removed unused 'os' import in console
wow, sequence had two remove_gene methods. now it has one.
removed unused imports in gffreader
removed 'remove_mrnas_with_cds_shorter_than' methods in console controller and gene; they are replaced by filters
cosmetic improvements to sequence.py
removed unused variables from seq.get_longest_etc.
more unused variables removed from sequence
removed dangerous default value of [] from gene_part.write_tbl
removed unused 'i' in gene_part.invalidate_region
removed unused imports from console controller
cosmetic enhancements to console controller
removed default [] in mrna.__init__
removed clean_up_indices from gene, mrna and gene_part; not used
removed 'remove_invalid_stuff' commands from gene, mrna, gene_part. maybe i can sleep tonight