def build(self, cursor):
switch_to_db(cursor, get_compara_name(cursor))
for leaf in self.leafs:
leaf.tax_id = species2taxid(cursor, leaf.name)
leaf.is_leaf = True
self.node[leaf.tax_id] = leaf
# build the tree using ncbi_tax.nodes
# fill in the names using ncbi_tax.names
switch_to_db(cursor, get_ncbi_tax_name(cursor))
for leaf in self.leafs:
parent_id = taxid2parentid(cursor, leaf.tax_id)
leaf.parent_id = parent_id
current_id = leaf.tax_id
# move to the root
while current_id:
current_node = self.node[current_id]
parent_id = taxid2parentid(cursor, parent_id)
if (not parent_id or current_id == parent_id):
current_node.is_root = True
self.root = self.node[current_id]
current_id = None
else:
# does parent exist by any chance
if self.node.has_key(parent_id):
parent_node = self.node[parent_id]
parent_node.children.append(current_node)
# we are done here
current_id = None
else: # make new node
parent_name = taxid2name(cursor, parent_id)
parent_node = Node(parent_name)
parent_node.tax_id = parent_id
# grampa:
parent_node.parent_id = taxid2parentid(
cursor, parent_id)
parent_node.children.append(current_node)
self.node[parent_id] = parent_node
# attach the current node to the parent
current_id = parent_id
# shortcircuit nodes with a single child
new_root = self.root.__cleanup__()
if (new_root):
new_root.is_root = True
self.root = new_root
del_ids = []
for node_id, node in self.node.iteritems():
if node.is_leaf:
continue
if (not node.children):
del_ids.append(node_id)
for node_id in del_ids:
del self.node[node_id]
self.__set_parent_ids__(self.root)
def find_mammals(cursor, trivial_name_list):
mammals = []
for trivial_name in trivial_name_list:
switch_to_db(cursor, get_compara_name(cursor))
tax_id = trivial2taxid (cursor, trivial_name)
parent_id = taxid2parentid (cursor, tax_id)
tax_id = parent_id
is_mammal = False
while tax_id:
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'";
rows = search_db (cursor, qry)
if rows and rows[0][0]:
if 'mammal' in rows[0][0].lower():
is_mammal = True
break
elif 'vertebrat' in rows[0][0].lower():
# if the thing wasa mammal, we would have found it by now
is_mammal = False
break
parent_id = taxid2parentid (cursor, tax_id)
if parent_id and parent_id>1:
tax_id = parent_id
else:
tax_id = None
if is_mammal:
mammals.append(trivial_name)
return mammals
def find_mammals(cursor, trivial_name_list):
mammals = []
for trivial_name in trivial_name_list:
switch_to_db(cursor, get_compara_name(cursor))
tax_id = trivial2taxid(cursor, trivial_name)
parent_id = taxid2parentid(cursor, tax_id)
tax_id = parent_id
is_mammal = False
while tax_id:
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'"
rows = search_db(cursor, qry)
if rows and rows[0][0]:
if 'mammal' in rows[0][0].lower():
is_mammal = True
break
elif 'vertebrat' in rows[0][0].lower():
# if the thing wasa mammal, we would have found it by now
is_mammal = False
break
parent_id = taxid2parentid(cursor, tax_id)
if parent_id and parent_id > 1:
tax_id = parent_id
else:
tax_id = None
if is_mammal:
mammals.append(trivial_name)
return mammals
def build (self, cursor):
switch_to_db(cursor, get_compara_name(cursor))
for leaf in self.leafs:
leaf.tax_id = species2taxid (cursor, leaf.name)
leaf.is_leaf = True
self.node[leaf.tax_id] = leaf
# build the tree using ncbi_tax.nodes
# fill in the names using ncbi_tax.names
switch_to_db(cursor, get_ncbi_tax_name(cursor))
for leaf in self.leafs:
parent_id = taxid2parentid (cursor, leaf.tax_id)
leaf.parent_id = parent_id
current_id = leaf.tax_id
# move to the root
while current_id:
current_node = self.node[current_id]
parent_id = taxid2parentid (cursor, parent_id)
if (not parent_id or current_id == parent_id):
current_node.is_root = True
self.root = self.node[current_id]
current_id = None
else:
# does parent exist by any chance
if self.node.has_key(parent_id):
parent_node = self.node[parent_id]
parent_node.children.append(current_node)
# we are done here
current_id = None
else: # make new node
parent_name = taxid2name(cursor, parent_id)
parent_node = Node(parent_name)
parent_node.tax_id = parent_id
# grampa:
parent_node.parent_id = taxid2parentid (cursor, parent_id)
parent_node.children.append(current_node)
self.node[parent_id] = parent_node
# attach the current node to the parent
current_id = parent_id
# shortcircuit nodes with a single child
new_root = self.root.__cleanup__()
if (new_root):
new_root.is_root = True
self.root = new_root
del_ids = []
for node_id, node in self.node.iteritems():
if node.is_leaf:
continue
if (not node.children):
del_ids.append(node_id)
for node_id in del_ids:
del self.node[node_id]
self.__set_parent_ids__ (self.root)
def add(self, cursor, name):
leaf = Node(name)
# get tax ids from the gene_db table in compara database
switch_to_db(cursor, get_compara_name(cursor))
leaf.tax_id = species2taxid(cursor, leaf.name)
leaf.is_leaf = True
self.leafs.append(leaf)
self.node[leaf.tax_id] = leaf
def add(self, cursor, name):
leaf = Node(name)
# get tax ids from the gene_db table in compara database
switch_to_db(cursor, get_compara_name(cursor))
leaf.tax_id = species2taxid (cursor, leaf.name)
leaf.is_leaf = True
self.leafs.append(leaf)
self.node[leaf.tax_id] = leaf
def get_common_name (cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
tax_id = species2taxid (cursor, species)
switch_to_db(cursor,get_ncbi_tax_name (cursor))
qry = "select name_txt from names where "
qry += "tax_id = %d and " % tax_id
qry += "name_class = 'genbank common name'"
rows = search_db (cursor, qry)
if rows:
if ('ERROR' in rows[0]):
search_db (cursor, qry, verbose = True)
return ""
else:
return rows[0][0]
return ""
def get_common_name(cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
tax_id = species2taxid(cursor, species)
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select name_txt from names where "
qry += "tax_id = %d and " % tax_id
qry += "name_class = 'genbank common name'"
rows = search_db(cursor, qry)
if rows:
if ('ERROR' in rows[0]):
search_db(cursor, qry, verbose=True)
return ""
else:
return rows[0][0]
return ""
