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



Create random samples of DNA from known genomes



    echo '83333.1 | svr_generate_dna_samples -n 200 -s 550

would produce a 2-column table. The first column would contain the genome ID (83333.1) and the second a 550 bp piece of DNA from the genome. There would be 200 rows in the table


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 genome for which sequence is being requested. If some other column contains the genomes, use

    -c N

where N is the column (from 1) that contains the genome ID 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 genomes is not the last.

-s [default: 500]

Size of the requested fragments.

-n [number of rows to output for each input genome]

Note that this times the number of input lines gives the number of fragments.

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (a fragment of DNA)