Documentation read from 01/25/2012 11:58:34 version of /scratch/FIGdisk.server/FIG/bin/svr_neighbors_of.



    svr_neighbors_of <gene_ids.tbl >neighbor_ids.tbl

Get neighbors of protein-encoding genes (PEGs)

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the PEG for which a list of neighbors is being requested. If some other column contains the feature IDs, use

    -c n

where n is the column (from 1) that contains the PEG in each case. You are allowed to specify the number of neighbors you want using

     -N n 

where n in this case is the number to each side of a given PEG. That is, a value of 5 would lead to a result composed of the 5 genes to the left and the 5 genes to the right.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c Column

This is used only if the column containing PEGs is not the last.

-N number-neighbors

This value is the number to the left and the number to the right of the given gene. Hence, you would normally get twice this number as the detected set of neighbors. You may get less if the given gene occurs near the beginning or end of a contig.

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (i.e., the column containing the comma-separated list of neighbors).


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