Add a warning to usage for assembly_comparison.py
order_assembly.py based on assembly_comparison.py

The layout ordering from assembly_comparison.py isn't always what
we want for re-ordering an assembly FASTA file.
Add warning to assembly_comparison.py suggesting order_assembly.py
TODO comment regarding constants as command line options
Ignore length of pre-hit sequence in query for order_assembly.py

For drawing in assembly_comparison.py need to consider this; perhaps can
be solved with separation of the visual layout offset and a weighted
sort key?
Avoid median problem of phantom placement