import h5py
f = h5py.File('my.hal', 'r')
print(f['Anc00']['SEQNAME_ARRAY'])
gives:
...
File "h5py/h5t.pyx", line 435, in h5py.h5t.TypeID.dtype.__get__
File "h5py/h5t.pyx", line 951, in h5py.h5t.TypeIntegerID.py_dtype
TypeError: data type '<i15' not understood
I am out of my depth here but: 8 * 15 = 120 and 8 * 14 = 112, so it's like the python library is considering this field as 8 lots of 14(15)-bit integers instead of the other way around.
Or maybe it's just that there's no appropriate numpy type for this sort of variable length integer?
For one reason or another, I want to parse the hal file output from cactus in python.
Using h5py, like:
gives:
Using h5dump to look at the header:
Same as above, but look at another genome (
Pfa
):and:
I am out of my depth here but:
8 * 15 = 120
and8 * 14 = 112
, so it's like the python library is considering this field as 8 lots of 14(15)-bit integers instead of the other way around.Or maybe it's just that there's no appropriate numpy type for this sort of variable length integer?
Thanks very much for your time.