changed {} to None as default function parameters and more

It is advised not to use mutable object (such as {} and []) as default
parameters to avoid possible bugs. See
http://satyajit.ranjeev.in/2012/01/12/python--dangerous-default-value-as-argument.html
for details.

Also fixed a typo
Add descriptive error to add_alpha_to_mapping_file

The library function was changed to check for the existance of the
specified rarefaction depth; it will now raise an exception if a
non-existant depth is passed. This exception is now catched from the
script interface and displayed using option_parser.error.

The test suite was updated accordingly for this module.

An unnecessary type cast was also removed from the script interface.

This should fix #827
Add available depths to the exception message
Add default depth as the highest

Mean alpha is now retrieve the highest available rarefaction depth when
None is specified. Script usage and unit tests were updated accordingly.

A new option was added to the script interface to indicate when the user
is trying to pass collated data as the input, since --depth is no longer
required to determine whether or not the execution will be over collated
or non-collated data, there was a redundancy that this option resolves.
Add --output_fp to print_metadata_stats.py

Add a new option to save the results of the script in a file. Add a new
script usage example with a corresponding update to the test_data
directory.

This is in favor the integration with Galaxy and should fix item 3 of #633
Add option to save the output of fix_arb_fasta.py

One usage example was added plus an update to the fix_arb_fasta folder
in the qiime_test_data.

This should fix item 2 of #633
Addd --output_fp option to relatedness.py

Add new script usage example where results are saved into a file.

This should fix item 5 of #633.
Change -i to -f in script_usage examples
Merge pull request #775 from RNAer/master

changed {} to None as default function parameters and more
Fixed typos

Thanks @jrrideout
Merge pull request #871 from ElDeveloper/print_metadata_stats_633

Add --output_fp to print_metadata_stats.py
Merge pull request #872 from ElDeveloper/fix_arb_fasta_633

Add option to save the output of fix_arb_fasta.py
Merge pull request #873 from ElDeveloper/relatedness_633

Addd --output_fp option to relatedness.py
replaced program name with %prog
modified language in output_fp option for clarity
fixed failure on metadata category with spaces

this fixes #765
Merge pull request #877 from gregcaporaso/doc-edits

Doc edits
Merge pull request #879 from gregcaporaso/issue-765

fixed failure on metadata category with spaces
Change redundant if else statement

Thanks @gregcaporaso!
Merge pull request #840 from ElDeveloper/issue_827

Add descriptive error to add_alpha_to_mapping_file