reStructuredText markup in `--help` output

[mr-c]

This was an early design decision on my part to enable richer formatting in the auto generated scripts documentation.

Since we specify the method or attribute name to sphinx-contrib.autoprogram of the argparse.ArgumentParser to use we can programmatically manipulate it before usage in the script itself.

Bonus: instead of down converting the rST syntax to plain text, use blessings to add bold or italics effects as is useful.

[mr-c]

Example from normalize-by-median.py --help:

With :option:`-s`/:option:`--savetable`, the k-mer counting table
will be saved to the specified file after all sequences have been
processed. With :option:`-d`, the k-mer counting table will be
saved every d files for multifile runs; if :option:`-s` is set,
the specified name will be used, and if not, the name `backup.ct`
will be used.  :option:`-l`/:option:`--loadtable` will load the
specified k-mer counting table before processing the specified
files.  Note that these tables are are in the same format as those
produced by :program:`load-into-counting.py` and consumed by
:program:`abundance-dist.py`.

Specifically:

`:option:`-l`/:option:`--loadtable`

could be rendered as -l,--loadtable and

:program:`load-into-counting.py`

could be rendered as load-into-counting.py and

`backup.ct`

could be rendered using underline (which is not possible to demonstrate in this comment)

All together:

With -s,--savetable, the k-mer counting table will be saved to the specified file after all sequences have been processed. With -d, the k-mer counting table will be saved every d files for multifile runs; if -s is set, the specified name will be used, and if not, the name backup.ct will be used. -l,--loadtable will load the specified k-mer counting table before processing the specified files. Note that these tables are are in the same format as those produced by load-into-counting.py and consumed by abundance-dist.py.

[mr-c]

Note that blessings will turn off terminal effects automatically if connected to a pipe https://pypi.python.org/pypi/blessings#pipe-savvy

[ctb]

s/problematically/programmatically/

[mr-c]

@ctb thx