added trace to have a n idea of the time needed to retrieve the number of reacors in the input fastq file

added trace to have a n idea of the time needed to retrieve the number of reacors in the input fastq file

* 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.

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