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.
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
Fix loader to read line by line (instead of whole file)
Merge pull request #131 from mlangill/change_precalc_format

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