refactor a lot

analyze-cut.py

analyze-cycle.py

count_cdc.py

flower_snarks.py

graph_parameters.py

graph_tools/__init__.py

graph_tools/__main__.py

graph_tools/all.py

graph_tools/definitions.py

graph_tools/misc.py

graph_tools/parameters.py

graph_tools/sequences.py

graph_tools/tests.py

graph_tools/utils.py

test_cycle.py

utils.py