Update EMBL.pm

When unable to open file for reading add the reason for failure.
Update Fastaq.pm

When unable to open file for reading add the reason for failure.
Update SwissPfam.pm

When unable to open file for reading add the reason for failure.
Update GeneBank.pm

When unable to open file for reading add the reason for failure.
Update Qual.pm

When unable to open file for reading add the reason for failure.
Update Fasta.pm

When unable to open file for reading add the reason for failure.
Update bp_oligo_count.pl

When unable to open file for writing add the reason for failure.
Update GenBank.pm

fix typo $1/$!
Massive check of file open lines. Changed bareword filehandles
to lexical with three-argument opens calls, added die/throw
and reason of failure $! where missing, and made error messages
more uniform and consistent with Florent Angly messages for Root
(like quoting of filenames). Also deleted a few unused open
filehandles and some unnecessary parenthesis. Tests pass.
Changed some open calls from 2 to 3 arguments,
and added a few missing "die" messages