RNACONNECT

This project aims to build the interactive RNA-Protein interaction network on webserver, where people can submit their Proteins/RNAs code and get their neighbor interactions and perform the Breadth-First Search (BFS).

The BFS

The BFS_func.cpp can be served as independent program to search the shortest distance, as well as providing all shortest paths between 2 vertices.

Usage

You can compile this file by:
g++ BFS_func.cpp -o BFS_func
or
make BFS_func

Then type ./BFS_func -h for more information of the usage:

Options:
  -h [ --help ]                   Print the help message.
  -s [ --start ] arg              Start node.
  -e [ --end ] arg                End node.
  -g [ --graph ] arg              Adjacency dictionary in json format. If graph is not provided, the program will use a demo graph.
  -o [ --outfile ] arg            Export result as json format file.
  -d [ --distance_only ]          Only return shortest distance, not the path.
  -i [ --distance_information ]	  Perform the BFS faster with the known distances stored in json format file.

Notes

• When --graph option is not called, the program will use the graph in demo_graph.json in the directory by default. There is also a file larger_demo_graph.json, which is much larger in the directory, you can try it as an input.
• When --graph is called, make sure that your json file contains only string type information.
• If there is no path between Start node and End node, their distance is set to -1 and no path is provided.
• If one node is used for both Start and End node, if it's self-interacted, the distance will be 1, otherwise 0.
• The program will be much faster with the --distance_only mode than the return-paths mode.
• --distance_information field is a filename. That json format file contains information about distances. Check the distance_infor.json for the example.