Added output filename argument

[Jason Vander Heiden]

We might want to allow overwrite of the input file and/or explicit specification of the output file name with an optional --overwrite argument. We would have to write to a tempfile, then move the tempfile after the task is done, but that shouldn't require much of a change if we tie it to an optional argument.

[Jason Vander Heiden]

Okay, I'm going to go with "no" on the --overwrite argument, but we can add an explicit output file name argument instead (as per -o in changeo). At the same time, we can do #62 as well as swap things to the simpler interface that doesn't load everything into SeqRecord objects.

[Jason Vander Heiden]

Well that was tedious. Done in d069248. Still needs some testing though.