katerinakazantseva / strainy

Graph-based assembly phasing
Other
65 stars 5 forks source link

Fix Pandas SettingWithCopyWarning #30

Closed mikolmogorov closed 1 year ago

mikolmogorov commented 1 year ago

This warning indicates a potential problem in pandas matrices handing: https://www.dataquest.io/blog/settingwithcopywarning/

Currently the warning is suppressed by the line pd.options.mode.chained_assignment = None in build_adj_matrix.py. But we need to find the cause and fix it for good. It is likely due to chained use of indexing (A[x][y] = Z), which should be converted to (A[x, y] = Z)