def testMapto(self):
r = Interval.mapto(self.d, self.c)
self.assertListEqual(
r,
[[3, 4, 'a', 'I'], [3, 7, 'b', 'I'], [4, 6, 'e', 'I'],
[4, 7, 'd', 'I'], [5, 7, 'f', 'I'], [10, 11, 'd', 'II'],
[10, 12, 'x', 'II'], [16, 20, 'x', 'III'], [16, 17, 'h', 'III'],
[18, 20, 'i', 'III'], [23, 24, 'x', 'IV']], 'Failed in Mapto')
def parse_indel(read_info, target_name, target, bond_name=None, gDNA=False):
min_indel = None
indel_info = []
target_len = target[target_name]['total']
if not gDNA: # donor
left_bond = target[bond_name]['left_bond']
right_bond = target[bond_name]['right_bond']
dis = 5
else: # gDNA
left_bond = 0
right_bond = 0
cut_left = target[target_name]['cut_left']
cut_right = target[target_name]['cut_right']
dis = 20
for index1, index2, start, end, strand, aln, alignment in read_info:
if strand == '+':
interval = target[target_name]['interval']
else:
interval = target[target_name]['rev_interval']
# reverse start and end
start, end = target_len - end, target_len - start
aln_info = '{}|{}|{}|{}|{}|{}'.format(strand, start, end, index1,
index2, aln)
if start >= dis or target_len - end >= dis:
target_tag = 'partially'
seg_type = '-'.join(
x[2] for x in Interval.mapto([start, end], interval))
else:
target_tag = 'full'
if strand == '+':
seg_type = 'L-LH-C-RH-R' if gDNA else 'LH-I-RH'
else:
seg_type = 'R-RH-C-LH-L' if gDNA else 'RH-I-LH'
cut_indel = 0
total_indel = 0
reference_pos = start
read_tag = 'full'
for n, (num, t) in enumerate(alignment):
if t in ('S', 'H'):
if n == 0: # first postion
if num - left_bond >= dis:
read_tag = 'partially'
else: # last position
if num - right_bond >= dis:
read_tag = 'partially'
if gDNA:
if t == 'I' and cut_left <= reference_pos <= cut_right:
cut_indel += num
if t in ('D', 'U'):
if (cut_left <= reference_pos + num
and reference_pos <= cut_right):
cut_indel += num
if t in ('M', 'U', 'D'):
reference_pos += num
else:
if t in ('D', 'U', 'I'):
cut_indel += num
if t in ('D', 'U', 'I'):
total_indel += num
if target_tag == 'partially' or read_tag == 'partially':
tag = 'partially'
else:
tag = 'full'
if min_indel is None or total_indel < min_indel:
min_indel = total_indel
min_cut_indel = cut_indel
final_tag = tag
indel_info.append('{}|{}|{}|{}|{}'.format(target_name, seg_type,
total_indel, cut_indel,
aln_info))
return [indel_info, final_tag, min_indel, min_cut_indel, target_name]