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
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:
