def sqlite_enabled(): """ Detects whether sqlite3 is functional on the current system """ from pygr.sqlgraph import import_sqlite try: sqlite = import_sqlite() # from 2.5+ stdlib, or pysqlite2 except ImportError, exc: msg = 'sqlite3 error: %s' % exc warn(msg) return False
import os from pygr import sqlgraph, annotation as anno sqlite = sqlgraph.import_sqlite() CREATE_SCHEMA = '''CREATE TABLE annotations (syn TEXT PRIMARY KEY, name TEXT, seq_id TEXT, start INT, stop INT, orientation INT, description TEXT, type TEXT DEFAULT 'gene'); ''' CREATE_SCHEMA_IG = '''CREATE TABLE ig_annotations (k INTEGER PRIMARY KEY, prev_gene_id INT, next_gene_id INT, name TEXT, seq_id TEXT, start INT, stop INT, type TEXT DEFAULT 'intergenic'); ''' class BagsAnnotationMaker(object): def __init__(self, filename, initialize=True): if initialize: