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import sys
import numpy as np
from .utils import Strand, log, breakpoint, new_strand, rev_cmpl
# ------------------------------------------------------------------------
# Node class: one visit along a path
class Node(object):
"""docstring for Node"""
def __init__(self, blk, num, strand):
self.blk = blk
self.num = num
self.strand = strand
def __str__(self):
return f"({self.blk}, {self.num}, {self.strand})"
def __repr__(self):
return str(self)
def __eq__(self, other):
return self.blk.id == other.blk.id and self.strand == other.strand
def __hash__(self):
return hash((self.blk.id, self.strand))
@classmethod
def from_dict(cls, d, blks):
N = Node()
N.blk = blks[d['id']]
N.num = d['num']
N.strand = Strand(d['strand'])
return N
def to_dict(self):
return {'id': self.blk.id, 'num': self.num, 'strand': int(self.strand)}
def length(self, name):
return self.blk.len_of(name, self.num)
# ------------------------------------------------------------------------
# Path class: (circular) list of blocks
class Path(object):
"""docstring for Path"""
def __init__(self, name, nodes, offset):
super(Path, self).__init__()
self.name = name
self.nodes = nodes if isinstance(nodes, list) else [nodes]
self.offset = offset
self.position = np.cumsum([0] + [n.length(name) for n in self.nodes])
def __str__(self):
return f"{self.name}: {[str(n) for n in self.nodes]}"
def __repr__(self):
return str(self)
@classmethod
def from_dict(cls, d):
P = Path()
P.name = d['name']
P.offset = d['offset']
P.nodes = [Node.from_dict(n) for n in d['nodes']]
return P
def to_dict(self):
return {'name': self.name, 'offset': self.offset, 'nodes': [n.to_dict() for n in self.nodes]}
def blocks(self):
return set([n.blk for n in self.nodes])
def sequence(self, verbose=False):
seq = ""
for n in self.nodes:
s = n.blk.extract(self.name, n.num, strip_gaps=True, verbose=verbose)
if n.strand == Strand.Plus:
seq += s
else:
seq += rev_cmpl(s)
if self.offset != 0:
seq = seq[self.offset:] + seq[:self.offset]
return seq
def rm_nil_blks(self):
good, popped = [], set()
for i, n in enumerate(self.nodes):
if n.blk.id in popped:
continue
if n.blk.is_empty(self.name, n.num):
if (self.name, n.num) not in n.blk.muts:
breakpoint("malformed mutation bookkeeping!")
n.blk.muts.pop((self.name, n.num))
else:
good.append(i)
if not n.blk.has(self.name):
popped.add(n.blk.id)
self.nodes = [self.nodes[i] for i in good]
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
# TODO: debug cases w/ multiple runs
def merge(self, start, stop, new):
N = 0
while True:
ids = [n.blk.id for n in self.nodes]
try:
i, j = ids.index(start[0]), ids.index(stop[0])
if N > 0:
breakpoint("HIT")
if self.nodes[i].strand == start[1]:
beg, end, s = i, j, Strand.Plus
else:
beg, end, s = j, i, Strand.Minus
if beg < end:
self.nodes = self.nodes[:beg] + [Node(new, N, s)] + self.nodes[end+1:]
else:
self.offset += sum(n.blk.len_of(self.name, N) for n in self.nodes[beg:])
self.nodes = [Node(new, N, s)] + self.nodes[end+1:beg]
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
N += 1
except:
return
def replace(self, blk, tag, new_blks, blk_map):
new = []
for n in self.nodes:
if n.blk.id == blk.id and n.num == tag[1]:
os = n.strand
mk = lambda b,ns,merged: Node(b, blk_map[b.id][blk.id][tag][1], new_strand(os, ns)) if merged else Node(b, n.num, new_strand(os, ns))
tmp = [mk(blk,ns,flag) for blk, ns, flag in new_blks]
if os == Strand.Minus:
tmp = tmp[::-1]
new.extend(tmp)
else:
new.append(n)
self.nodes = new
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
def position_of(self, blk, num):
index = { n.num:i for i, n in enumerate(self.nodes) if n.blk == blk }
if not num in index:
return None
return (self.position[index[num]], self.position[index[num]+1])
# TODO: pull out common functionality into a helper function
# TODO: merge with other sequence function
def sequence_range(self, start=None, stop=None):
beg = start or 0
end = stop or self.position[-1]
l, r = "", ""
# if start == 159 and stop == 3659:
# breakpoint("test")
if beg < 0:
if len(self.nodes) > 1:
l = self.sequence_range(self.position[-1]+beg,self.position[-1])
beg = 0
if end > self.position[-1]:
if len(self.nodes) > 1:
r = self.sequence_range(0,end-self.position[-1])
end = self.position[-1]
if beg > end:
beg, end = end, beg
i = np.searchsorted(self.position, beg, side='right') - 1
j = np.searchsorted(self.position, end, side='left')
m = ""
if i < j:
if j >= len(self.position):
breakpoint("what?")
if i == j - 1:
m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):(end-self.position[i])]
else:
m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):]
for n in self.nodes[i+1:j-1]:
m += n.blk.extract(self.name, n.num)
n = self.nodes[j-1]
b = n.blk.extract(self.name, n.num)
m += b[0:(end-self.position[j-1])]
return l + m + r
def __getitem__(self, index):
if isinstance(index, slice):
beg = index.start or 0
end = index.stop or self.position[-1]
l, r = [], []
if beg < 0:
if len(self.nodes) > 1:
l = self[(self.position[-1]+beg):self.position[-1]]
beg = 0
if end > self.position[-1]:
if len(self.nodes) > 1:
r = self[0:(end-self.position[-1])]
end = self.position[-1]
if beg > end:
beg, end = end, beg
i = np.searchsorted(self.position, beg, side='right') - 1
j = np.searchsorted(self.position, end, side='left')
if i > j:
breakpoint(f"not sorted, {beg}-{end}")
return l + [n.blk for n in self.nodes[i:j]] + r
elif isinstance(index, int):
i = np.searchsorted(self.position, index, side='right') - 1
return self.nodes[i].blk
else:
raise ValueError(f"type '{type(index)}' not supported as index")
def __len__(self):
return self.position[-1]
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