Old question, but first hit on Google and no correct answer.
Those files are "lock"-files, usually created by an editor. Lock files come in many different shapes, but both
joe creates symlinks named like in your example - as .#[original-filename].
Lock files are used to prevent multiple instances from editing the same file, simultaneous (eg. 2 different users wanting to edit the same file).
If you run
$ joe netMHC3.2.py
a lock-file will be created named
When the editor closes, the file gets deleted. If the editor crashes, its left behind and becomes a "stale lock". You can delete the file manually at this point, but most editors give you that option automatically when editing the file next time.