'''run as executable to process the pb.dmp.nr.trees.184 trees file and save them to save_path'''
import ivy
import graph_tool.all as gt
import NCBIgraph
import tree_to_graph
import convex_colored_subtrees
import string
ncbiG, ncbiG_tid2v, ncbiG_name2v = NCBIgraph.load_taxonomy_graph("db.xml")
tid2name, name2tid = NCBIgraph.fetch_tid2name_name2tid(ncbiG)
ncbiG_v2tid = ncbiG.vertex_properties['taxid']
Eukaryota_tid = name2tid['Eukaryota']
merged_nodes = NCBIgraph.fetch_mergednodes_dict()
del_nodes = NCBIgraph.fetch_delnodes()
ivy.newick.add_label_chars('/#&-')
save_path = '/home/jstevensstein/Desktop/convex_subtrees_3/'
f = open("pb.dmp.nr.trees.184")
data = open(save_path + "tree_data.txt", "w")
i = 0
for line in f:
try:
i += 1
print i
'''run as executable to load the NCBI hierarchy and associated structures'''
import ivy
import graph_tool.all as gt
import NCBIgraph
import tree_to_graph
import convex_colored_subtrees
ncbiG, ncbiG_tid2v, ncbiG_name2v = NCBIgraph.load_taxonomy_graph("db.xml")
tid2name, name2tid = NCBIgraph.fetch_tid2name_name2tid(ncbiG)
ncbiG_v2tid = ncbiG.vertex_properties['taxid']
merged_nodes = NCBIgraph.fetch_mergednodes_dict()
del_nodes = NCBIgraph.fetch_delnodes()
