_r"][j] = np.nan
# reset codon
d_vars["codon"][j] = ""
return d_vars
def _update_ORF_frame(self, i, nuc, j, frame, d_vars):
d_vars["codon"][j] = d_vars["codon"][j] + nuc
if len(d_vars["codon"][j]) == 3:
# test for start forward (if none already found)
is_start = d_vars["codon"][j] in self._codons_start
if is_start & np.isnan(d_vars["pos_ATG_f"][j]):
d_vars["pos_ATG_f"][j] = i-2
# test for stop forward
is_stop = d_vars["codon"][j] in self._codons_stop
if is_stop:
d_vars["end_f"][j] = i
# test is length of CDS or ORF found is enough to be in output
if self._type_filter == "CDS":
len_to_filter = d_vars["end_f"][j] - d_vars["pos_ATG_f"][j] # len_CDS
else:
len_to_filter = d_vars["end_f"][j] - d_vars["begin_f"][j] # len_ORF
if len_to_filter > self._threshold:
len_ORF = d_vars["end_f"][j] - d_vars["begin_f"][j]
len_CDS = d_vars["end_f"][j] - d_vars["pos_ATG_f"][j]
self._ORF_pos.append([d_vars["begin_f"][j],d_vars["end_f"][j],\
frame+1, d_vars["pos_ATG_f"][j], len_ORF, len_CDS])
d_vars["begin_f"][j] = i+1
d_vars["pos_ATG_f"][j] = np.nan
# test for start reverse
is_start_rev = d_vars["codon"][j] in self._codons_start_rev
if is_start_rev :
d_vars["pos_ATG_r"][j] = i
# test for stop reverse
is_stop_rev = d_vars["codon"][j] in self._codons_stop_rev
if is_stop_rev:
d_vars["end_r"][j] = i-3
# test is length of CDS or ORF found is enough to be in output
if self._type_filter == "CDS":
len_to_filter = d_vars["pos_ATG_r"][j] - d_vars["begin_r"][j]# len_CDS
else:
len_to_filter = d_vars["end_r"][j] - d_vars["begin_r"][j] # len_ORF
if len_to_filter > self._threshold:
len_ORF = d_vars["end_r"][j] - d_vars["begin_r"][j]
len_CDS = d_vars["pos_ATG_r"][j] - d_vars["begin_r"][j]
self._ORF_pos.append([d_vars["begin_r"][j],d_vars["end_r"][j],\
-(frame+1), d_vars["pos_ATG_r"][j], len_ORF, len_CDS])
d_vars["begin_r"][j] = i-3+1
d_vars["pos_ATG_r"][j] = np.nan
# reset codon
d_vars["codon"][j] = ""
return d_vars