cast main_utils.InputDerivedDataArgs.mean_virome to int for py3 compatibility of string multiplication.

* IData_handling.genomeFastaRecovery had an extra open() of the file,
and was reading the file without closing it, unsafely. Removed unneeded
open().
* main_utils.checkFastaFile was using "U" option in opening files, not
needed and deprecated.
* read_Coverage_res was using time.clock() in a couple of places, which
is deprecated. replaced with time.time().

Changed _modules/ and PhageTerm.py and
test_functions_PhageTerm_for_multi.py to use py3-style print functions.

Py2-compatible due to __future__ imports.

Also added both-versions compatible translate method in
_modules/utilities.py.

 - Test arguments (e.g. which test dataset to run) are not checked for validity, which leads to a confusing
error. I added a check for this (an else block) with an informative
error message.
 - I unpinned libcxx in env.yml file to work for me.

work in process for processing the mapping results produced by the GPU on several cores accross the cluster

added comments in doxygen format for doc generation, added traces in debug mode, removed unuseful parameter