class Line:
"""
Represents a line in the SAM file.
"""
TYPE_HEADER = 0
TYPE_ALIGNMENT = 1
def __init__(self, line_string):
self.type = self.TYPE_HEADER if line_string.startswith('@') \
else self.TYPE_ALIGNMENT
if self.type == self.TYPE_HEADER:
self.fields = [line_string]
return
self.fields = line_string.split()
pos, cigar = self.fields[3], self.fields[5]
if cigar == '*':
raise CigarUnavailableError
md = next(filter(lambda field: field.startswith('MD:Z:'), self.fields))
md = md.replace('MD:Z:', '')
self.alignment = Alignment(pos, cigar, md)
def soft_clip(self, start, stop):
if self.type == self.TYPE_HEADER:
return
self.strip_paired_end_info()
self.fields[2] = '{}:{}-{}'.format(self.fields[2], start, stop)
self.alignment.soft_clip(start, stop)
self.fields[3] = str(self.alignment.pos)
self.fields[5] = self.alignment.cigar
self.fields = list(map(
lambda field: 'MD:Z:'+self.alignment.md if \
field.startswith('MD:Z:') else field,
self.fields))
def strip_paired_end_info(self):
'''
fields[1]: Bitwise flags according to the SAM specifications:
1 -- template having multiple segments in sequencing
2 -- each segment properly aligned according to the aligner
4 -- segment unmapped
8 -- next segment in template unmapped
16 -- SEQ being reverse complemented
32 -- SEQ of the next segment in the template being reversed
complemented
64 -- the first segment in the template
128 -- the last segment in the template
...
fields[6]: reference sequence name of the primary alignment of the next
read in the template; '*' when information is unavailable.
fields[7]: 1-based position of the primary alignment of the next read in
the template; '0' when information is unavailable.
fields[8]: signed observed template length; '0' for single-segment
template, or when information is unavailable.
'''
flags = int(self.fields[1])
flags &= 0b00111100
self.fields[1] = str(flags)
self.fields[6:9] = ['*', '0', '0']
def __repr__(self):
return '\t'.join(self.fields)
def test_alignment_soft_clip(pre_clip, to_clip, post_clip):
alignment_original = Alignment(*pre_clip)
alignment_original.soft_clip(*to_clip)
assert alignment_original == Alignment(*post_clip)
