Python Tree.graft方法代码示例

# 需要导入模块: import Tree [as 别名]
# 或者: from Tree import graft [as 别名]

#.........这里部分代码省略.........
		self.unique_stop_sequence = list()
		
		# initialise the tree and branches
		self.tree = Tree()
		self.branches = list()
		
		# initialise other attributes
		self.paths = list() # all tree paths
		self.no_paths = None
		self.frame_paths = dict() # all paths per frame
		self.sorted_frame_paths = dict() # sorted by length
		
		self.frameshift_sequences = dict()
		
		# get the raw start sequence
		self.get_start_sequence()
		if verbose: print >> sys.stderr, "Generated start sequence of length %d..." % len( self.start_sequence )
		
		# get the raw stop sequence
		self.get_stop_sequence()
		if verbose: print >> sys.stderr, "Generated stop sequence of length %d..." % len( self.stop_sequence )
		
		# sanitise the raw stop sequence
		self.sanitise_stop_sequence()
		if verbose: print >> sys.stderr, "Generated unique stop sequence of length %d..." % len( self.unique_stop_sequence )
		
		# create a list of branches
		self.create_branches()
		if verbose: print >> sys.stderr, "Creating branches..."
		
		# graft the branches to the tree
		if verbose: print >> sys.stderr, "Grafting branches to tree..."
		for B in self.branches:
			self.tree.graft( B, verbose )
		
		# get the paths
		self.paths = self.tree.get_paths( simplify=True )
		self.no_paths = len( self.paths )
		if verbose: print >> sys.stderr, "Found %d paths in tree." % self.no_paths
		
		# get paths per frame
		for frame in xrange( 3 ):
			self.frame_paths[frame] = self.tree.get_frame_paths( frame )
			
		# sort frame paths by length
		sorted_frame_paths = dict()
		for frame in xrange( 3 ):
			for path in self.frame_paths[frame]:
				path_len = len( path )
				if path_len not in sorted_frame_paths:
					sorted_frame_paths[path_len] = [ path ]
				else:
					sorted_frame_paths[path_len] += [ path ]
		
		all_path_len = sorted_frame_paths.keys()
		all_path_len.sort()
		
		for a in all_path_len:
			if a not in self.sorted_frame_paths:
				self.sorted_frame_paths[a] = sorted_frame_paths[a]
			else:
				self.sorted_frame_paths[a] += sorted_frame_paths[a]
		
		# get all frameshift sequences
		for frame in self.frame_paths:
			for path in self.frame_paths[frame]:

# 需要导入模块: import Tree [as 别名]
# 或者: from Tree import graft [as 别名]
def main():
	s = RandomFSSequence( no_of_shifts=2, min_length=50, max_length=100 )
	s.generate()
	
	print s.info( "without UGA" )
	
	# a Sequence object
	#t = BiologicalSequence( s.sequence )
	#t = BiologicalSequence( "GCTGGTGGGGTAGCAGGTGTTTCTGTTGACTTGATATTATTTCCTCTGGATACCATTAAAACCAGGCTGCAGAGTCCCCAAGGATTTAGTAAGGCTGGTGGTTTTCATGGAATATATGCTGGCGTTCCTTCTGCTGCTATTGGATCCTTTCCTAATG" )
	t = BiologicalSequence( "AAATGACGAACACAGAGGAAAGAAGAGAGGCAACTGCTGAGGTCCCCTAGGCCTTTGAGAAAACGGAGTTGTACCTTTGGCAACATAAGTGCATATCTACAAGAAAGGCGATAATGTAGACACCAAGGGAATGGGTACTGTCCAAAAAGAAATGCCTCACAAATGTCACCATGGCAAAACTAAAAGAGTCTACAAAGTTACCTAGCATGCTGTTGGCATCATTGTAAACAAACAAGTTAAGGGCAAGATTCTTGCCAAGAGAATTAATATGCATATTGGGCATATTAAGCACTCTAAGAGCCAAGATGATTTCCTGAAAGTGTGTGAAGGAAAATAACCAGCATAAAGAGGGAAGCTAAAGAGAAACCTGAAGCTGCAGCCTGTTCCACCCAGAGAAGCACACTTTGTAAGAACCAATGAAAAGGAGCCTGAGCTGCTGGAGTCTATTAACTGAATTCATGGT" )
	#t = RandomSequence( 100 )
	#t.generate()
	# t.stops.append( "UGA" )
		
	print 
	print t.info()
	for i in xrange( 3 ):
		print t.colour_frame( i, sep="" )
	print "         |"*(( s.length )//10 )
	
	t.get_stop_sequence()
	
	print "The raw stop sequence (%s)..." % len( t.stop_sequence )
	print t.stop_sequence
	print
	
	# now to create paths
	p = Paths( t.stop_sequence )
	
	print "The sanitised stop sequence (%d)..." % len( p.unique_frame_sequence )
	print p.unique_frame_sequence
	print
	
	print "Create the branches from the stop sequence..."
	p.create_branches()
	print
	
	print "Create a tree..."
	T = Tree()
	
	print "View and graft the branches..."
	for B in p.branches:
		#print B
		T.graft( B )
	
	print T
	
	print "Build the paths..."
	
	paths = T.get_paths( simplify=True )
	print paths
	print
	
	for frame in xrange( 3 ):
		print "Frameshift sequences for frame %d:" % frame
		for j in T.get_frame_paths( frame ):
			print len( j ), " : ", j
		print
	
	"""
	frameshifted_sequence, fragments = t.frameshift_from_path( all_paths[0] )
	q = BiologicalSequence( s.sequence )
	print s.info()
	for i in xrange( 3 ):
		print q.colour_frame( i, sep="" )
	print "         |"*(( s.length )//10 )
	print
	
	print " ".join( fragments )
	print
	
	print t.path
	print t.colour_frameshifted_sequence( sep="" )
	print "         |"*(( s.length )//10 )
	"""
	
	for i in xrange( 3 ):
		all_paths = T.get_frame_paths( i )
		for a in all_paths:
			frameshifted_sequence, fragments, frameshift_signals = t.frameshift_from_path( a )
			print t.path
			print t.colour_frameshifted_sequence( sep="" )
			print " ".join( fragments )
			print " ".join( frameshift_signals )
			print

# 需要导入模块: import Tree [as 别名]
# 或者: from Tree import graft [as 别名]
def main():
	t = Tree()
	b1 = Branch( Node( 1, 0 ), Node( 0, 1 ), Node( 2, 2 ))
	t.graft( b1 )
	print t
	print
	b2 = Branch( Node( 0, 1 ), Node( 2, 2 ), Node( 1, 4 ))
	t.graft( b2 )
	print t
	print
	b3 = Branch( Node( 2, 2 ), Node( 1, 4 ), Node( 0, 5 ))
	t.graft( b3 )
	print t
	print
	b4 = Branch( Node( 1, 4 ), Node( 0, 5 ), Node( 2, -1 ))
	t.graft( b4 )
	print t
	print
	b5 = Branch( Node( 0, 5 ), Node( 1, 6 ), Node( 2, -1 ))
	t.graft( b5 )
	print t
	print
	b6 = Branch( Node( 1, 6 ), Node( 0, -1 ), Node( 2, -1 ))
	t.graft( b6 )
	print t
	print
	
	paths = t.get_paths()
	print paths
	simple_paths = [ map( lambda x: ( x.name, x.value ), path ) for path in paths ]
	print len( paths )
	for p in simple_paths:
		print p