def __mapping_promoter(self):
with open(self.PROMOTOR_OUT, 'r') as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.tRNA(name, strand, start, end, feature, sequence)
self.session.add(obj)
self.session.commit()
def generate_db():
# for debugging, please set echo=True
engine = species.create_engine('sqlite:///db/ecli.db', echo=False)
# create table to DB
species.metadata.create_all(engine)
# create session object
Session = species.sessionmaker()
Session.configure(bind=engine)
# session start!
session = Session()
# data registration to sqlite3
with open("data/CDS_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.CDS(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/rRNA_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.rRNA(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/tRNA_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.tRNA(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/promoter_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.Promoter(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/terminator_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature,
sequence) = line[:-1].split("\t")
obj = species.Terminator(name, strand, start, end, feature,
sequence)
session.add(obj)
session.commit()
def generate_db():
# for debugging, please set echo=True
engine = species.create_engine('sqlite:///db/ecli.db', echo=False)
# create table to DB
species.metadata.create_all(engine)
# create session object
Session = species.sessionmaker()
Session.configure(bind=engine)
# session start!
session = Session()
# data registration to sqlite3
with open("data/CDS_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature, sequence) = line[:-1].split("\t")
obj = species.CDS(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/rRNA_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature, sequence) = line[:-1].split("\t")
obj = species.rRNA(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/tRNA_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature, sequence) = line[:-1].split("\t")
obj = species.tRNA(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/promoter_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature, sequence) = line[:-1].split("\t")
obj = species.Promoter(name, strand, start, end, feature, sequence)
session.add(obj)
with open("data/terminator_annotation.tbl", "r") as f:
for line in f:
(name, strand, start, end, feature, sequence) = line[:-1].split("\t")
obj = species.Terminator(name, strand, start, end, feature, sequence)
session.add(obj)
session.commit()