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



    svr_ids_to_figfams <gene_ids.tbl >figfam_data.tbl 2> 

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

This script takes as input a tab-delimited file with gene IDs at the end of each line. For each gene ID, the FIGfam containing the gene and that FIGfam's associated function are appended to the line. The functional is placed first and the FIGfam follows.

If the --idsOnly option is specified, then the orginal input is discarded, and only the FIGfam ID and the role will be output. Duplicate FIGfam IDs will be conflated, so that you get a complete list of the FIGfams covered by the input genes.

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 FIGfams, there may be more output items than input lines.

Command-Line Options


If specified, only the IDs of the FIGfams found will be output, and duplicate IDs will be conflated. Use this to get a list of all the FIGfams for a specified list of genes.


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.


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.