Dark-matter

Added `--readCountColor` and `--defaultReadCountColor` to
`proteins-to-pathogens-civ.py` for differential coloring of read
counts. Added `citrus yellow` to plant-only virus name regex in
`dark/taxonomy.py`.

Added a const value for `--pathogenPanelFilename` in `proteins-to-pathogens-civ.py`.

Added `--dnaOnly` and `--maxGenomeLength` args to `make-protein-database.py`.
Improved `isRNAVirus` function so it returns `True` on retroviridae.
Improved the log output of the same script. Added a test (for HIV as an RNA
virus) and some small clean-ups.

Fixed incorrect `with` statement in `taxonomy.py`. Improved description of
fields in civ proteins HTML.

Standardized scripts that need a taxonomy database to use
`--taxonomyDatabase` on the command line and two utility functions in
`dark/taxonomy.py` to read them and also look in the
`DARK_MATTER_TAXONOMY_DATABASE` environment variable.

Added `dryRun`, `useStderr`, and handling of keyword arguments to the
`Executor.execute` method (in `dark/process.py`).

Add `LineageElement` to `taxonomy.py`. Get rid of `_preprocessLineage`
function and instead just have the `Taxonomy.lineageFromTaxid` method
adjust the 'no rank' ranks to be `-`. Added `skipFunc` and `stopFunc` to
lineage processing.

Make it so `get-taxonomy.py` and `get-hosts.py` can accept a name (e.g.,
Hymenoptera) as well as a taxonomy id or accession number.