Are there any pci-e controllers that take like a SPI signal, or USB and then lets me hookup a pci-e x1 card to it?
Usually the PCIe root complex is a part of the SoC. If PCIe is needed you just select an SoC that has it built-in. Example: i.MX6, Sitara.

It could of course be designed in an FPGA and connected by SPI or anything to the SoC, but that defeats the main point of PCIe, which is high-bandwidth applications. Having SPI on the host side could work but would make in unbearably slow.