search

nanoporetech / minknow_api

Protobuf and gRPC specifications for the MinKNOW API
Other
55 stars 12 forks source link

how can we modify the start_protocol.py to obtain zlib_compres fast5 #28

Closed neuropathbasel closed 3 years ago

neuropathbasel commented 3 years ago

We did not find a switch to define zlib_compres fast5 as output option and do seem to obtain (by default?) vbz_compres fast5. Essentially we would like to obtain fast5 identical to those generated by starting a run with MinKnow UI. Currently we do use the SQK-RBK004 kit. Looking forward to your reply. Best wishes Claus

0x55555555 commented 3 years ago

Hello, you would need to adjust this line:

https://github.com/nanoporetech/minknow_api/blob/master/python/minknow_api/tools/protocols.py#L316:


    if fast5_arguments:
        protocol_args.extend(
            ["--fast5_data", "trace_table", "fastq", "raw", "vbz_compress"] # zlib_compress instead of vbz_compress here

VBZ is become the default with MinKNOW UI, in the latest release so these are now in sync. I will raise the ability to configure this option from the script with the development group.

neuropathbasel commented 3 years ago

Thanks! We had tried this yesterday with success - but I thought there was a different way, other than modifying the protocols.py script. Best, Jürgen