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 __init__(self, seqs, num_support_position, Cell2PPls, initial_seq_builder, OutFileName):
self.cut = num_support_position
Align = MegaAlignment()
self.ini_seqs_builder = seqs
self.CellLs, self.Cell2Seq = Align.name2seq(seqs)
self.SNVnum = len(self.Cell2Seq[self.CellLs[0]])
self.InMeg = Align.AddNormal(seqs)
IniCellLs, self.Cell2iniSeq = Align.name2seq(initial_seq_builder)
self.Cell2PPls = Cell2PPls
self.out_file_name = OutFileName