qc broken b.c. it expects auxiliary folder to simultaneously exist and not exist #160
Description
The qc subcommand requires an 'auxiliary' folder to exist to work. This folder is intended to be provided by train. However, chrombpnet will not allow for this folder to exist due to the usage of os.makedirs(..., exist_ok=False) in chrombpnet_qc() and in the block that handles qc as an input subcommand. Thus it's impossible for qc to work correctly. I recommend changing that flag to True within that block, and in chrombpnet_qc().
For completeness, here's the error when the train folders are provided:
Traceback (most recent call last):
File "/opt/conda/bin/chrombpnet", line 33, in <module>
sys.exit(load_entry_point('chrombpnet', 'console_scripts', 'chrombpnet')())
File "/scratch/chrombpnet/chrombpnet/CHROMBPNET.py", line 26, in main
os.makedirs(os.path.join(args.output_dir,"auxiliary"), exist_ok=False)
File "/opt/conda/lib/python3.9/os.py", line 225, in makedirs
mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/projectTest/output/auxiliary'
Exit code: 1
and here's when they're not provided:
Traceback (most recent call last):
got the model
loading peaks...
File "/opt/conda/bin/chrombpnet", line 33, in <module>
sys.exit(load_entry_point('chrombpnet', 'console_scripts', 'chrombpnet')())
File "/scratch/chrombpnet/chrombpnet/CHROMBPNET.py", line 29, in main
pipelines.chrombpnet_qc(args)
File "/scratch/chrombpnet/chrombpnet/pipelines.py", line 196, in chrombpnet_qc
predict.main(args_copy)
File "/scratch/chrombpnet/chrombpnet/training/predict.py", line 105, in main
test_generator = initializers.initialize_generators(args, mode="test", parameters=None, return_coords=True)
File "/scratch/chrombpnet/chrombpnet/training/data_generators/initializers.py", line 69, in initialize_generators
peak_regions=pd.read_csv(args.peaks,header=None,sep='\t',names=NARROWPEAK_SCHEMA)
File "/opt/conda/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/opt/conda/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/opt/conda/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1448, in __init__
self._engine = self._make_engine(f, self.engine)
File "/opt/conda/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1705, in _make_engine
self.handles = get_handle(
File "/opt/conda/lib/python3.9/site-packages/pandas/io/common.py", line 863, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/projectTest/output/auxiliary/filtered.peaks.bed'
Exit code: 1
Model: "model"