After running the process_asts function I noticed I only get one line at the output.
I checked my input file (from calc_asts) and noticed I should have over one hundred testable genes.
After going through the source code I noticed that the script process.py (https://github.com/LappalainenLab/lorals/tree/master/lorals/process.py in the function _process_asts has a wrong indentation. It seems that starting at line 118 it should be indented out one level.
After I fixed this locally, I was able to run the script successfully.
After running the
process_astsfunction I noticed I only get one line at the output.I checked my input file (from
calc_asts) and noticed I should have over one hundred testable genes.After going through the source code I noticed that the script
process.py(https://github.com/LappalainenLab/lorals/tree/master/lorals/process.py in the function_process_astshas a wrong indentation. It seems that starting at line 118 it should be indented out one level.After I fixed this locally, I was able to run the script successfully.