Empty results produces error

[jhrcook]

An empty rows list in "i_o.py" causes the following error:

Traceback (most recent call last):
  File "wext/find_sets.py", line 158, in <module>
    if __name__ == '__main__': run( get_parser().parse_args(sys.argv[1:]) )
  File "wext/find_sets.py", line 156, in run
    output_enumeration_table( args, k, setToPval, setToRuntime, setToFDR, setToObs, args.fdr_threshold )
  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/WExT/wext/wext/i_o.py", line 71, in output
    k = len(rows[0][0].split(', '))
IndexError: list index out of range

I inserted a quick print statement of rows just before line 71 (it is normally line 67, I believe) and it produced:

[]

Let me know if you need any more information for this small bug. Thank you for putting this package together for the community and being responsive to issues,
Josh Cook

[matthewreyna]

Josh,

Thank you for raising this issue. As you noticed, an error occurs when the results are empty, which can happen if no gene set meets the given FDR threshold (-fdr/-fdr_threshold in the find_sets.py script, which is 0.5 by default). We will update the code to fix this, but for an immediate solution, please indent line 66 through line 73 and add if rows: before line 66 in the i_o.py script, i.e., replace

k = len(rows[0][0].split(', '))
tbl_header = create_tbl_header( k )
header = 'Gene set\t{0}{1} P-value\t{0}{1} FDR\t{0}{1} '\
         'Runtime\tT\tZ\t{2}'.format(args.test, method_paren, tbl_header)

# Output to file
OUT.write('#{}\n'.format(header))
OUT.write( '\n'.join([ '\t'.join(map(str, row)) for row in rows ]) )

with

if rows:
    k = len(rows[0][0].split(', '))
    tbl_header = create_tbl_header( k )
    header = 'Gene set\t{0}{1} P-value\t{0}{1} FDR\t{0}{1} '\
             'Runtime\tT\tZ\t{2}'.format(args.test, method_paren, tbl_header)

    # Output to file
    OUT.write('#{}\n'.format(header))
    OUT.write( '\n'.join([ '\t'.join(map(str, row)) for row in rows ]) )

Best,
Matt