* 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().