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



    svr_ids_to_subsystems <gene_ids.tbl >subsystems.tbl 2> lines from input file having no subsystem match

List the subsystems for each specified gene ID STDOUT. List on STDERR those lines where the id does not have a subsystem.

This script takes as input a tab-delimited file with gene IDs at the end of each line. For each gene ID, the subsystem containing the gene is appended to the line.

This is a pipe command: the input is taken from the standard input and the output is to the standard output.

Note that because some genes belong to multiple subsystems, there may be more output items than input lines.

Command-Line Options


Database source of the IDs specified-- SEED for FIG IDs, GENE for standard gene identifiers, or LocusTag for locus tags. In addition, you may specify RefSeq, CMR, NCBI, Trembl, or UniProt for IDs from those databases. Use mixed to allow mixed ID types (though this may cause problems when the same ID has different meanings in different databases). Use prefixed to allow IDs with prefixing indicating the ID type (e.g. uni|P00934 for a UniProt ID, gi|135813 for an NCBI identifier, and so forth). The default is SEED.


The URL for the Sapling server, if it is to be different from the default.


Include the subsystem role in the output. The role will appear after the subsystem name.


Column index. If specified, indicates that the input IDs should be taken from the indicated column instead of the last column. The first column is column 1.