Error encountered during Pandas pivot

[evanseitz]

The use of Pandas pivot throws an error for me about repeated entries, which halts the program laid out in [1].

I only encountered this error using my own synthetic data (which can have some duplicate sequence/bin combinations, hence the error). I can confirm that no such error arises when using the demo sort-seq file provided (2010, file_S2.txt). I was able to correct it using the recommendation at [2], by making the following change:

pivot_df = sub_df.pivot(index='x', values='ct', columns='bin').fillna(0).astype(int) #before
pivot_df = sub_df.pivot_table(index='x', values='ct', columns='bin').fillna(0).astype(int) #after

[1] https://mavenn.readthedocs.io/en/latest/datasets/dataset_sortseq.html
[2] https://stackoverflow.com/questions/11232275/pandas-pivot-warning-about-repeated-entries-on-index