)
# if no arguments, print usage and exit
if len(sys.argv) < 2:
print version
print
parser.print_usage()
print
print "Use -h for details."
sys.exit(2)
# parse arguments
args = parser.parse_args()
# instantiate database and load knowledge file, if any
db = loki_db.Database(testing=args.test_data, updating=((args.update != None) or (args.update_except != None)))
db.setVerbose(args.verbose)
db.attachDatabaseFile(args.knowledge)
# list sources?
if args.list_sources != None:
srcSet = set()
for srcList in args.list_sources:
srcSet |= set(srcList)
if (not srcSet) or ('+' in srcSet):
print "available source loaders:"
srcSet = set()
else:
print "source loader options:"
moduleVersions = db.getSourceModuleVersions(srcSet)
moduleOptions = db.getSourceModuleOptions(srcSet)
if mapped_size / float(region[1] - region[0]) >= self._minFrac:
mapped_reg = (first_seg[5], new_start, new_end)
return mapped_reg
if __name__ == "__main__":
from loki import loki_db
if len(sys.argv) < 5:
print "usage: %s <input> <lokidb> <output> <unmap> [oldhg=19] [newhg=38]" % (
sys.argv[0], )
sys.exit(2)
db = loki_db.Database(sys.argv[2])
old = int(sys.argv[5]) if (len(sys.argv) > 5) else 19
new = int(sys.argv[6]) if (len(sys.argv) > 6) else 38
#lo = liftOver(db, old, new, False)
f = (sys.stdin if (sys.argv[1] == '-') else file(sys.argv[1], 'r'))
m = (sys.stdout if (sys.argv[3] == '-') else file(sys.argv[3], 'w'))
u = (sys.stderr if (sys.argv[4] == '-') else file(sys.argv[4], 'w'))
def generateInputs(f):
for l in f:
wds = l.split()
if wds[0].lower().startswith('chr'):
wds[0] = wds[0][3:]
yield (l.strip().replace(" ", ":").replace("\t", ":"),
db.chr_num.get(wds[0], -1), int(wds[1]), int(wds[2]), None)
# if m < 1024*1024*1024:
# print "WARNING: ignoring '%s' memory allotment, the updater requires ~1gb at minimum" % args.memory
# else:
# print "using ~%1.1fMB of memory" % (m / (1024 * 1024))
# memLimit = max(memLimit, m - 1024*1024*1024)
# #if args.memory
# set $TMPDIR so sqlite will use it for vacuum etc.
if args.temp_directory:
if not os.path.isdir(args.temp_directory):
print "ERROR: '%s' is not a directory"
sys.exit(1)
os.environ['TMPDIR'] = os.path.abspath(args.temp_directory)
# instantiate database object
db = loki_db.Database(testing=args.test_data, updating=True)
db.setVerbose(args.verbose)
db.attachDatabaseFile(args.knowledge)
# list sources?
if args.list_sources != None:
srcSet = set()
for srcList in args.list_sources:
srcSet |= set(srcList)
if (not srcSet) or ('+' in srcSet):
print "available source loaders:"
srcSet = set()
else:
print "source loader options:"
moduleVersions = db.getSourceModuleVersions(srcSet)
moduleOptions = db.getSourceModuleOptions(srcSet)
# print "WARNING: ignoring '%s' memory allotment, the updater requires ~1gb at minimum" % args.memory
# else:
# print "using ~%1.1fMB of memory" % (m / (1024 * 1024))
# memLimit = max(memLimit, m - 1024*1024*1024)
# #if args.memory
# set $TMPDIR so sqlite will use it for vacuum etc.
if args.temp_directory:
if not os.path.isdir(args.temp_directory):
print "ERROR: '%s' is not a directory"
sys.exit(1)
os.environ['TMPDIR'] = os.path.abspath(args.temp_directory)
# instantiate database object
db = loki_db.Database(testing=args.test_data,
updating=True,
taxID=args.taxonomy_id)
db.setVerbose(args.verbose or (not args.quiet))
# list sources?
if args.list_sources != None:
srcSet = set()
for srcList in args.list_sources:
srcSet |= set(srcList)
if (not srcSet) or ('+' in srcSet):
print "available source loaders, versions, supported species and options:"
srcSet = set()
else:
print "source loader versions, supported species and options:"
moduleVersions = db.getSourceModuleVersions(srcSet)
moduleSpecies = db.getSourceModuleSpecies(srcSet)