def alignAndFilter(self, reads, ref_storage, mode):
# type: (Iterable[Contig], ContigStorage, str) -> Generator[AlignmentPiece]
filter = self.filters[mode]
read_storage = ContigStorage(reads, False)
als = []
for rec in self.align(read_storage, list(ref_storage.unique()), mode):
if rec.is_unmapped:
continue
if len(als) > 0 and rec.query_name != als[0].seg_from.contig.id:
res = list(filter(als))
for al in res:
yield al
als = []
if len(als) > 0:
seq_from = als[0].seg_from.contig
else:
seq_from = read_storage[rec.query_name]
seq_to = ref_storage[rec.tname]
tmp = AlignmentPiece.FromSamRecord(seq_from, seq_to, rec)
if tmp is not None:
if mode == "dotplot":
als.extend(tmp.splitRef())
elif (mode == "local"):
als.extend(tmp.splitRead())
elif (mode == "ava-pb"):
als.extend(tmp.splitRead())
else:
als.append(tmp)
if len(als) > 0:
res = list(filter(als))
for al in res:
yield al
def printAlignments(sam_handler, reference_handler, reads_handler):
print "Loading reference"
cc = ContigStorage(add_rc=False).loadFromFasta(reference_handler, False)
print "Loading query"
reads = ContigStorage().loadFromFasta(reads_handler, False)
print "Loading result"
res = []
for rec in sam_parser.Samfile(sam_handler):
if rec.query_name in reads.items and cc[rec.tname] is not None:
al = AlignmentPiece.FromSamRecord(reads[rec.query_name], cc[rec.tname], rec)
if al is None:
print rec.query_name, rec.tname
continue
if al.seg_to.contig not in cc:
al = al.rc
res.append(al)
print "Printing result", len(res)
res = sorted(res, key = lambda al: al.seg_to.left)
# res = sorted(res, key = lambda al: len(al))[::-1]
up = 0
down = 0
for al in res:
print al
print list(al.splitRead())
s1, s2 = al.asMatchingStrings()
up += s1.count("-")
down += s2.count("-")
s = []
if len(list(al.splitRead())) > 1:
nums = []
for al1 in al.splitRead():
nums.append(al1.seg_from.left)
nums.append(al1.seg_from.right - 1)
cur_num = 0
cur = al.seg_from.left
for c in s1:
if cur == nums[cur_num] and c != "-":
if cur_num % 2 == 0:
s.append("[")
else:
s.append("]")
cur_num += 1
else:
if cur_num % 2 == 0:
s.append("-")
else:
s.append("+")
if c != "-":
cur += 1
print "".join(s)
print s1
print s2
print up, down