Documentation read from 04/17/2019 22:07:28 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_sphinx_indexing.



Use sphinx indexes to match a keyword query (returning a table [peg,weight,annotation] By default it returns PEGs from pubSEED. The -c option supports coreSEED instead. ------


    svr_sphinx_indexing -k 'ribosomal protein streptococcus s1p'

would produce a 3-column table. The first column would contain PEG IDs for genes that somehow matched the keywords.

Command-Line Options

-k keywords

Make sure you enclose the list of keywords with apostrophes


Use coreSEED, rather than pubSEED

Output Format

The standard output is a 3-column tab-delimited file.

    column 1:  a PEG ID
    column 2:  a weight (the higher, the more solid the match)                                       
    column 3:  the annotation stored in the indexes (it may be out of date)