def upshift(self, refseq):
"""Shifts event start coordinate upstream for repeat-involved event"""
if self.snv_type in ('ins', 'dup', 'ITD', 'PTD') or self.snv_type == 'del':
if self.snv_type in ('ins', 'dup', 'ITD', 'PTD'):
if tools.is_homopolymer(self.var_seq):
size = 1
seq = self.var_seq[0]
else:
size = len(self.var_seq)
seq = self.var_seq
else:
if tools.is_homopolymer(self.ref_seq):
size = 1
seq = self.ref_seq[0]
else:
size = len(self.ref_seq)
seq = self.ref_seq
start = int(self.ref_start) - size
# skip if 0-size event
if size == 0:
sys.stderr.write("error in upshift size 0 contig:%s %s\n" % (self.var, self.ref_seq))
return
# continues checking upstream sequence to see if it's repeat of sequence in question
while start > 1:
upstream = refseq.GetSequence(self.ref, start + 1, start + size)
if seq.upper() != upstream.upper():
break
start = start - size
# changed reference start coordinate (and end coordinate too if deletion)
if start + size < self.ref_start:
if self.snv_type in ('ins', 'dup', 'ITD', 'PTD'):
sys.stderr.write("shifted %s %s %s %s to %d\n" % (self.var, self.snv_type, self.ref, self.ref_start, start+size))
self.ref_start = self.ref_end = start + size
else:
sys.stderr.write("shifted %s %s %s %s to %d\n" % (self.var, self.snv_type, self.ref, self.ref_start, start+size+1))
self.ref_start = start + size + 1
self.ref_end = self.ref_start + len(self.ref_seq) - 1
def expand_contig_region(self, contig_sequence, query_strand):
"""Expand read-support checking region if repeats are involved"""
if not self.snv_type in ('ins', 'dup', 'ITD', 'PTD', 'del'):
return None
# skip if deleted/inserted sequence is longer than contig sequence
if self.snv_type == 'del' and len(self.ref_seq) > len(contig_sequence):
return None
if self.snv_type in ('ins', 'dup', 'ITD', 'PTD') and len(self.var_seq) > len(contig_sequence):
return None
if self.snv_type in ('ins', 'dup', 'ITD', 'PTD'):
seq = self.var_seq[:]
else:
seq = self.ref_seq[:]
if len(seq) == 0:
return None
if tools.is_homopolymer(seq) or len(seq) == 1:
h**o = True
else:
h**o = False
# keep a record of previous value for reporting expansion
region_before = self.confirm_contig_region[:]
# arbitrary big number
limit = 100000
# forward
expand = 0
for i in range(limit):
if h**o:
changed_base = seq[0].upper()
else:
changed_base = seq[i % len(seq)].upper()
downstream_base = None
if self.snv_type == 'del':
if query_strand == '+':
if int(self.var_end) + i < len(contig_sequence) and int(self.var_end) + i >= 0:
downstream_base = contig_sequence[int(self.var_end) + i].upper()
else:
if int(self.var_end) - 2 - i >= 0 and int(self.var_end) - 2 - i < len(contig_sequence):
downstream_base = tools.reverse_complement(contig_sequence[int(self.var_end) - 2 - i]).upper()
elif self.snv_type in ('ins', 'dup', 'ITD', 'PTD'):
if query_strand == '+':
if int(self.var_end) + i < len(contig_sequence) and int(self.var_end) + i >= 0:
downstream_base = contig_sequence[int(self.var_end) + i].upper()
else:
if int(self.var_start) - i - 2 >= 0 and int(self.var_start) - i - 2 < len(contig_sequence):
downstream_base = tools.reverse_complement(contig_sequence[int(self.var_start) - i - 2]).upper()
if changed_base == downstream_base:
expand += 1
else:
break
multiples = expand/len(seq)
if multiples > 0:
if query_strand == '+':
self.confirm_contig_region[1] += multiples * self.snv_len
else:
self.confirm_contig_region[0] -= multiples * self.snv_len
# reverse
seq = seq[::-1]
expand = 0
for i in range(limit):
if h**o:
changed_base = seq[0].upper()
else:
changed_base = seq[i%len(seq)].upper()
upstream_base = None
if self.snv_type == 'del':
if query_strand == '+':
if int(self.var_start) - i - 1 >= 0 and int(self.var_start) - i - 1 < len(contig_sequence):
upstream_base = contig_sequence[int(self.var_start) - i - 1].upper()
else:
if int(self.var_start) + i - 1 < len(contig_sequence) and int(self.var_start) + i - 1 >= 0:
upstream_base = tools.reverse_complement(contig_sequence[int(self.var_start)+i-1]).upper()
elif self.snv_type in ('ins', 'dup', 'ITD', 'PTD'):
if query_strand == '+':
if int(self.var_start) - i - 2 >= 0 and int(self.var_start) - i - 2 < len(contig_sequence):
upstream_base = contig_sequence[int(self.var_start) - i - 2].upper()
else:
if int(self.var_end) + i < len(contig_sequence) and int(self.var_end) + i >= 0:
upstream_base = tools.reverse_complement(contig_sequence[int(self.var_end) + i]).upper()
if changed_base == upstream_base:
expand += 1
else:
break
multiples = expand/len(seq)
if multiples > 0:
if query_strand == '+':
self.confirm_contig_region[0] -= multiples * self.snv_len
else:
self.confirm_contig_region[1] += multiples * self.snv_len
expanded_sequence = contig_sequence[self.confirm_contig_region[0]-1:self.confirm_contig_region[1]]
# coordinate given in 1-based
if region_before[0] != self.confirm_contig_region[0] or region_before[1] != self.confirm_contig_region[1]:
self.expansion = (self.confirm_contig_region[1] - self.confirm_contig_region[0] + 1) / self.snv_len
sys.stderr.write("expand confirm contig region %s %s -> %s %s %s %sx\n" % (self.var, region_before, self.confirm_contig_region, expanded_sequence, len(expanded_sequence), self.expansion))
