don't rely on data/rank_thresholds.csv

[nhoffman]

Problem: tax_ids missing from the version of the file rank_thresholds.csv that is distributed with the package will never be included in a classification because the corresponding threshold will be NA (this is seen after joining blast_results with rank_thresholds around line 650 of classifier.py).

We need to do a few things to address this:

• remove data/rank_thresholds.csv entirely from the repository
• make sure that data/rank_threshold_defaults.csv is distributed with the package (currently it appears in the repo, but doesn't seem to be installed along with the package)
• the default behavior should be to apply default thresholds according to rank (not tax_id)
• a user may still specify a rank thresholds file (using --rank-thresholds); in this case, use thresholds for any tax_ids that are represented, and fill in defaults by rank. If the rank thresholds file is provided, there should be an info-level logging message when defaults are used for missing tax_ids.
• classifier.py should exit with an error if any thresholds are missing after the above operations (look for specific thresholds, fill in with defaults)

At this point we should focus on implementing the above as opposed to refactoring tax2thresholds

[crosenth]

Summary dev steps:

1. The default thresholds will be defined and input using this file and format: (https://github.com/nhoffman/bioy/blob/master/bioy_pkg/data/rank_threshold_defaults.csv).
2. Users can provide additional rank_thresholds with the --rank-thresholds argument and same four column file format.
3. Users would define default behavior by rank and taxon (via tax_id). For example, a global default taxonomic threshold would be defined by "root" and propagated to any member of the "root" lineage. Users can override a global, root threshold by defining more specific taxon. For example, a user could additionally define overriding genus level thresholds for all Bacillus species.
4. classifier.py should exit with an error if any thresholds are missing after the above operations or any thresholds input is invalid.

tax2thresholds will be DEPRECATED

Previously we corrected a rank_thresholds bug in v1.9 associated with issue https://github.com/nhoffman/bioy/issues/32. All users should upgrade to at least 1.9.1 (or preferably the latest tagged version of bioy) to avoid this bug.