psites HDF5 file fails to be created

My run failed for my dataset, that has all genes set to equal length. What happens is this (I here display the partial hdf5 file):

  group           name       otype dclass        dim
0     /        p_sites H5I_DATASET   VLEN 551 x 1000
1     / transcript_ids H5I_DATASET STRING       1000

You see the "psites_number" table is not made, because it fails at inserting the "p_sites" table properly. I think the newest h5py with anaconda (3.6.0) version does not work now as the code is implemented, or am I wrong here?

ERROR is:

Traceback (most recent call last):
  File "/home/roler/anaconda3/envs/ribocode_env/bin/RiboCode", line 10, in <module>
    sys.exit(main())
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/RiboCode.py", line 40, in main
    tpsites_sum, total_psites_number = process_bam.psites_count(configIn.configList,transcript_dict,thread_num=1)
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 111, in psites_count
    tpsites_sum,total_psites_number = read_bam(configList[0])
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 84, in read_bam
    write_psites(tpsites,psites_number, name + "_psites.hd5")
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 26, in write_psites
    fout.create_dataset("p_sites",data=list(tpsites.values()),dtype=dt, compression="gzip")
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/h5py/_hl/group.py", line 149, in create_dataset
    dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds)
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/h5py/_hl/dataset.py", line 145, in make_new_dset
    dset_id.write(h5s.ALL, h5s.ALL, data)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5d.pyx", line 232, in h5py.h5d.DatasetID.write
  File "h5py/_proxy.pyx", line 145, in h5py._proxy.dset_rw
  File "h5py/_conv.pyx", line 784, in h5py._conv.ndarray2vlen
AttributeError: 'int' object has no attribute 'dtype'

I tried to make the h5 file from scratch, but it still fails with this error:

Traceback (most recent call last):
  File "/home/roler/anaconda3/envs/ribocode_env/bin/RiboCode", line 10, in <module>
    sys.exit(main())
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/RiboCode.py", line 40, in main
    tpsites_sum, total_psites_number = process_bam.psites_count(configIn.configList,transcript_dict,thread_num=1)
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 111, in psites_count
    tpsites_sum,total_psites_number = read_bam(configList[0])
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 49, in read_bam
    tpsites,psites_number = load_psites(name + "_psites.hd5" )
  File "/home/roler/anaconda3/envs/ribocode_env/lib/python3.9/site-packages/RiboCode/process_bam.py", line 35, in load_psites
    psites_number = fin["psites_number"].value
AttributeError: 'Dataset' object has no attribute 'value'

It now says there is no ".value" getter, which might be because ".value" is deprecated? Relevant link: https://stackoverflow.com/questions/67409919/attributeerror-dataset-object-has-no-attribute-value

xryanglab / RiboCode

psites HDF5 file fails to be created #32