The example provided by your team is ok. When I test my own data, I met errors in find_sets.py. I don't know how to solve it so that I paste my script and the log file here. Please give some suggestions. Thank you!
------------------------------ Input Mutation Data -----------------------------
- Genes: 6249
- Patients: 43
- Genes mutated in >=2 patients: 2028
------------------------------- Enumerating Sets -------------------------------
k=2: 2055378 sets...
- Output 2042825 sets
Removed 12553 sets with NaN or invalid P-values
Ignored 0 sets with Z >= T or a gene with no exclusive mutations
Traceback (most recent call last):
File "/data2/database/opt/common/wext/wext-1.3.0/find_sets.py", line 158, in <module>
if __name__ == '__main__': run( get_parser().parse_args(sys.argv[1:]) )
File "/data2/database/opt/common/wext/wext-1.3.0/find_sets.py", line 156, in run
output_enumeration_table( args, k, setToPval, setToRuntime, setToFDR, setToObs, args.fdr_threshold )
File "/data2/database/opt/common/wext/wext-1.3.0/wext/i_o.py", line 66, in output_enumeration_table
k = len(rows[0][0].split(', '))
IndexError: list index out of range
Hello,
The example provided by your team is ok. When I test my own data, I met errors in
find_sets.py. I don't know how to solve it so that I paste my script and the log file here. Please give some suggestions. Thank you!(venv) [xxx@xxx wext]$ python /data2/database/opt/common/wext/wext-1.3.0/find_sets.py -mf data/mutation.exonic.json -wf weights.npy -s exclusivity -k 2 -c $num_cores -f 2 -o exclusivity_results -v 1