NameError: name 'cmd_biomart' is not defined; NameError: name 'time' is not defined

[ossmith]

From an email sent to me: a couple of bugs I didn't catch in testing since I run <400 annotations through BioMart. It's safe to correct these as suggested, but I should add a test which would catch this in the future.

Bug 1:

/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/lib/python3.11/site-packages/intersect.py:164: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
  raw_df = pd.read_csv(argumentClass.gwas, sep="\t", header=0, index_col=False) # sep="\t"
Traceback (most recent call last):
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/bin/hare", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/lib/python3.11/site-packages/hare.py", line 122, in main
    run_intersect(intargs)
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/lib/python3.11/site-packages/hare.py", line 36, in run_intersect
    intersect.main(**intersect_args)
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/lib/python3.11/site-packages/intersect.py", line 705, in main
    locations_filepath = biomart_locate(annotation_filepath, hareParameters, hareSettings)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-env/lib/python3.11/site-packages/intersect.py", line 481, in biomart_locate
    os.system(cmd_biomart)
              ^^^^^^^^^^^
NameError: name 'cmd_biomart' is not defined. Did you mean: 'run_biomart'?

Bug 2:

/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/lib/python3.11/site-packages/intersect.py:164: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
  raw_df = pd.read_csv(argumentClass.gwas, sep="\t", header=0, index_col=False) # sep="\t"
Traceback (most recent call last):
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/bin/hare", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/lib/python3.11/site-packages/hare.py", line 122, in main
    run_intersect(intargs)
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/lib/python3.11/site-packages/hare.py", line 36, in run_intersect
    intersect.main(**intersect_args)
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/lib/python3.11/site-packages/intersect.py", line 705, in main
    locations_filepath = biomart_locate(annotation_filepath, hareParameters, hareSettings)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work/home/ac1q5qmtwi/softwares/miniconda3/envs/hare-revised-env/lib/python3.11/site-packages/intersect.py", line 484, in biomart_locate
    time.sleep(0.5) # Prevent lockout of BioMart from rate limit
    ^^^^
NameError: name 'time' is not defined