Find Roles That Occur Close Together¶
p3-generate-close-roles.pl [options] <roles.tbl >pairs.tbl
This script is part of a pipeline to compute functionally-coupled roles. It takes a file of locations and roles, then outputs a file of pairs of roles with the number of times features containing those two roles occur close together on the chromosome. Such roles typically have related functions in a genome.
The input file must contain the following four fields.
contig (sequence) ID
location in the sequence
The default script assumes the four columns are in that order. This can all be overridden with command-line options.
The input file must be sorted by genome ID and then by sequence ID within genome ID. Otherwise, the results will be incorrect. Use p3-sort to sort the file.
The location is a PATRIC location string, either of the form start
Given a set of genome IDs in the file
genomes.tbl, you can generate the proper file using the following pipe.
p3-get-genome-features --attr sequence_id --attr location --attr product <genomes.tbl | p3-function-to-role
(If PATRIC does not yet have roles defined, you will need to use an additional command-line option on p3-function-to-role.)
There are no positional parameters.
The standard input can be overriddn using the options in Input Options.
Additional command-line options are
The index (1-based) or name of the column containing the genome ID. The default is
The index (1-based) or name of the column containing the sequence ID. The default is
The index (1-based) or name of the column containing the location string. The default is
The index (1-based) or name of the column containing the role description. The default is
The maximum space between two features considered close. The default is
The minimum number of occurrences for a pair to be considered significant. The default is