def adjust_cell_genotype1(self):
Align = MegaAlignment()
tree_builder = MegaML()
tree_analyzer = TreeAnalizer()
status = tree_builder.do_mega_ml(self.InMeg, 'Noresun')
if status == True:
tree1 = tree_builder.newick_trees
else:
print('failed to run megaML')
Tree_Rooted1 = tree_analyzer.RootTree_rootBottom(tree1, 'Normal')
InferAncestor = MegaAncestor()
InferAncestor.alignment_file = self.InMeg
InferAncestor.input_tree_file = Tree_Rooted1
self.ancestor_states, self.offspring2ancestor, cell2code, self.code2cell = InferAncestor.retrieve_ancestor_states(
)
ancestor2offspring, self.node2cellclade = InferAncestor.report_anc2dec_lin(
)
for code in self.code2cell:
if self.code2cell[code].find('Node_') == -1:
self.node2cellclade[code] = [self.code2cell[code]]
self.Cellclade_withSupport2SupportCount = self.count_support3()
self.Clone2CellLs = self.get_clone3()
def __init__(self, id0, seqs, PPcut): #seqs is list format of mega alignment
self.PPcut=PPcut
Align = MegaAlignment()
tree_builder = MegaML()
tree_analyzer = TreeAnalizer()
self.InMeg = Align.AddNormal(seqs)
status = tree_builder.do_mega_ml(self.InMeg, id0)
if status == True:
tree = tree_builder.newick_trees
else:
print 'failed to run megaML'
self.Tree_rooted = tree_analyzer.RootTree(tree, 'Normal')
def save_without_cloneID(self, Cell2BestSeq):
Align = MegaAlignment()
tree_builder = MegaML()
tree_analyzer = TreeAnalizer()
BestSeq_builder_3 = Align.UpMeg(Cell2BestSeq, self.CellLs)
Align.save_mega_alignment_to_file(self.out_file_name,
BestSeq_builder_3)
def Compute_PP(self):
Align = MegaAlignment()
tree_analyzer = TreeAnalizer()
PP_builder = MegaPP()
Input=self.Tree_rooted
print 'input for inferring missing',Input
Meg=self.InMeg
NameOrder, self.Cell2megSeq=Align.name2seq_with_normal(Meg)
id = 'All_alignment'
status = PP_builder.do_mega_pp(self.InMeg, self.Tree_rooted, id)
if status == True:
self.Cell2PP = PP_builder.retrieve_pp_states()
else:
print 'failed to run megaPP'