svr_upstream

    svr_upstream <gene_ids.tbl >upstream_dna.fasta

Retrieve upstream regions from the Sapling Server.

This script takes as input a tab-delimited file with feature IDs at the end. For each feature ID, the upstream DNA is computed and written to the output file in FASTA format. Sections of DNA that occur inside a feature are shown in upper case. DNA between known features is shown in lower case.

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

Command-Line Options

skipGene

If specified, then only the upstream region is output. Otherwise, the upstream region and the feature interior are output together.

size

Number of base pairs to show in the upstream region. The default is 200.

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.