LocalNeighborhood

Local Neighborhood Docker image

A simple pathway reconstruction algorithm used to welcome new contributors. The algorithm takes a network and a list of nodes as input. It outputs all edges in the network that have a node from the list as an endpoint.

New contributors complete the Dockerfile to wrap the implementation in local_neighborhood.py.

Usage

$ python local_neighborhood.py -h
usage: local_neighborhood.py [-h] --network NETWORK --nodes NODES --output OUTPUT  

Local neighborhood pathway reconstruction

optional arguments:
  -h, --help         show this help message and exit
  --network NETWORK  Path to the network file with '|' delimited node pairs
  --nodes NODES      Path to the nodes file
  --output OUTPUT    Path to the output file that will be written

Example behavior

Network file:

A|B
C|B
C|D
D|E
A|E

Nodes file:

A
B

Output file:

A|B
C|B
A|E