def get_cfg_db(self):
db = connect_to_mysql()
cursor = db.cursor()
qry = "show databases like'%exoloc%config%'"
rows = search_db (cursor, qry, verbose=False)
if (not rows):
print "config database not found (by guessing)"
print "pls fix config_reader.py"
cursor.close()
db.close()
exit (1)
self.cfg_db_name = rows[0][0]
#print "reading config from ", self.cfg_db_name
cursor.close()
db.close()
qry_leaf = leaf
tree.build(cursor)
#find cousins for the qry leaf (recursively)
cousins = find_cousins(qry_leaf)
return [qry_species] + cousins
#####################################
if __name__ == '__main__':
local_db = False
if local_db:
db = connect_to_mysql()
else:
db = connect_to_mysql(user="******",
passwd="sqljupitersql",
host="jupiter.private.bii",
port=3307)
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species(cursor)
tree = Tree()
for species in all_species:
tree.add(cursor, species)
tree.build(cursor)
print tree.nhx_string()
def load_cfg(self):
'''
Load a configuration file and add the
key, value pairs to the internal configuration dictionary
'''
db = connect_to_mysql(self.user, self.passwd, self.host, self.port)
cursor = db.cursor()
switch_to_db (cursor, self.cfg_db_name)
# utils
qry = "select name, path from util_path"
rows = search_db (cursor, qry, verbose=False)
if (not rows):
print "no util_path info in %s" % self.cfg_db_name
cursor.close()
db.close()
sys.exit (1)
for row in rows:
[name, path] = row
if (self.check and not os.path.exists(path)):
print path, " not found "
sys.exit (1)
self.util_path[name] = path
# utils
qry = "select name, path from dir_path"
rows = search_db (cursor, qry, verbose=False)
if (not rows):
print "no dir_path info in %s" % self.cfg_db_name
cursor.close()
db.close()
sys.exit (1)
for row in rows:
[name, path] = row
if (self.check and not os.path.exists(path)):
print path, " not found "
sys.exit (1)
self.dir_path[name] = path
# utils
qry = "select name, value from parameter"
rows = search_db (cursor, qry, verbose=False)
if (not rows):
print "no dir_path info in %s" % self.cfg_db_name
cursor.close()
db.close()
sys.exit (1)
for row in rows:
[name, value] = row
if value.isdigit():
value= int(value)
else:
try:
value = float(value)
except:
pass
self.parameter_value[name] = value
cursor.close()
db.close()
tree = Tree()
for species in all_species:
leaf = Node(species)
tree.leafs.append(leaf)
if leaf.name == qry_species:
qry_leaf = leaf
tree.build(cursor)
#find cousins for the qry leaf (recursively)
cousins = find_cousins (qry_leaf)
return [qry_species]+cousins
#####################################
if __name__ == '__main__':
local_db = False
db = connect_to_mysql()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
tree = Tree()
for species in all_species:
tree.add(cursor, species)
tree.build(cursor)
print tree.nhx_string()
