Drizzle olive oil into a saucepan. Add onions, chile pepper, garlic, anchovy filet, red pepper flakes, and salt; place over medium-high heat. Stir and cook until onions and garlic just start to turn golden, 3 or 4 minutes.

Stir in wine and simmer until wine is reduced by about half, 3 to 5 minutes. Add clam juice, tomatoes, and oregano. Bring to a boil, reduce heat to medium-low, and simmer gently for about 15 minutes.

Gently stir in calamari and simmer until tender, 35 to 45 minutes. Remove from heat. Stir in parsley.

Bring a large pot of lightly salted water to a boil. Cook spaghetti in the boiling water, stirring occasionally until tender yet firm to the bite, about 12 minutes. Drain.

Stir some sauce into the hot, drained pasta. Serve in warm bowls topped with more marinara sauce and grated cheese.