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 taxonomy as a valid string

When using taxonomy as a header key in parse_classic_otu_table, this
function would fail. Fixes #866.
updated to reduce the frequency of a stochastic failure
updated some comments
Merge pull request #869 from gregcaporaso/issue-864

addresses one of the stochastic failures noted in #864
Modified qiime/pick_otus.py so reference based OTU picking (usearch 5.X and 6.1) will create the failures file, even if there are no failures to write to address issue #868
Merge pull request #870 from walterst/gregs-edits

Modified qiime/pick_otus.py so reference based OTU picking (usearch 5.X ...
Merge pull request #867 from ElDeveloper/issue_866

Add taxonomy as a valid string
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