def compress_miso(output_filename, input_dirs,
comp_ext=".misozip"):
"""
Compress a directory containing MISO files.
Traverse directories, one by one, and look for directories
that contain
"""
output_filename = utils.pathify(output_filename)
for input_dir in input_dirs:
if not os.path.isdir(input_dir):
print "Error: Cannot find directory %s" %(input_dir)
sys.exit(1)
if not os.path.basename(output_filename).endswith(comp_ext):
print "Error: Compressed output filename must end in %s" \
%(comp_ext)
sys.exit(1)
if os.path.isfile(output_filename):
print "Error: Output filename exists. Please delete %s to overwrite." \
%(output_filename)
sys.exit(1)
t1 = time.time()
miso_comp = MISOCompressor()
miso_comp.compress(output_filename, input_dirs)
t2 = time.time()
print "Compression took %.2f minutes." %((t2 - t1)/60.)
def compress_miso(output_filename, input_dirs,
comp_ext=".misozip"):
"""
Compress a directory containing MISO files.
Traverse directories, one by one, and look for directories
that contain
"""
output_filename = utils.pathify(output_filename)
for input_dir in input_dirs:
if not os.path.isdir(input_dir):
print "Error: Cannot find directory %s" %(input_dir)
sys.exit(1)
if not os.path.basename(output_filename).endswith(comp_ext):
print "Error: Compressed output filename must end in %s" \
%(comp_ext)
sys.exit(1)
if os.path.isfile(output_filename):
print "Error: Output filename exists. Please delete %s to overwrite." \
%(output_filename)
sys.exit(1)
t1 = time.time()
miso_comp = MISOCompressor()
miso_comp.compress(output_filename, input_dirs)
t2 = time.time()
print "Compression took %.2f minutes." %((t2 - t1)/60.)
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--compress",
dest="compress",
nargs=2,
default=None,
help="Compress a directory containing MISO output. "
"Takes as arguments: (1) the output filename of the "
"compressed file, (2) a comma-separated list of "
"directory names to be compressed. "
"Example: --compress output.misozip dirname1,dirname2")
parser.add_option("--uncompress",
dest="uncompress",
nargs=2,
default=None,
help="Uncompress a file generated by compress_miso. "
"Takes as arguments: (1) the filename to be "
"uncompressed, and (2) the directory to place the "
"uncompressed representation into. "
"Example: --uncompress output.misozip outputdir")
(options, args) = parser.parse_args()
if (options.compress is None) and (options.uncompress is None):
greeting()
sys.exit(1)
elif (options.compress is not None) and (options.uncompress is not None):
# Can't be given both.
greeting()
print "Error: Cannot process --compress and --uncompress at same time."
sys.exit(1)
if options.compress is not None:
output_filename = utils.pathify(options.compress[0])
input_dirs = [utils.pathify(d) \
for d in options.compress[1].split(",")]
compress_miso(output_filename, input_dirs)
if options.uncompress is not None:
compressed_filename = utils.pathify(options.uncompress[0])
output_dir = utils.pathify(options.uncompress[1])
uncompress_miso(compressed_filename, output_dir)
def view_miso_db(db_fname):
db_fname = misc_utils.pathify(db_fname)
if not os.path.isfile(db_fname):
print "Error: %s does not exist." %(db_fname)
sys.exit(1)
curr_db = miso_db.MISODatabase(db_fname)
event_names = curr_db.get_all_event_names()
num_events = len(event_names)
print "Database contains %d events" %(num_events)
for event in event_names:
print event
def view_miso_db(db_fname):
db_fname = misc_utils.pathify(db_fname)
if not os.path.isfile(db_fname):
print "Error: %s does not exist." % (db_fname)
sys.exit(1)
curr_db = miso_db.MISODatabase(db_fname)
event_names = curr_db.get_all_event_names()
num_events = len(event_names)
print "Database contains %d events" % (num_events)
for event in event_names:
print event
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--compress", dest="compress", nargs=2, default=None,
help="Compress a directory containing MISO output. "
"Takes as arguments: (1) the output filename of the "
"compressed file, (2) a comma-separated list of "
"directory names to be compressed. "
"Example: --compress output.misozip dirname1,dirname2")
parser.add_option("--uncompress", dest="uncompress", nargs=2, default=None,
help="Uncompress a file generated by compress_miso. "
"Takes as arguments: (1) the filename to be "
"uncompressed, and (2) the directory to place the "
"uncompressed representation into. "
"Example: --uncompress output.misozip outputdir")
(options, args) = parser.parse_args()
if (options.compress is None) and (options.uncompress is None):
greeting()
sys.exit(1)
elif (options.compress is not None) and (options.uncompress is not None):
# Can't be given both.
greeting()
print "Error: Cannot process --compress and --uncompress at same time."
sys.exit(1)
if options.compress is not None:
output_filename = utils.pathify(options.compress[0])
input_dirs = [utils.pathify(d) \
for d in options.compress[1].split(",")]
compress_miso(output_filename, input_dirs)
if options.uncompress is not None:
compressed_filename = utils.pathify(options.uncompress[0])
output_dir = utils.pathify(options.uncompress[1])
uncompress_miso(compressed_filename, output_dir)
def is_miso_rawdir(dirname, miso_ext=".miso"):
"""
Return true if the given directory is one which contains
raw MISO output (i.e. if it contains MISO chromosome directories.)
"""
dirname = utils.pathify(dirname)
if not os.path.isdir(dirname):
return False
filenames = glob.glob(os.path.join(dirname, "*.miso"))
# If all of the subdirectories of the current directory
# contain raw MISO (*.miso) files, consider it a raw MISO
# output directory.
if len(filenames) == 0:
return False
for fname in filenames:
if not fname.endswith(miso_ext):
return False
return True
def is_miso_rawdir(dirname, miso_ext=".miso"):
"""
Return true if the given directory is one which contains
raw MISO output (i.e. if it contains MISO chromosome directories.)
"""
dirname = utils.pathify(dirname)
if not os.path.isdir(dirname):
return False
filenames = glob.glob(os.path.join(dirname, "*.miso"))
# If all of the subdirectories of the current directory
# contain raw MISO (*.miso) files, consider it a raw MISO
# output directory.
if len(filenames) == 0:
return False
for fname in filenames:
if not fname.endswith(miso_ext):
return False
return True