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import h5py
import warnings
from ont_fast5_api import fast5_file as f5f
class FileToDict(object):
def __init__(self):
self.contents = {}
def scan(self, name, obj):
if isinstance(obj, h5py.Group):
self.contents[name] = 'group'
else:
self.contents[name] = 'dataset'
self.contents['{}.data'.format(name)] = \
str(f5f._sanitize_data_for_reading(obj))
self.contents['{}.cols'.format(name)] = obj.dtype.names
attrdict = {}
for item in obj.attrs:
attrdict[item] = \
str(f5f._sanitize_data_for_reading(obj.attrs[item]))
self.contents['{}.attrs'.format(name)] = attrdict
return None
def compare_hdf_files(file1, file2):
""" Compare two hdf files.
:param file1: First file to compare.
:param file2: Second file to compare.
:returns True if they are the same.
"""
warnings.simplefilter("default")
warnings.warn("'compare_hdf_files': HDF5 comparison is deprecated. \n"
"If this feature is still required please contact the project maintainers",
DeprecationWarning)
data1 = FileToDict()
data2 = FileToDict()
scanner1 = data1.scan
scanner2 = data2.scan
with h5py.File(file1, 'r') as fh1:
fh1.visititems(scanner1)
with h5py.File(file2, 'r') as fh2:
fh2.visititems(scanner2)
return data1.contents == data2.contents
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