TAB and space issue and deprecated functions.

[Former user]

There are a couple place in the scripts that used TAB as new line indent, should be consistent as others are using 4 spaces. Aslo there are a couple functions that have been removed from Python 3, including: upper become str.upper() join become sep.join(str) has_key() become key in dictionary

But after fixing all these, still could not run with an error:

Traceback (most recent call last):
  File "ROSE_main.py", line 497, in <module>
    main()
  File "ROSE_main.py", line 354, in main
    referenceCollection = ROSE_utils.gffToLocusCollection(inputGFFFile)
  File "/fast/users/a1692215/Rose/young_computation-rose-feb35cb1d955/ROSE_utils.py", line 534, in gffToLocusCollection
    return LocusCollection(lociList,window)
  File "/fast/users/a1692215/Rose/young_computation-rose-feb35cb1d955/ROSE_utils.py", line 332, in __init__
    for lcs in loci: self.__addLocus(lcs)
  File "/fast/users/a1692215/Rose/young_computation-rose-feb35cb1d955/ROSE_utils.py", line 341, in __addLocus
    for n in self.__getKeyRange(lcs):
  File "/fast/users/a1692215/Rose/young_computation-rose-feb35cb1d955/ROSE_utils.py", line 348, in __getKeyRange
    return range(start,end)
TypeError: 'float' object cannot be interpreted as an integer