fgvieira
commented
1 year ago 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?
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'