jverma / hdf5-to-json-converter Goto Github PK

Hi,
I am new in python and interested in using this python code to convert the .biom file from hdf5 format to a json one. However it does not sucess:

python HDF5toJSON.py my_file.biom my_fileJ.biom

Traceback (most recent call last):
File "HDF5toJSON.py", line 26, in
h5file = open_file(sys.argv[1])
NameError: name 'open_file' is not defined

Can you show an example on how to use the python code? Thanks a lot!!

This is what I get when I try to convert:
[764:6296:0813/122557:VERBOSE1:crash_service_main.cc(68)] Session start. cmdline is [--reporter-url=https://ticinocrashreporter.azurewebsites.net/crash --application-name=VSCode --v=1]
[764:6296:0813/122558:VERBOSE1:crash_service.cc(142)] window handle is 000B0EB6
[764:6296:0813/122558:VERBOSE1:crash_service.cc(290)] pipe name is .\pipe\VSCode Crash Service
dumps at C:\Users\johnp\AppData\Local\Temp\VSCode Crashes
[764:6296:0813/122558:VERBOSE1:crash_service.cc(294)] checkpoint is C:\Users\johnp\AppData\Local\Temp\VSCode Crashes\crash_checkpoint.txt
server is https://ticinocrashreporter.azurewebsites.net/crash
maximum 128 reports/day
reporter is electron-crash-service
[764:6296:0813/122558:VERBOSE1:crash_service_main.cc(84)] Ready to process crash requests
[764:16632:0813/122558:VERBOSE1:crash_service.cc(323)] client start. pid = 4428
[764:16632:0813/122558:VERBOSE1:crash_service.cc(323)] client start. pid = 5424
[6368:8124:0813/122558:VERBOSE1:crash_service_main.cc(68)] Session start. cmdline is [--reporter-url=https://ticinocrashreporter.azurewebsites.net/crash --application-name=VSCode --v=1]
[6368:8124:0813/122558:VERBOSE1:crash_service.cc(142)] window handle is 00060E68
[6368:8124:0813/122558:VERBOSE1:crash_service.cc(290)] pipe name is .\pipe\VSCode Crash Service
dumps at C:\Users\johnp\AppData\Local\Temp\VSCode Crashes
[6368:8124:0813/122558:VERBOSE1:crash_service.cc(294)] checkpoint is C:\Users\johnp\AppData\Local\Temp\VSCode Crashes\crash_checkpoint.txt
server is https://ticinocrashreporter.azurewebsites.net/crash
maximum 128 reports/day
reporter is electron-crash-service
[6368:8124:0813/122558:ERROR:crash_service.cc(301)] could not start dumper