.. _cli::p3-find-in-clusters:


###################
p3-find-in-clusters
###################


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Identify Clusters Containing Input Features
*******************************************



.. code-block:: perl

     p3-find-in-clusters.pl [options] realClusterFile


This script takes as input a list of features and compares it to a list of physical clusters (the output of :ref:`cli::p3-identify-clusters`).
If a features is within the bounds of a cluster, or within the gap distance of either end, it will be output with the cluster ID appended.

Parameters
==========


The positional parameter is the name of the file containing the cluster information. This must be a tab-delimited file with the following
columns-- (1) cluster ID, (2) genome ID, (3) sequence ID, (4) start location, and (5) end location. This is the output format from
:ref:`cli::p3-identify-clusters`.

The standard input can be overriddn using the options in :ref:`cli-input-options`. The standard input should contain feature IDs in the
key column (specified using the options in :ref:`cli-column-options`) plus the feature location and the ID of the containing sequence.
The following additional options are supported.


- maxGap
 
 The maximum number of base pairs allowed between two features in the same cluster. The default is \ ``2000``\ .
 


- location
 
 In index (1-based) or name of the column containing the feature location. The default is \ ``location``\ .
 


- sequence
 
 The index (1-based) or name of the column containing the sequence ID. The defahult is \ ``sequence_id``\ .