svr_ach_lookup

    svr_ach_lookup <gene_ids.tbl >assertions.tbl

Find protein assertions from the Annotation Clearinghouse.

This script takes as input a tab-delimited file with gene or protein IDs at the end of each line. For each ID, the assertions related to the identified protein sequence are returned in another tab-delimited file. Assertions for all genes that have the same sequence as the identified protein will be returned.

The IDs should be in prefixed form, e.g. cmd|4808340, gi|21221828, uni|Q9X8I1.

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

1. The incoming ID.
2. The ID of the gene whose assertion was found in the database.
3. The text of the assertion.
4. The source of the assertion, usually a user name or institution identifier.
5. A flag that is TRUE if the assertion is by a human expert, else FALSE.

Command-Line Options

url

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

c

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.