def get_frames(seq1, seq2, shift_left, shift_right, all_frames):
"""Take output of check_input function and insert into flanking sequences.
take from database all miRNA results and check if ends of input is suitable
for flanking sequences.
If first value == and miRNA_end_5 second value == miRNA_end_3 then simply
concatenate
sequences flanks5_s + first_sequence + loop_s + second_sequence + flanks3_s.
If any end is different function has to modify end of the insert:
Right end:
if miRNA_end_5 < first_end
add to right site of second sequence additional nucleotides
(as many as |miRNA_end_5 - first_end|)
like (dots are nucleotides to add, big letter are flanking sequences, small are input):
AAAGGGGCTTTTagtcttaga
TTTCCCCGAA....agaatct
if miRNA_end_5 > first_end
cut nucleotides from rigth site of flanks3_s and/or from right site of
second sequence
before cut:
AAAGGGGCTTTTagtcttaga
TTTCCCCGAAAATTcctcagaatct (-2, +2)
After
AAAGGGGCTTTTagtcttaga
TTTCCCCGAAAAtcagaatct
Returns list of tuples (frame, sequence_1 sequence_2)
input: string, string, int, int, pri-miRNA objects
output: List of list of Backbone object, 1st strand 2nd strand """
frames = []
for elem in all_frames:
frame = Backbone(**elem)
if shift_left == frame.miRNA_end_5 and shift_right == frame.miRNA_end_5:
frames.append([frame, seq1, seq2])
else:
_seq1 = seq1[:]
_seq2 = seq2[:]
#miRNA 5 end (left)
if frame.miRNA_end_5 < shift_left:
if frame.miRNA_end_5 < 0 and shift_left < 0:
_seq2 += reverse_complement(
frame.flanks5_s[frame.miRNA_end_5:shift_left])
elif frame.miRNA_end_5 < 0 and shift_left > 0:
frame.flanks5_s = frame.flanks5_s[:frame.miRNA_end_5]
_seq2 += reverse_complement(_seq1[:shift_left])
elif shift_left == 0:
_seq2 += reverse_complement(
frame.flanks5_s[:frame.miRNA_end_5])
elif frame.miRNA_end_5 == 0:
_seq2 += reverse_complement(_seq1[:frame.miRNA_end_5])
else:
_seq2 += reverse_complement(
_seq1[frame.miRNA_end_5:shift_left])
elif frame.miRNA_end_5 > shift_left:
if frame.miRNA_end_5 > 0 and shift_left < 0:
frame.flanks5_s += reverse_complement(
_seq2[frame.miRNA_end_5:])
frame.flanks3_s = frame.flanks3_s[frame.miRNA_end_5:]
elif frame.miRNA_end_5 > 0 and shift_left > 0:
frame.flanks5_s += reverse_complement(
frame.flanks3_s[shift_left:frame.miRNA_end_5])
elif shift_left == 0:
frame.flanks5_s += reverse_complement(
frame.flanks3_s[:frame.miRNA_end_5])
elif frame.miRNA_end_5 == 0:
frame.flanks5_s += reverse_complement(_seq2[shift_left:])
else:
frame.flanks5_s += reverse_complement(
_seq2[shift_left:frame.miRNA_end_5])
#miRNA 3 end (right)
if frame.miRNA_end_3 < shift_right:
if frame.miRNA_end_3 < 0 and shift_right > 0:
frame.loop_s = frame.loop_s[-frame.miRNA_end_3:]
frame.loop_s += reverse_complement(
_seq1[-shift_right:])
elif frame.miRNA_end_3 > 0 and shift_right > 0:
frame.loop_s += reverse_complement(
_seq1[-shift_right:-frame.miRNA_end_3])
elif frame.miRNA_end_3 == 0:
frame.loop_s += reverse_complement(_seq1[-shift_right:])
elif shift_right == 0:
frame.loop_s += reverse_complement(
frame.loop_s[:-frame.miRNA_end_3])
else:
frame.loop_s += reverse_complement(
frame.loop_s[-shift_right:-frame.miRNA_end_3])
elif frame.miRNA_end_3 > shift_right:
if frame.miRNA_end_3 > 0 and shift_right < 0:
_seq1 += reverse_complement(
_seq2[:-shift_right])
frame.loop_s = frame.loop_s[:-frame.miRNA_end_3]
elif frame.miRNA_end_3 > 0 and shift_right > 0:
_seq1 += reverse_complement(
frame.loop_s[-frame.miRNA_end_3:-shift_right])
elif shift_right == 0:
_seq1 += reverse_complement(
frame.loop_s[:frame.miRNA_end_3])
elif frame.miRNA_end_3 == 0:
_seq1 += reverse_complement(_seq2[:-shift_right])
else:
_seq1 += reverse_complement(
_seq2[-frame.miRNA_end_3:-shift_right])
frames.append([frame, _seq1, _seq2])
return frames
def get_frames(seq1, seq2, shift_left, shift_right, all_frames):
"""Take output of check_input function and insert into flanking sequences.
take from database all miRNA results and check if ends of input is suitable
for flanking sequences.
If first value == and miRNA_end_5 second value == miRNA_end_3 then simply
concatenate
sequences flanks5_s + first_sequence + loop_s + second_sequence + flanks3_s.
If any end is different function has to modify end of the insert:
Right end:
if miRNA_end_5 < first_end
add to right site of second sequence additional nucleotides
(as many as |miRNA_end_5 - first_end|)
like (dots are nucleotides to add, big letter are flanking sequences, small are input):
AAAGGGGCTTTTagtcttaga
TTTCCCCGAA....agaatct
if miRNA_end_5 > first_end
cut nucleotides from rigth site of flanks3_s and/or from right site of
second sequence
before cut:
AAAGGGGCTTTTagtcttaga
TTTCCCCGAAAATTcctcagaatct (-2, +2)
After
AAAGGGGCTTTTagtcttaga
TTTCCCCGAAAAtcagaatct
Returns list of tuples (frame, sequence_1 sequence_2)
input: string, string, int, int, pri-miRNA objects
output: List of list of Backbone object, 1st strand 2nd strand """
frames = []
for elem in all_frames:
frame = Backbone(**elem)
if shift_left == frame.miRNA_end_5 and shift_right == frame.miRNA_end_5:
frames.append([frame, seq1, seq2])
else:
_seq1 = seq1[:]
_seq2 = seq2[:]
#miRNA 5 end (left)
if frame.miRNA_end_5 < shift_left:
if frame.miRNA_end_5 < 0 and shift_left < 0:
_seq2 += reverse_complement(
frame.flanks5_s[frame.miRNA_end_5:shift_left])
elif frame.miRNA_end_5 < 0 and shift_left > 0:
frame.flanks5_s = frame.flanks5_s[:frame.miRNA_end_5]
_seq2 += reverse_complement(_seq1[:shift_left])
elif shift_left == 0:
_seq2 += reverse_complement(
frame.flanks5_s[:frame.miRNA_end_5])
elif frame.miRNA_end_5 == 0:
_seq2 += reverse_complement(_seq1[:frame.miRNA_end_5])
else:
_seq2 += reverse_complement(
_seq1[frame.miRNA_end_5:shift_left])
elif frame.miRNA_end_5 > shift_left:
if frame.miRNA_end_5 > 0 and shift_left < 0:
frame.flanks5_s += reverse_complement(
_seq2[frame.miRNA_end_5:])
frame.flanks3_s = frame.flanks3_s[frame.miRNA_end_5:]
elif frame.miRNA_end_5 > 0 and shift_left > 0:
frame.flanks5_s += reverse_complement(
frame.flanks3_s[shift_left:frame.miRNA_end_5])
elif shift_left == 0:
frame.flanks5_s += reverse_complement(
frame.flanks3_s[:frame.miRNA_end_5])
elif frame.miRNA_end_5 == 0:
frame.flanks5_s += reverse_complement(_seq2[shift_left:])
else:
frame.flanks5_s += reverse_complement(
_seq2[shift_left:frame.miRNA_end_5])
#miRNA 3 end (right)
if frame.miRNA_end_3 < shift_right:
if frame.miRNA_end_3 < 0 and shift_right > 0:
frame.loop_s = frame.loop_s[-frame.miRNA_end_3:]
frame.loop_s += reverse_complement(_seq1[-shift_right:])
elif frame.miRNA_end_3 > 0 and shift_right > 0:
frame.loop_s += reverse_complement(
_seq1[-shift_right:-frame.miRNA_end_3])
elif frame.miRNA_end_3 == 0:
frame.loop_s += reverse_complement(_seq1[-shift_right:])
elif shift_right == 0:
frame.loop_s += reverse_complement(
frame.loop_s[:-frame.miRNA_end_3])
else:
frame.loop_s += reverse_complement(
frame.loop_s[-shift_right:-frame.miRNA_end_3])
elif frame.miRNA_end_3 > shift_right:
if frame.miRNA_end_3 > 0 and shift_right < 0:
_seq1 += reverse_complement(_seq2[:-shift_right])
frame.loop_s = frame.loop_s[:-frame.miRNA_end_3]
elif frame.miRNA_end_3 > 0 and shift_right > 0:
_seq1 += reverse_complement(
frame.loop_s[-frame.miRNA_end_3:-shift_right])
elif shift_right == 0:
_seq1 += reverse_complement(
frame.loop_s[:frame.miRNA_end_3])
elif frame.miRNA_end_3 == 0:
_seq1 += reverse_complement(_seq2[:-shift_right])
else:
_seq1 += reverse_complement(
_seq2[-frame.miRNA_end_3:-shift_right])
frames.append([frame, _seq1, _seq2])
return frames
