Documentation read from 04/17/2019 22:07:26 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_expressed_genes_in_range.



    svr_expressed_genes_in_range --min=minLevel --max=maxLevel <genome_ids.tbl >genome_data.tbl

Compute the genes in the specified genomes that are expressed a particular fraction of the time, where the fraction is a number between 0 and 1. The fraction is specified as a range from a minimum to a maximum value. If the minimum is 1, then only genes expressed all the time are returned. If the maximum is 0, then only genes that are never expressed are returned.

The expression level is computed by taking all the experiment results called on and dividing them by the total number of results called either on or off. In other words, results that are called as indeterminate are ignored in the computation.

This script takes as input a tab-delimited file with genome IDs at the end of each line. For each genome ID, multiple output lines will be generated-- one per qualified gene-- and each generated line will have a level fraction and a FIG gene ID appended to it.

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

The following command-line options are supported.


The URL to use for the server. This is primarily a debugging option, and is used to specify an alternate server script.


The index (1-based) of the column containing the genome ID. If this option is omitted, the last column is used.


The minimum acceptable expression level. The default is 0, meaning all genes with an expression level less than or equal to the maximum will be returned.


The maximum acceptable expression level. The default is 1, meaning all genes with an expression level greater than or equal to the minimum level will be returned.