search

velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
159 stars 83 forks source link

Velocyto python analysis tutorial error #213

Open Sethupathy-Lab opened 5 years ago

Sethupathy-Lab commented 5 years ago

In the analysis tutorial (http://velocyto.org/velocyto.py/tutorial/analysis.html), the step on saving the vlm object has a function that didn't work.

vlm.dump_hdf5("my_velocyto_analysis")

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-8-38636c55e1ff> in <module>
----> 1 vlm.dump_hdf5("375KO-villi_velocyto_analysis")

AttributeError: 'VelocytoLoom' object has no attribute 'dump_hdf5'

Using vlm.to_hdf5 instead of dump_hdf5 worked though.

Best, Matt

hbandukw commented 3 years ago

I am also unable to read the hdf5 file with 

load_velocyto_hdf5("KO_velocity.hdf5")
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-ca1f1b1cdbb9> in <module>
----> 1 load_velocyto_hdf5("KO_velocity.hdf5")

NameError: name 'load_velocyto_hdf5' is not defined

my hdf5 file was made with vlm.to_hdf5.

maminby commented 1 year ago

I encounter the same problem, you solve it yet?