Ignore compiled python files.
Check if keys exist before converting to float.
Remove commented out code.
Extract sequence from postscript files.

This fixes several bugs with regexes, flake8 complaints and transformations. In
addition I changed around the use of the Base class. All this combines to create
something which can extract the sequence for and E. coli 16S. This will probably
work for 16S 2D's but possibly not others.
Add infrastructure to generate 2D positions.

We need to load the nt information from somewhere, deal with missing nts and
output the new data. This commit adds most of that. We can't yet deal with
missing nts inside the structure, but that is fixable. This assumes that the nt
data will be stored in a json file and should be written to a json file. It can
add entries for missing nts at the beginning or end.