Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples
The problem was that if the match within bedtools_window is empty, the dataframe was not correctly constructed and column names were not properly created.
This caused a KeyError in compute_metrics.py when sorting the variable matched.
The fix is to explicitly name the columns when creating the empty dataframe.
The else statement is now extended to rename the columns from the non-empty (i.e. number of rows > 0) directly.
I locally debugged the solution and it seems to work in that the variable matched is created with corresponding column names and the sorting successfully finishes. The metrics sensitivity and precision are evaluated to 0, as expected.
Checklist
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] My code follows the templates/style guidelines of the repository
[x] Results, logs or other output is not commited to the repository
The problem was that if the match within
bedtools_windowis empty, the dataframe was not correctly constructed and column names were not properly created. This caused a KeyError incompute_metrics.pywhen sorting the variablematched.The fix is to explicitly name the columns when creating the empty dataframe. The
elsestatement is now extended to rename the columns from the non-empty (i.e. number of rows > 0) directly.I locally debugged the solution and it seems to work in that the variable
matchedis created with corresponding column names and the sorting successfully finishes. The metrics sensitivity and precision are evaluated to 0, as expected.Checklist