Issue when running in denovo mode

[JannikSchneider12]

Hello,

I wanted to run the model in denovo mode, but I am getting this error:

File "/home/jannik/Masterthesis/de_novo_peptide_sequencing/ContraNovo/ContraNovo/ContraNovo.py", line 198, in main
writer.set_metadata(
AttributeError: 'NoneType' object has no attribute 'set_metadata'

Which is related to this part of the implementation

https://github.com/BEAM-Labs/ContraNovo/blob/main/ContraNovo/ContraNovo.py#L197-L200

writer = None
writer.set_metadata(
config, peak_path=peak_path, model=model, config_filename=config_fn
)

If I see this right, the writer class should be instanciated before?

Thanks for your time and help

[Chryzl]

Hello,

I encountered the issue myself.

Since ContraNovo and Casanovo are similar in code structure, I found that Casanovo's writer can be inserted.

If you look at the ms_io.py file within Casanovo, you can find a fitting MztabWriter. Simply copy the code into the ContraNovo repo (e.g. into ContraNovo/data/) and insert the writer.

I fixed it like so:

from .data import ms_io
...
writer = ms_io.MztabWriter(Path(output).with_suffix(".mztab"))
writer.set_metadata(
    config, peak_path=peak_path, model=model, config_filename=config_fn
)
writer.set_ms_run([peak_path])
...
writer.save()

I hope this works for you

[irleader]

Hello,

I encountered the issue myself.

Since ContraNovo and Casanovo are similar in code structure, I found that Casanovo's writer can be inserted.

If you look at the ms_io.py file within Casanovo, you can find a fitting MztabWriter. Simply copy the code into the ContraNovo repo (e.g. into ContraNovo/data/) and insert the writer.

I fixed it like so:

from .data import ms_io
...
writer = ms_io.MztabWriter(Path(output).with_suffix(".mztab"))
writer.set_metadata(
    config, peak_path=peak_path, model=model, config_filename=config_fn
)
writer.set_ms_run([peak_path])
...
writer.save()

I hope this works for you

#4 Can you help to check this error please?