prune_ngsLD.py error

[Andrew-N-Black]

Hello, I'm receiving an error trying to prune sites in a conda env. Both pandas and graph-tool are loading, running python3. Can you help debug?

#Command
~/ngsLD/scripts/prune_ngsLD.py --input LD/test --max_dist 5000 --min_weight 0.5 --out LD/testLD_unlinked.pos

#stout
Checking if file is gzipped...
Reading in data...
Traceback (most recent call last):
File "/home/blackan/ngsLD/scripts/prune_ngsLD.py", line 94, in
G = load_graph_from_csv(args.input, directed = False,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/blackan/.conda/envs/cent7/2020.11-py38/ld/lib/python3.11/site-packages/graph_tool/init.py", line 3486, in load_graph_from_csv
name = g.add_edge_list(itertools.chain([line], r), hashed=hashed,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/blackan/.conda/envs/cent7/2020.11-py38/ld/lib/python3.11/site-packages/graph_tool/init.py", line 2507, in add_edge_list
libcore.add_edge_list_hashed(self.__graph, edge_list,
File "/home/blackan/.conda/envs/cent7/2020.11-py38/ld/lib/python3.11/site-packages/graph_tool/init.py", line 2493, in
yield (val if i < 2 else converti - 2
^^^^^^^^^^^^^^^^^^^
File "/home/blackan/.conda/envs/cent7/2020.11-py38/ld/lib/python3.11/site-packages/graph_tool/init.py", line 275, in convert
return vtype(val)
^^^^^^^^^^
ValueError: invalid literal for int() with base 10: 'dist'

[fgvieira]

I just released a more efficient alternative to the pruning scripts (check the README); do you think you could give it a try and see if you get the same error?

If you do, can you send me the input file you are using?