Python 2/3 compatibility

[nvictus]

This is probably still incomplete and requires more testing, so maybe keep in another branch until ready. In short, the consequential changes:

• shebang and executable permissions added to HiCPlotter.py. Should have no effect on windows.
• print statements replaced with print functions and real division activated using __future__ imports
• xrange replaced with range
• Deprecated for line in file.xreadlines() replaced with for line in file:
• max in cmatrix = log2(pow(2, ceil(log2(max(matrix))/log2(2)))) replaced with np.nanmax

Issues that will probably arise will involve integer division and incompatibility of comparing objects of different types (e.g. int > list). Other hangups can most likely be resolved with the six package.

Style-wise, the changes are:

• tabs to spaces :)
• other pep8 formatting changes in the upper functions, but not comprehensive
• added some numpydoc-style docstrings
• deleted lots of .DS_Store junk files and added a .gitignore

EDIT: oh, and also, fixed the default end point for read_Cooldata to end = c.chromsizes[chrom], as we discussed :P

[lachlansimpson]

These changes look good on the face of it. I've only just found this now, having already made HiCPlotter exec and added the #!/bin/env python.

Any reason for not merging?

[akdemirlab]

Million thanks to Nezar! 😃
No reason for not merging, I just need some free time for testing python3 functions.