svr_aliases_to_pegs

Convert aliases to PEGs

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Example:

    svr_aliases_to_pegs -protein < aliases > plus_PEGs 2> no.matches

assumes that the files aliases ends with a column containing aliases. An extra column containing PEGs will be added, and those aliases that do not match PEGs will be 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 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.

-protein=1 (optional)

If TRUE, then all FIG IDs for equivalent proteins will be returned. The default is FALSE, meaning that only FIG IDs for the same gene will be returned.

-source

Specifies the source of the incoming IDs. The default is prefixed, which means the type of the incoming ID will be determined by its prefix (gi for NCBI numbers, uni for UniProt IDs). Otherwise, use the name of the database from which the IDs were taken: RefSeq, CMR, NCBI, Trembl, or UniProt.

Output Format

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