svr_which_genus_species

Try to identify genus and species of DNA fragments

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Example:

    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.

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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.