svr_dna_seq

    svr_dna_seq <ids.tbl >sequences.tbl

Produce DNA strings for contigs, FIG feature IDs, and/or locations.

This script takes as input a tab-delimited file with contig IDs and locations at the end of each line. For each one, the appropriate DNA or protein sequence is written to the output file. If the --fasta option is specified, the sequence is written in FASTA format.

This is a pipe command: the input is taken from the standard input and the output to the standard output. The columns of data preceding the first will be supplied as comments to each FASTA string.

Command-Line Options

fasta

If specified, the output sequences will be FASTA format, otherwise just simple character strings. The default is FALSE. In this case the output file will look the same as the input file but with DNA sequences tacked onto the end of each line.

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.