def merge_chunks_multicore(chunks, db):
if len(chunks) <= 1:
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "indexing final database."
shutil.move(chunks[0], db)
main_conn = sqlite3.connect(db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
return db
else:
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "merging", len(chunks), "chunks."
procs = []
sub_merges = get_chunks_to_merge(chunks)
tmp_dbs = get_temp_dbs(len(sub_merges),
os.path.dirname(sub_merges[0][0]))
for sub_merge, tmp_db in zip(sub_merges, tmp_dbs):
cmd = get_merge_chunks_cmd(sub_merge, tmp_db)
procs.append(subprocess.Popen(cmd, shell=True))
wait_until_finished(procs)
cleanup_temp_db_files(chunks)
merge_chunks_multicore(tmp_dbs, db)
def merge_chunks_multicore(chunks, db):
if len(chunks) <= 1:
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "indexing final database."
shutil.move(chunks[0], db)
main_conn = sqlite3.connect(db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
return db
else:
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "merging", len(chunks), "chunks."
procs = []
sub_merges = get_chunks_to_merge(chunks)
tmp_dbs = get_temp_dbs(len(sub_merges), os.path.dirname(sub_merges[0][0]))
for sub_merge, tmp_db in zip(sub_merges, tmp_dbs):
cmd = get_merge_chunks_cmd(sub_merge, tmp_db)
procs.append(subprocess.Popen(cmd, shell=True))
wait_until_finished(procs)
cleanup_temp_db_files(chunks)
merge_chunks_multicore(tmp_dbs, db)
def build_indices_and_disconnect(self):
"""
Create the db table indices and close up
db connection
"""
# index our tables for speed
database.create_indices(self.c)
# commit data and close up
database.close_and_commit(self.c, self.conn)
def build_indices_and_disconnect(self):
"""
Create the db table indices and close up
db connection
"""
# index our tables for speed
database.create_indices(self.c)
# commit data and close up
database.close_and_commit(self.c, self.conn)
def finalize_merged_db(tmp_db, db):
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "indexing final database."
main_conn = sqlite3.connect(tmp_db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
shutil.move(tmp_db, db)
def finalize_merged_db(tmp_db, db):
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
print st, "indexing final database."
main_conn = sqlite3.connect(tmp_db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
gemini_db.add_max_aaf(main_curr)
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
shutil.move(tmp_db, db)
def merge_db_chunks(args):
# open up a new database
if os.path.exists(args.db):
os.remove(args.db)
gemini_db.create_tables(
args.db,
gemini_load_chunk.get_extra_effects_fields(args) if args.vcf else [])
main_conn = sqlite3.connect(args.db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
databases = []
for database in args.chunkdbs:
databases.append(database)
for idx, database in enumerate(databases):
db = database[0]
append_variant_info(main_curr, db)
# we only need to add these tables from one of the chunks.
if idx == 0:
append_sample_genotype_counts(main_curr, db)
append_sample_info(main_curr, db)
append_resource_info(main_curr, db)
append_version_info(main_curr, db)
append_vcf_header(main_curr, db)
append_gene_summary(main_curr, db)
append_gene_detailed(main_curr, db)
else:
update_sample_genotype_counts(main_curr, db)
if args.index:
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
def merge_db_chunks(args):
# open up a new database
if os.path.exists(args.db):
os.remove(args.db)
main_conn = sqlite3.connect(args.db)
main_conn.isolation_level = None
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
# create the gemini database tables for the new DB
gemini_db.create_tables(main_curr, gemini_load_chunk.get_extra_effects_fields(args) if args.vcf else [])
databases = []
for database in args.chunkdbs:
databases.append(database)
for idx, database in enumerate(databases):
db = database[0]
append_variant_info(main_curr, db)
# we only need to add these tables from one of the chunks.
if idx == 0:
append_sample_genotype_counts(main_curr, db)
append_sample_info(main_curr, db)
append_resource_info(main_curr, db)
append_version_info(main_curr, db)
append_vcf_header(main_curr, db)
append_gene_summary(main_curr, db)
append_gene_detailed(main_curr, db)
else:
update_sample_genotype_counts(main_curr, db)
if args.index:
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()
def merge_db_chunks(args):
# open up a new database
if os.path.exists(args.db):
os.remove(args.db)
main_conn = sqlite3.connect(args.db)
main_conn.isolation_level = None
main_conn.row_factory = sqlite3.Row
main_curr = main_conn.cursor()
main_curr.execute('PRAGMA synchronous = OFF')
main_curr.execute('PRAGMA journal_mode=MEMORY')
# create the gemini database tables for the new DB
gemini_db.create_tables(main_curr)
databases = []
for database in args.chunkdbs:
databases.append(database)
for idx, database in enumerate(databases):
db = database[0]
append_variant_info(main_curr, db)
# we only need to add these tables from one of the chunks.
if idx == 0:
append_sample_genotype_counts(main_curr, db)
append_sample_info(main_curr, db)
append_resource_info(main_curr, db)
append_version_info(main_curr, db)
else:
update_sample_genotype_counts(main_curr, db)
gemini_db.create_indices(main_curr)
main_conn.commit()
main_curr.close()