I am currently testing SGVFinder2 for my analysis. When I ran the following code:
vsgv, dsgv = work_on_collection(
samp_to_map=smp_map,
max_spacing=10,
min_samp_cutoff=2,
delsdetectthresh=0.25,
real_del_thresh=0.95,
dels_cooc_thresh=0.25,
vsgv_dissim_thresh=0.125,
vsgv_clip_quantile=0.02,
vsgv_fit_interval=0.95,
vsgv_fit_method='betaprime',
x_coverage=0.01,
rate_param=10,
vsgv_dense_perc=85,
browser_path=None,
taxonomypath=None,
genepospath=None,
frames_path=None
)
I encountered warning messages similar to the following:
doing var regions XXXXXXX
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/lib/function_base.py:520: RuntimeWarning: Mean of empty slice.
avg = a.mean(axis, **keepdims_kw)
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
~miniconda3/envs/SV/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
warnings.warn(stats.ConstantInputWarning(warn_msg))
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/lib/function_base.py:520: RuntimeWarning: Mean of empty slice.
avg = a.mean(axis, **keepdims_kw)
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
=== All done! ===
Despite these warnings, the code completed successfully and produced the vsgv and dsgv output files. I am unsure why these warnings appeared and whether my output results are accurate. Specifically, I am concerned that some samples might not contain valid values in the output.
I am currently testing SGVFinder2 for my analysis. When I ran the following code:
vsgv, dsgv = work_on_collection(
samp_to_map=smp_map,
max_spacing=10,
min_samp_cutoff=2,
delsdetectthresh=0.25,
real_del_thresh=0.95,
dels_cooc_thresh=0.25,
vsgv_dissim_thresh=0.125,
vsgv_clip_quantile=0.02,
vsgv_fit_interval=0.95,
vsgv_fit_method='betaprime',
x_coverage=0.01,
rate_param=10,
vsgv_dense_perc=85,
browser_path=None,
taxonomypath=None,
genepospath=None,
frames_path=None
)
I encountered warning messages similar to the following:
doing var regions XXXXXXX
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/lib/function_base.py:520: RuntimeWarning: Mean of empty slice.
avg = a.mean(axis, **keepdims_kw)
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
~miniconda3/envs/SV/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
warnings.warn(stats.ConstantInputWarning(warn_msg))
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/lib/function_base.py:520: RuntimeWarning: Mean of empty slice.
avg = a.mean(axis, **keepdims_kw)
~miniconda3/envs/SV/lib/python3.10/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
=== All done! ===
Despite these warnings, the code completed successfully and produced the vsgv and dsgv output files. I am unsure why these warnings appeared and whether my output results are accurate. Specifically, I am concerned that some samples might not contain valid values in the output.