def test_sanity(reads, n_frag, len_frag):
'''Perform sanity checks on supposedly good reads'''
if not test_integrity(reads):
return False
if not test_coh(reads):
return False
if not test_fragment_assignment(reads, n_frag, len_frag):
return False
return True
def trim_primers(reads, frag_pos, include_tests=False):
'''Trim inner primers
- frag_pos are the coordinates of the fragment trimmed of inner primers
'''
# Note: this function is robust against fuzzy ends, i.e. it works also if the
# insert reads into the adapters and crap like that.
# Because we accept short inserts, the primer can also be at the end
if include_tests:
if test_integrity(reads):
print 'trim_primers (entry):'
import ipdb; ipdb.set_trace()
tampered = False
for read in reads:
# FWD primer
if read.pos < frag_pos[0]:
tampered = True
ref_pos = read.pos
read_pos = 0
cigar = read.cigar[::-1]
for i, (bt, bl) in enumerate(read.cigar):
if bt == 0:
# Strictly greater, because we dump the CIGAR ending at the
# right position. In the corner case, ref_pos == frag_pos[0]
# and we add the whole block (and do not move read_pos).
if ref_pos + bl > frag_pos[0]:
cigar[-1] = (bt, ref_pos + bl - frag_pos[0])
read_pos += frag_pos[0] - ref_pos
ref_pos = frag_pos[0]
break
cigar.pop(-1)
read_pos += bl
ref_pos += bl
elif bt == 1:
cigar.pop(-1)
read_pos += bl
elif bt == 2:
# Starting with a deletion is not allowed
cigar.pop(-1)
ref_pos += bl
if ref_pos > frag_pos[0]:
break
cigar = cigar[::-1]
# If you cut away everything, trash
if not len(cigar):
return True
seq = read.seq
qual = read.qual
read.pos = ref_pos
read.seq = seq[read_pos:]
read.qual = qual[read_pos:]
read.cigar = cigar
# REV primer
ref_pos = read.pos + sum(bl for (bt, bl) in read.cigar if bt in (0, 2))
if ref_pos > frag_pos[1]:
tampered = True
read_pos = read.rlen
cigar = read.cigar
for i, (bt, bl) in enumerate(read.cigar[::-1]):
if bt == 0:
# Strictly less, because we dump the CIGAR starting at the
# right position. In the corner case, ref_pos == frag_pos[1]
# and we add the whole block (and do not move read_pos).
if ref_pos - bl < frag_pos[1]:
cigar[-1] = (bt, frag_pos[1] - (ref_pos - bl))
read_pos -= ref_pos - frag_pos[1]
break
cigar.pop(-1)
read_pos -= bl
ref_pos -= bl
elif bt == 1:
cigar.pop(-1)
read_pos -= bl
elif bt == 2:
# Ending with a deletion is not allowed
cigar.pop(-1)
ref_pos -= bl
if ref_pos < frag_pos[1]:
break
# If you cut away everything, trash
if not len(cigar):
return True
seq = read.seq
qual = read.qual
read.seq = seq[:read_pos]
read.qual = qual[:read_pos]
read.cigar = cigar
# Fix mate pair
if tampered:
i_fwd = reads[0].is_reverse
i_rev = not i_fwd
reads[i_fwd].mpos = reads[i_rev].pos
reads[i_rev].mpos = reads[i_fwd].pos
isize = reads[i_rev].pos + sum(bl for bt, bl in reads[i_rev].cigar
if bt in (0, 2)) - reads[i_fwd].pos
reads[i_fwd].isize = isize
reads[i_rev].isize = -isize
if include_tests:
if test_integrity(reads):
print 'trim_primers (exit):'
import ipdb; ipdb.set_trace()
return False