Removed some parentheses
Bio::Root::IO::file() now reports filename and mode in array context
and associated code changes to take advantage of this [Florent Angly]
Missed a change during the Root merge
More consistent IO error messages

1/ use of the past tense
2/ quoting of filenames to catch subtle errors such as trailing spaces
3/ use of throw() instead of die
Separate method for clean filename and mode, for backward compatibility

Also renamed $obj to $self for consistency
More concise skip_all message [Florent Angly]
Fixed bad filename

Was "sample_dataset.tigr " instead of "sample_dataset.tigr" (no trailing space)
Also made style more consistent
Fixed filename in test

Should be ">$o_file" and not "> $o_file"
Also did miscellaneous cleaning (tabs, parentheses)