search

theislab / scib

Benchmarking analysis of data integration tools
MIT License
294 stars 63 forks source link

provide number of columns to `pd.read_table` #381

Closed johnarevalo closed 1 year ago

johnarevalo commented 1 year ago

It may be the case that the first row of any of the graph_lisi*txt files does not contain values for all of the n_neighbors (e.g. files attached), thus the line

https://github.com/theislab/scib/blob/cce7aaa65ccc18649e141e30464361d1fc67ea77/scib/metrics/lisi.py#L451

raises an exception: ParserError: Error tokenizing data. C error: Expected 21 fields in line 2, saw 91. (more info).

This PR explictly provides column names to make sure it allocates the total number of columns.

graph_lisi_indices_0.txt graph_lisi_distances_0.txt

johnarevalo commented 1 year ago

NVM, I just saw this is addressed in https://github.com/theislab/scib/pull/380.