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



Try to identify genus and species of DNA fragments



    echo '83333.1 | svr_which_genus_species -n 200 -s 550 | svr_which_genus_species

would produce a 3-column table. The first column would contain the genome ID (83333.1), the second a 550 bp piece of DNA from the genome, and the third would be the predicted species. Fragments that could not be predicted are written to STDERR.


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 sequence for which the species is desired. If some other column contains the fragments, use

    -c N

where N is the column (from 1) that contains the sequence in each case.

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 sequences is not the last.

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (a prediction). Input that does not result in a prediction is written to STDERR.