svr_aligns_with_prot

    svr_aligns_with_prot         < fid-md5 > table-with-2-more-columns
    svr_aligns_with_prot --roles < fid-md5 > table-with-4-more-columns
    svr_aligns_with_prot --text  < fid-md5 > textual-descriptions

Get the list of alignments associated with each specified protein or fid.

This script takes as input a tab-delimited file with gene or protein IDs at the end of each line. For each ID, the associated alignment data are retrieved and appended.

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

If a single ID is associated with multiple alignments, there will be one output line for each alignment.

Similarly, the --roles option adds one line per role found in the tree

Command-Line Options

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.

roles

Add two additional columns with roles and their counts in the alignment. The number of roles is capped at 25 most commonly occurring.

text

Output data in a more human friendly manner. Implies -roles.

url

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