-
Notifications
You must be signed in to change notification settings - Fork 1
/
test_hdf5.py
23 lines (19 loc) · 695 Bytes
/
test_hdf5.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
import logging
import sys
FORMAT = '%(asctime)-20s\t%(levelname)s\t%(name)-25s\t%(message)s'
logging.basicConfig(level=logging.DEBUG,format=FORMAT)
from PyMAF import get_track
from PyMAF.maf_hdf5 import MAFBlockDB
db = MAFBlockDB('/scratch/data/maf/mm10_60way/maf/chrM.maf.hdf5')
for x in db.query_interval('mm10', 'chrM', 0, 9):
print ">>>block"
for y in x:
print str(y)
#for x in db.query_interval('mm10', 'chrM', 65, 100):
#print ">>>block"
#for y in x:
#print str(y)
sys.exit(1)
maf = get_track('/scratch/data/genomes', '/scratch/data/maf/mm10_60way/maf', 'mm10')
print maf.get_oriented('chrM', 15, 50, '+')
print maf.get_oriented('chrM', 15, 50, '+')