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#!/usr/bin/env python
"""A data structure currently superseded by indel_positions.py.
Multiple Sequence Alignment Using Partial Order Graphs
Bioinformatics 2002 18:452-464
Christopher Lee, Catherine Grasso, & Mark Sharlow
"""
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
def pog_traceback(pogs, aligned_positions):
full_pogs = [getattr(pog, 'full', pog) for pog in pogs]
upto = [0, 0]
align_builder = POGBuilder(pogs)
full_builder = POGBuilder(full_pogs)
full_coords = []
full_count = 0
full_aligned_positions = []
for posn in aligned_positions:
# Find equivalent position in the full POG
# which includes all of the original sites
full_posn = []
for (pog,pos) in zip(pogs, posn):
if pos is not None:
pos = pog.full_coords[pos]
full_posn.append(pos)
# Add all skipped over positions to the full POG
for (dim, pos) in enumerate(full_posn):
if pos is not None:
for p in range(upto[dim]+1, pos+1):
full_builder.addAligned([(dim, p)])
full_count += 1
fp = [None, None]
fp[dim] = p - 1
full_aligned_positions.append(fp)
upto[dim] = pos+1
# Add this position to the full POG
full_merged_origins = []
fap = []
for (dim, pos) in enumerate(full_posn):
if pos is not None:
full_merged_origins.append((dim,pos+1))
fap.append(pos+1)
else:
fap.append(None)
full_builder.addAligned(full_merged_origins)
full_count += 1
full_aligned_positions.append(fap)
# Add this position to the minimal POG which does not
# include sequence which has been called as an insert.
merged_origins = []
for (dim, pos) in enumerate(posn):
if pos is not None:
merged_origins.append((dim,pos+1))
align_builder.addAligned(merged_origins)
full_coords.append(full_count-1)
result_pog = align_builder.getPOG()
result_pog.aligned_positions = aligned_positions
# Add leftover positions to the full POG
for (dim, pos) in enumerate([len(p) for p in full_pogs]):
if pos is not None:
for p in range(upto[dim]+1, pos+1):
full_builder.addAligned([(dim, p)])
full_count += 1
fp = [None, None]
fp[dim] = p - 1
full_aligned_positions.append(fp)
upto[dim] = pos+1
result_pog.full = full_builder.getPOG()
result_pog.full_coords = full_coords
result_pog.full.aligned_positions = full_aligned_positions
return result_pog
class POGBuilder(object):
def __init__(self, children):
self.children = children
self.remap = [{} for child in children]
self.started = [False, False]
self.last = [None, None]
self.result = [[]]
self.origins = [[]]
def addAligned(self, nodes):
pre_merged = set()
origins_merged = []
for (dim, pos) in nodes:
if pos is None:
continue
if not self.started[dim]:
pre_merged.add(0)
self.started[dim] = True
pog = self.children[dim]
pre = pog.pred_sets[pos]
origins_merged.append((dim,pos))
pre = [self.remap[dim].get(n, None) for n in pre]
pre_merged.update([p for p in pre if p is not None])
self.remap[dim][pos] = len(self.result)
self.last[dim] = pos
self.result.append(pre_merged)
self.origins.append(origins_merged)
def getPOG(self):
end = set(self.remap[dim][self.last[dim]] for dim in [0,1])
self.result.append(end)
self.origins.append([])
return POG(self.result, self.origins)
class POG(object):
def __init__(self, pog, origins):
self.origins = origins
if origins is not None:
assert len(origins) == len(pog), (len(origins), len(pog))
for (i, pred_set) in enumerate(pog):
for pre in pred_set:
assert 0 <= pre < i, pog
self.pred_sets = pog
def traceback(self, other, aligned_positions):
return pog_traceback([self, other], aligned_positions)
def asListOfPredLists(self):
return [list(pre) for pre in self.pred_sets]
def getAlignedPositions(self):
return self.aligned_positions
def getFullAlignedPositions(self):
return self.full.aligned_positions
def __len__(self):
return len(self.pred_sets) - 2
def __getitem__(self, index):
if index.start is None:
start = 1
else:
start = index.start + 1
if index.stop is None:
end = len(self.pred_sets)-2 + 1
else:
end = index.stop + 1
pred = [list(pre) for pre in self.pred_sets[start:end]]
origins = ['s'] + list(self.origins[start:end]) + ['e']
before = self.pred_sets[1:start]
after = self.pred_sets[end:]
ends = []
for (i,p) in enumerate(after):
for pre in p:
if pre < end:
ends.append(max(pre-start+1, 0))
pog = [[]] + [[max(0, pre-start+1) for pre in p] for p in pred]
pog.append(ends)
return POG(pog, origins)
def backward(self):
# Switches predecessors / successors
pog = [[]]
for (i,p) in enumerate(self.pred_sets[1:]):
pog.append([])
for pre in p:
pog[pre].append(len(self.pred_sets)-i-2)
pog.reverse()
return POG(pog, None)
def writeToDot(self, dot):
print >>dot, 'digraph POG {'
for (i, preds) in enumerate(self.pred_sets):
#print i, preds
for pred in preds:
print >>dot, ' ', ('node%s -> node%s' % (pred, i))
if i == 0:
label = 'START'
elif i == len(self.pred_sets) - 1:
label = 'END'
else:
label = ','.join(c for c in self.origins[i])
print >>dot, ' ', ('node%s' % i), '[label="%s"]' % label
print >>dot, '}'
print >>dot, ''
class LeafPOG(POG):
def __init__(self, length):
pog = [set([i]) for i in range(length)]
pog = [[]] + pog + [[len(pog)]]
self.pred_sets = pog
self.full = self
self.full_coords = range(len(pog))
self.length = length
cap = [(0, None)]
self.origins = [cap] + [[(0, i)]
for i in range(length)] + [cap]
def __len__(self):
return len(self.pred_sets) - 2
def backward(self):
return LeafPOG(self.length)
def leaf2pog(leaf):
return LeafPOG(len(leaf))
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