I am working on integrating Identipy into a quality control application and I have been having some issues working with the config file. Specifically, the decoy database option and the parameter optimization do not seem to be activated/changed by the contents of the config file. The first was easy to work around with command line arguments, but the second not so.
Decoy database search
Including the following in the config file did not cause a decoy database to be created and used:
[input] add decoy: yes decoy method: reverse prefix: DECOY_
The config file was provided to Identipy using the -cfg argument, but did not seem to change how the search ran. There were no decoy hits in the pepXML output. However, adding the appropriate arguments to the command line (i.e. -ad, -method, -prefix) did work.
Search parameter optimization
I would also like to include the following in the config file:
[misc] first stage: identipy.extras.optimization
but again, this did not seem to change the search. The pepXML output is identical whether or not this is included in the config file. Even if it is changed in the default config file there is no change. In this case, I don't see a way to invoke the optimization from the command line. Is identipy.extras.optimization the default even when it is not specified in the config file?
I am calling Identipy from inside a .NET application, and in order to avoid some of the python warnings from popping up I am calling
> python -W ignore [path to identipy-script.py] [arguments] instead of the Identipy exe directly.