Find Neighbors

Beyond the basics of finding aliases and function, a more advanced analysis might require finding the PEGs that are in the neighborhood of a given PEG. This command takes as input a tab-separated table where the last field in each line contains the PEG for which a list of neighbors is being requested. It takes an argument telling how many neighbors to find to the left and right. The output file is the input file with an extra column appended at the end (containing a list of neighbors).

svr_neighbors_of n < table_of_gene_ids

Note that this script uses stdin and stdout and is designed to be part of a processing pipeline. 

The code for this server is here. The man page is here.

Here is an example of running this command:

> svr_all_features 3702.1 peg | svr_neighbors_of 5
fig|3702.1.peg.1 fig|3702.1.peg.2,fig|3702.1.peg.3,fig|3702.1.peg.4,fig|3702.1.peg.5,fig|3702.1.peg.6
fig|3702.1.peg.2 fig|3702.1.peg.1,fig|3702.1.peg.3,fig|3702.1.peg.4,fig|3702.1.peg.5,fig|3702.1.peg.6,fig|3702.1.peg.7
fig|3702.1.peg.3 fig|3702.1.peg.1,fig|3702.1.peg.2,fig|3702.1.peg.4,fig|3702.1.peg.5,fig|3702.1.peg.6,fig|3702.1.peg.7,fi
fig|3702.1.peg.4 fig|3702.1.peg.1,fig|3702.1.peg.2,fig|3702.1.peg.3,fig|3702.1.peg.5,fig|3702.1.peg.6,fig|3702.1.peg.7,fi
fig|3702.1.peg.5 fig|3702.1.peg.1,fig|3702.1.peg.2,fig|3702.1.peg.3,fig|3702.1.peg.4,fig|3702.1.peg.6,fig|3702.1.peg.7,fi