for nodeid in taxa:
parentid = node2parent[nodeid]
while nodeid != parentid: #costruiamo un nuovo dizionario per i soli taxa che abbiamo identificato nel campione
ass_node2parent[nodeid] = parentid
nodeid = parentid
parentid = node2parent[nodeid]
node2parentid = {}
for nodeid in ass_node2parent.keys():
parentid = ass_node2parent[nodeid]
# Stores node connections
all_ids.update([nodeid, parentid])
# Creates a new TreeNode instance for each new node in file
n = TreeNode()
# Sets some TreeNode attributes
n.add_feature("name", node2name[nodeid])
n.add_feature("taxid", nodeid)
n.add_feature("Order", node2order[nodeid])
# updates node list and connections
node2parentid[n] = parentid
id2node[nodeid] = n
print len(id2node)
# Reconstruct tree topology from previously stored tree connections
print 'Reconstructing tree topology...'
for node in id2node.itervalues():
parentid = node2parentid[node]
parent = id2node[parentid]
# node with taxid=1 is the root of the tree
if node.taxid == "1":
t = node
def build_tax_tree():
import os
import sys
from string import strip
from ete2 import TreeNode, Tree
#print sys.argv[1]
#if len(sys.argv) == 1:
# print "Usage: taxid2lineage file_with_taxids.txt"
#else:
# f = open(sys.argv[1], 'r')
# This sets Unbuffered stdout/auto-flush
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)
id2node= {}
id2rank={}
node2parentid = {}
all_ids = set([])
all_nodes = []
id2name= {}
# Loads info from NCBI taxonomy files
if os.path.exists("nodes.dmp"):
NODESFILE = open('nodes.dmp')
elif os.path.exists("nodes.dmp.bz2"):
import bz2
NODESFILE = bz2.BZ2File('nodes.dmp.bz2')
else:
print '"nodes.dmp" file is missing. Try to downloaded from: '
if os.path.exists("names_scientific.dmp"):
NAMESFILE = open('names_scientific.dmp')
elif os.path.exists("names_scientific.dmp.bz2"):
import bz2
NAMESFILE = bz2.BZ2File('names_scientific.dmp.bz2')
else:
print '"names_scientific.dmp" file is missing. Try to downloaded from: '
# Reads taxid/names transaltion
#print 'Loading species names from "names_scientific.dmp" file...',
for line in NAMESFILE:
line = line.strip()
fields = map(strip, line.split("|"))
nodeid, name = fields[0], fields[1]
id2name[nodeid] = name
# Reads node connections in nodes.dmp
#print 'Loading node connections form "nodes.dmp" file...',
for line in NODESFILE:
line = line.strip()
fields = map(strip, line.split("|"))
nodeid, parentid,rankid = fields[0], fields[1], fields[2]
id2rank[nodeid]=rankid
if nodeid =="" or parentid == "":
raw_input("Wrong nodeid!")
# Stores node connections
all_ids.update([nodeid, parentid])
# Creates a new TreeNode instance for each new node in file
n = TreeNode()
# Sets some TreeNode attributes
n.add_feature("name", id2name[nodeid])
n.add_feature("taxid", nodeid)
n.add_feature("rank",id2rank[nodeid])
# updates node list and connections
node2parentid[n]=parentid
id2node[nodeid] = n
#print len(id2node)
# Reconstruct tree topology from previously stored tree connections
#print 'Reconstructing tree topology...'
for node in id2node.itervalues():
parentid = node2parentid[node]
parent = id2node[parentid]
if node.taxid == "1":
t = node
else:
parent.add_child(node)
return id2node, id2name
def load_NCBI(species_file, names_file, nodes_file ):
if not os.path.isfile(species_file):
print "ERROR "+species_file+' can\'t be read. Exiting... '
sys.exit(8)
all_wanted_species={} # species_name: taxid (string)
print "Reading wanted species from file: "+species_file
ifile=open(species_file, 'r')
for iline in ifile:
species_name=iline.strip()
all_wanted_species[species_name]=-1
ifile.close()
# This sets Unbuffered stdout/auto-flush
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)
id2node= {}
node2parentid = {}
all_ids = set([])
all_nodes = []
id2name= {}
# Loads info from NCBI taxonomy files
if os.path.exists(nodes_file):
NODESFILE = open(nodes_file)
elif os.path.exists(nodes_file+"bz2"):
import bz2
NODESFILE = bz2.BZ2File(nodes_file+'.bz2')
else:
print nodes_file+' file is missing. '
sys.exit(8)
if os.path.exists(names_file):
NAMESFILE = open(names_file)
elif os.path.exists(names_file+"bz2"):
import bz2
NAMESFILE = bz2.BZ2File(names_file+'.bz2')
else:
print names_file +' file is missing. '
sys.exit(8)
# Reads taxid/names transaltion
print 'Loading species names from "names.dmp" file...',
for line in NAMESFILE:
# lines are redundant. synonyms are on different lines defined by the same id. So, we store only lines with "scientific name".
line = line.strip()
fields = map(strip, line.split("|"))
nodeid, name = fields[0], fields[1]
if all_wanted_species.has_key(name):
all_wanted_species[name]=nodeid
if fields[3]=='scientific name':
#storing name that will appear afterwards in the ete2 node
id2name[nodeid] = name
print len(id2name)
any_species_is_missing=0
for species_name in all_wanted_species:
if all_wanted_species[species_name]==-1:
print "ERROR the species name \""+species_name+"\" was not found!"
any_species_is_missing=1
if any_species_is_missing:
sys.exit(9)
# Reads node connections in nodes.dmp
print 'Loading node connections from "nodes.dmp" file...',
for line in NODESFILE:
line = line.strip()
fields = map(strip, line.split("|"))
nodeid, parentid = fields[0], fields[1]
if nodeid =="" or parentid == "":
raw_input("Wrong nodeid!")
# Stores node connections
all_ids.update([nodeid, parentid])
# Creates a new TreeNode instance for each new node in file
n = TreeNode()
# Sets some TreeNode attributes
n.add_feature("name", id2name[nodeid])
n.add_feature("taxid", nodeid)
# updates node list and connections
node2parentid[n]=parentid
id2node[nodeid] = n
print len(id2node)
# Reconstruct tree topology from previously stored tree connections
print 'Reconstructing tree topology...'
for node in id2node.itervalues():
parentid = node2parentid[node]
parent = id2node[parentid]
# node with taxid=1 is the root of the tree
if node.taxid == "1":
t = node
else:
parent.add_child(node)
return t, id2node, all_wanted_species
for nodeid in taxa:
parentid = node2parent[nodeid]
while nodeid != parentid: #costruiamo un nuovo dizionario per i soli taxa che abbiamo identificato nel campione
ass_node2parent[nodeid] = parentid
nodeid = parentid
parentid = node2parent[nodeid]
node2parentid = {}
for nodeid in ass_node2parent.keys():
parentid = ass_node2parent[nodeid]
# Stores node connections
all_ids.update([nodeid, parentid])
# Creates a new TreeNode instance for each new node in file
n = TreeNode()
# Sets some TreeNode attributes
n.add_feature("name", node2name[nodeid])
n.add_feature("taxid", nodeid)
n.add_feature("Order", node2order[nodeid])
# updates node list and connections
node2parentid[n] = parentid
id2node[nodeid] = n
print len(id2node)
# Reconstruct tree topology from previously stored tree connections
print 'Reconstructing tree topology...'
for node in id2node.itervalues():
parentid = node2parentid[node]
parent = id2node[parentid]
# node with taxid=1 is the root of the tree
if node.taxid == "1":
t = node
