New MSConvert CLI, hot off the presses

Emma ran over a new version of msconvert Austin recoded to accomodate the idiosyncracies in our isolation windows. He generated a new .config file, found here. Below is a side-by-side comparison of two different .config files. The one on the left is the original code, and the one on the right is the modified code.

I used the following code to convert one .raw file:

20170412_pwiz_testBuild_addMinWindowSize\msconvert.exe -c config_fix.txt 2017_January_23_envtstress_oyster1.raw

If this works, I’ll start converting all of my files! Emma will also take my converted file and run it through PECAN using a modified isolation scheme. You can track my progress with this Jupyter Notebook.

One possible caveat is that Laura and I have different isolation schemes and isolation window sizes. It’s possible that the .config file I’m using won’t be compatible with Laura’s data, and is only specific to my data for this experiment.