def __init__(self):
self.guided_ends = False
self.guided_assembly = False
self.transfrags = []
self.ref_transfrags = []
self.chrom = None
self.start = None
self.end = None
self.strand = None
self.tree_starts = IntervalTree()
self.tree_ends = IntervalTree()
self.ref_start_sites = set()
self.ref_stop_sites = set()
self.start_sites = set()
self.stop_sites = set()
self.expr_data = None
self.node_bounds = None
self.G = None
def _add_transfrags(self, transfrags):
self.transfrags = []
self.ref_transfrags = []
self.chrom = None
self.start = None
self.end = None
self.strand = None
self.ref_start_sites = set()
self.ref_stop_sites = set()
self.tree_starts = IntervalTree()
self.tree_ends = IntervalTree()
for t in transfrags:
if self.chrom is None:
self.chrom = t.chrom
elif self.chrom != t.chrom:
raise TacoError('chrom mismatch')
if self.strand is None:
self.strand = t.strand
elif self.strand != t.strand:
raise TacoError('strand mismatch')
if self.start is None:
self.start = t.start
else:
self.start = min(t.start, self.start)
if self.end is None:
self.end = t.end
else:
self.end = max(t.end, self.end)
if t.is_ref:
self.ref_start_sites.add(t.txstart)
self.ref_stop_sites.add(t.txstop)
self.ref_transfrags.append(t)
else:
self._add_to_interval_trees(t)
self.transfrags.append(t)
self.ref_start_sites = sorted(self.ref_start_sites)
self.ref_stop_sites = sorted(self.ref_stop_sites)
