svr_link_to_compare_regions

Get link to compare regions organized to show co-occuring genes

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Example:

    echo 'fig|83333.1.peg.4' | svr_link_to_compare_regions > 2-col.txt

would produce a 2-column table (in this case containing a single row). The first column would contain a PEG id (in this case fig|83333.1.peg.4) and the second a URL to illustrate conserved contiguity.

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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 PEG for which functions are being requested. If some other column contains the PEGs, use

    -c N

where N is the column (from 1) that contains the PEG 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 PEGs is not the last.

-b Base of URL (to the appropriate SEED) [default=http://pubseed.theseed.org which is the PubSEED]

This allows the user to specify which SEED he wishes the links to point at

-m Minimum Functional Coupling Score [default=10]

This parameter lets the user give a minimum FC score (which is the number of distinct OTUs in which co-occurrence has been detected).

-g GenomesFile [an optional file designating a restricted list of genomes for the links]

This allows the user to restrict the compare region to a limited set of genomes.

-show N [default is 10] k This gives the number of genomes to actually show.

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (the URL to produce the desired compare region).