more logo beautification
removed create_starts_and_stops command from console controller; it's all or nothing
added seq_fixer class
console controller now calls seq_fixer.fix(seq) on stats() call
sequence.remove_terminal_ns passed first test
sequence.remove_terminal_ns passed reverse test too
sequence.remove_terminal_ns seems trustworthy
added remove terminal ns call to seq_fixer; just one fix left to implement
lots of cleanup in console
cleaned up formatting on help messages
removed barf command from console controller; not sure what it did. hooray ignorance
removed barftofile from console controller
removed trim_region from console controller; it was hideous and nobody was calling it anyway
added ultra-complex console_controller.genome_is_loaded boolean function. don't try to read it, it'll make your brain explode
console won't let you try to fix, write, etc. if no genome is loaded
oops, i overdid it. console now lets you enter the load menu if nothing is loaded :)
added contains_mrna method to console controller
added contains_gene method to console controller
added mrna_id hints to write cds fasta; returns to main menu on success
write gene tbl and write gene gff now give hints, return to main menu on success