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()