Fix outputting of tab-delimited PICRUSt prediction

Previously, observation metadata field was hard-coded to "KEGG Pathways".
However, this changed to "KEGG_Pathways", but could also be COG based (COG_Category).
Even more complicated is that there may also be additional metadata fields (e.g "KEGG_Description").
Choice was made to output the metadata field containing .*Description (e.g. either KEGG_Description or COG_Description).
If KEGG_Pathway or COG_Category information is needed then user should output in BIOM format
and use categorize_by_function.py to get output in tab-delimited for the "level" they want.

Fix #114
Update predict_metagenomes.py testing files
Add better fallback for metadata in tab-delim output

In case the precalculated file does not contain a metadata field
with "*Description" in it, then just output the first obs_metadata,
and if no obs_metadata then don't output any.
Fix typo
Fix up metagenome_contributions.py

Remove unneeded options and update usage statements.
Also, update the selection of the precalculated file so it is
similar to predict_metagenomes.py.
Add script testing data for metagenome_contributions.py
Update BIOM version dependency to 1.1.2

Fixes #125
Update news
Merge pull request #115 from mlangill/issue114

Fix output of tab-delimited format for predict_metagenomes.py
Change predict_metagenomes.py to load tab-delim precalc file

This changes the default behaviour of predict_metagenomes.py to
load a new tab-delimited format. It can still load the old BIOM precalc file
by using the --load_precalc_file_in_biom option.

The new precalc format is tab-delimited with otu ids as row ids and trait ids (e.g. KO ids) as sample ids (note this is transposed from the BIOM format but is essential for easy partial loading of OTUs).

OTU and trait metadata is found by using the 'metadata_' prefix which is removed when loading into BIOM.

This speeds up loading tremendously in both time and memory usage. Now < 700mb memory and <20 seconds.
Change output to tab-delimited for predict_traits.py
Change options for calculating NSTI in predict_traits.py

If calculating NSTI, most of the time we don't need a separate file
with the measures since it is in the main output file (both tab or biom format),
so change -a option to a store_true option (instead of specifying a filepath).

Might still be convenient to get NSTI values without having to do all of the predict trait steps, so add option --output_accuracy_metric_results that takes a filepath and outputs NSTI to that file and exits before doing rest of predictions.
Merge pull request #129 from mlangill/issue125

Update news and biom version in docs
Change to not using BIOM format for precalc file

predict_traits.py defaults to outputting to new "precalc" format,
which is tab-delimited and embeds the metadata using the 'metadata_' prefix.

predict_metagenomes.py and normalize_by_copy_number.py takes this new
'precalc' format as input.
Update script testing files
Add parallel_predict_traits.py
Fix loader to read line by line (instead of whole file)
Improve memory usage when combining files

Simply code in parallel_predict_traits.py and more importantly
ensure only one of the output files is combined in memory at a single time.
Add delay option and speed up combine in parallel_predict_traits.py

Allow the user to add a delay (sleep) between each job submission in seconds.

Also, vastly speed up file combining by using += instead of = blah+blah
Merge pull request #131 from mlangill/change_precalc_format

Change PICRUSt precalculated file format from BIOM to in-house tab-delim format