Add --lineage option to convert_gff3_to_gbk.py
Add --include-sequence option to convert_gff3_to_gbk.py
Replace --include-sequence with --include_sequence for consistency.
Add --output_dir option: writes a single flat file for each input assembly.
Merge pull request #20 from jonathancrabtree/master

Add --lineage, --include_sequence, and --output_dir to convert_gff3_to_gbk.py