olsenlabmit / bcdb Goto Github PK

Hi all,

Cool project you have going here, and looking forward to see how it develops. Let me play my part by contributing a first issue.

OS: Mac 11.0.1

Problem:
Executing python tool.py as instructed gives following error:

Traceback (most recent call last):
File "/Users/cjg/Documents/elix/BCDB/platform/tool.py", line 20, in
chemistries = chemistry_table()
File "/Users/cjg/Documents/elix/BCDB/platform/BigSMILES_BigSmilesObj.py", line 491, in chemistry_table
chemistries = pd.read_csv("..\BigSMILES.csv")
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 610, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 462, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 819, in init
self._engine = self._make_engine(self.engine)
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 1050, in _make_engine
return mapping[engine](self.f, **self.options) # type: ignore[call-arg]
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 1867, in init
self._open_handles(src, kwds)
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/parsers.py", line 1362, in _open_handles
self.handles = get_handle(
File "/Users/cjg/miniconda3/envs/bcdb/lib/python3.9/site-packages/pandas/io/common.py", line 642, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '..\BigSMILES.csv'

Solution:
Change

to the following:
chemistries = pd.read_csv(os.path.join(os.path.dirname( __file__ ), os.pardir, "BigSMILES.csv"))
You will also need to import os in the same file.

Description:
os.path.join connects the arguments passed to it using the system's directory separator ("\" in Windows, but "/" in Mac and Linux). os.path.dirname( __file__ ) gets the directory of the current file. os.pardir references the "parent directory" symbol of the OS (".." for all 3). Works for me on Mac with these changes, and should be true for Linux, too. If you didn't have a chance to test your repo on Linux, I'd recommend it.