p3-uni-roles¶
Produce a Table of Singly-Occurring Roles For Genomes¶
p3-uni-roles.pl [options] outFile
Given an input list of genome IDs, this program produces a list of the roles that are singly-occurring. The output file will contain a genome ID in the first column, the domain in the second column, the seed protein sequence in the third column, and the additional columns will contain the IDs of the singly-occurring roles. The roles are taken from a typical roles.in.subsystems file, which contains a role ID in the first column, a role checksum in the second, and a role name in the third.
Status is displayed on the standard output.
Parameters¶
The positional parameter is the name of the output file.
The standard input can be overridden using the options in Input Options. Use the options in Column Options to identify the column containing genome IDs.
The following additional command-line options are supported.
roleFile
The
roles.in.subsystemsfile containing the roles to process. This is a tab-delimited file with no headers. Each line contains (0) a role ID, (1) a role checksum, and (2) a role name. The default isroles.unifiedin the SEEDtk global data directory.
resume
Use this option to restart an interrupted job. It specifies the genome ID of the last genome processed in the previous run. New results are appended to the output file.