def compress(self, output_filename, miso_dirnames):
"""
Takes a set of MISO input directories and compresses them
into 'output_filename'. This involves making SQL databases
for all the MISO directories and then additionally compressing the
results as a zip file.
"""
if os.path.isfile(output_filename):
print "Error: %s already exists. Please delete to overwrite." \
%(output_filename)
output_dir = "%s%s" % (output_filename, miso_db.MISO_DB_EXT)
if os.path.isdir(output_dir):
print "Error: Intermediate compressed directory %s " \
"exists. Please delete to overwrite." %(output_dir)
sys.exit(1)
for miso_dirname in miso_dirnames:
print "Processing: %s" % (miso_dirname)
if not os.path.isdir(miso_dirname):
print "Error: %s not a directory." % (miso_dirname)
sys.exit(1)
if os.path.isfile(output_filename):
print "Output file %s already exists, aborting. " \
"Please delete the file if you want " \
"compression to run."
sys.exit(1)
self.miso_dirs_to_compress = []
print "Copying source directory tree.."
shutil.copytree(miso_dirname,
output_dir,
ignore=self.collect_miso_dirs)
for dir_to_compress in self.miso_dirs_to_compress:
rel_path = os.path.relpath(dir_to_compress, miso_dirname)
comp_path = os.path.join(output_dir, rel_path)
# Remove the place holder directory
os.rmdir(comp_path)
comp_path = "%s%s" % (comp_path, miso_db.MISO_DB_EXT)
miso_db.miso_dir_to_db(dir_to_compress, comp_path)
# Zip directory using conventional zip
print "Zipping compressed directory with standard zip..."
t1 = time.time()
zipper(output_dir, output_filename)
print "Deleting intermediate directory: %s" % (output_dir)
shutil.rmtree(output_dir)
t2 = time.time()
print " - Standard zipping took %.2f minutes." \
%((t2 - t1)/60.)
print "To access the SQLite representation of raw MISO output "
print "(*.miso) files, simply unzip with the .miso_zip file "
print "with standard unzip utility:\n"
print " unzip %s" % (output_filename)
def compress(self, output_filename, miso_dirnames):
"""
Takes a set of MISO input directories and compresses them
into 'output_filename'. This involves making SQL databases
for all the MISO directories and then additionally compressing the
results as a zip file.
"""
if os.path.isfile(output_filename):
print "Error: %s already exists. Please delete to overwrite." \
%(output_filename)
output_dir = "%s%s" %(output_filename, miso_db.MISO_DB_EXT)
if os.path.isdir(output_dir):
print "Error: Intermediate compressed directory %s " \
"exists. Please delete to overwrite." %(output_dir)
sys.exit(1)
for miso_dirname in miso_dirnames:
print "Processing: %s" %(miso_dirname)
if not os.path.isdir(miso_dirname):
print "Error: %s not a directory." %(miso_dirname)
sys.exit(1)
if os.path.isfile(output_filename):
print "Output file %s already exists, aborting. " \
"Please delete the file if you want " \
"compression to run."
sys.exit(1)
self.miso_dirs_to_compress = []
print "Copying source directory tree.."
shutil.copytree(miso_dirname, output_dir,
ignore=self.collect_miso_dirs)
for dir_to_compress in self.miso_dirs_to_compress:
rel_path = os.path.relpath(dir_to_compress, miso_dirname)
comp_path = os.path.join(output_dir, rel_path)
# Remove the place holder directory
os.rmdir(comp_path)
comp_path = "%s%s" %(comp_path, miso_db.MISO_DB_EXT)
miso_db.miso_dir_to_db(dir_to_compress, comp_path)
# Zip directory using conventional zip
print "Zipping compressed directory with standard zip..."
t1 = time.time()
zipper(output_dir, output_filename)
print "Deleting intermediate directory: %s" %(output_dir)
shutil.rmtree(output_dir)
t2 = time.time()
print " - Standard zipping took %.2f minutes." \
%((t2 - t1)/60.)
print "To access the SQLite representation of raw MISO output "
print "(*.miso) files, simply unzip with the .miso_zip file "
print "with standard unzip utility:\n"
print " unzip %s" %(output_filename)
def pack_dirs(self, miso_dirnames):
"""
Takes a set of MISO input containing directories and packs them.
'miso_dirnames' are directory that have MISO output *somewhere*
in them -- could be arbitrarily nested within the directory.
This traverses the directory structure and converts raw *.miso text
containing directory into *.miso_db files that are much more compact
and are less of a burden for the filesystem.
"""
t1 = time.time()
for miso_dirname in miso_dirnames:
print "Processing: %s" %(miso_dirname)
if not os.path.isdir(miso_dirname):
print "Error: %s not a directory." %(miso_dirname)
sys.exit(1)
for dir_to_compress, subdirs, curr_fnames in os.walk(miso_dirname):
if miso_db.is_miso_unpacked_dir(dir_to_compress):
# It's a *.miso containing directory, so pack it
# into a MISO database
chrom_basename = os.path.basename(dir_to_compress)
if len(chrom_basename) == 0:
print "Error: Failed to pack MISO directory %s" \
%(miso_dirname)
raise Exception, "Basename for %s is empty!" \
%(dir_to_compress)
db_fname = \
os.path.join(os.path.dirname(dir_to_compress),
"%s%s" %(chrom_basename,
miso_db.MISO_DB_EXT))
# If packed file exists, move on
if os.path.isfile(db_fname):
continue
status = miso_db.miso_dir_to_db(dir_to_compress, db_fname)
# If packing was successful, delete the input directory
# containing the *.miso file
shutil.rmtree(dir_to_compress)
t2 = time.time()
print "Packing took %.2f minutes" %((t2 - t1)/60.)
def pack_dirs(self, miso_dirnames):
"""
Takes a set of MISO input containing directories and packs them.
'miso_dirnames' are directory that have MISO output *somewhere*
in them -- could be arbitrarily nested within the directory.
This traverses the directory structure and converts raw *.miso text
containing directory into *.miso_db files that are much more compact
and are less of a burden for the filesystem.
"""
t1 = time.time()
for miso_dirname in miso_dirnames:
print "Processing: %s" % (miso_dirname)
if not os.path.isdir(miso_dirname):
print "Error: %s not a directory." % (miso_dirname)
sys.exit(1)
for dir_to_compress, subdirs, curr_fnames in os.walk(miso_dirname):
if miso_db.is_miso_unpacked_dir(dir_to_compress):
# It's a *.miso containing directory, so pack it
# into a MISO database
chrom_basename = os.path.basename(dir_to_compress)
if len(chrom_basename) == 0:
print "Error: Failed to pack MISO directory %s" \
%(miso_dirname)
raise Exception, "Basename for %s is empty!" \
%(dir_to_compress)
db_fname = \
os.path.join(os.path.dirname(dir_to_compress),
"%s%s" %(chrom_basename,
miso_db.MISO_DB_EXT))
# If packed file exists, move on
if os.path.isfile(db_fname):
continue
status = miso_db.miso_dir_to_db(dir_to_compress, db_fname)
# If packing was successful, delete the input directory
# containing the *.miso file
shutil.rmtree(dir_to_compress)
t2 = time.time()
print "Packing took %.2f minutes" % ((t2 - t1) / 60.)
