Option parser for Slingshot only takes first letter from argument and discards the rest

[yutuyt01]

When passing arguments into run_Slingshot.py, the outPrefix argument seems to only take the first letter of the argument and discard the rest.
When this is run:

python scripts/runSlingshot.py --outPrefix output -p Synthetic/dyn-LI/PseudoTime.csv -e Synthetic/dyn-LI/ExpressionData.csv -c 1 -r 10

The following error occurs:

FileNotFoundError: [Errno 2] No such file or directory: 'o/PseudoTime.csv'

This happens with an absolute path as well, where it simply looks for "C/PsuedoTime.csv". Setting the default to such a string results in the same error, bizarrely (including passing a raw string).

This error was discussed and a solution was discussed here: StackOverflow - however, the solution only applies to the newer argparse and not optparse. I couldn't find a similar issue anywhere else. The nargs argument doesn't work in a similar fashion between the two parsing options.

Could possibly upgrade to argparse for a solution.

Also, for the instance when clusters = 1, a directory is not created for the output files with mkdir.

[yutuyt01]

Moved as the issue was opened under the wrong repository

[yutuyt01]

Kevin has pointed out the issue is that the script is trying to read outPaths as a list and iterating through each outPath for only the clusters = 1 case. Since this behavior is not present in the multiple clusters case, the behavior is changed to only try and read one path from outPaths. Will be solved in slingshot-docker branch.