.. _cli::p3-find-features:


################
p3-find-features
################


*************************************
Find Features By Filtering on a Field
*************************************



.. code-block:: perl

     p3-find-features.pl [options] keyName


This script finds features based on the value in one of several feature-identifying fields (other than \ ``patric_id``\ ).
It provides standard filtering parameters to otherwise limit the output. (So, for example, you can require that the
features output belong only to a specific genome using \ ``--eq genome_id``\ .)

Parameters
==========


The positional parameter is the name of the field used to match the incoming keys. The following fields are permitted.


- refseq_locus_tag
 
 The locus tag from REFSEQ
 


- protein_id
 
 The REFSEQ protein ID.
 


- gene
 
 The common gene name (e.g. \ ``rpoA``\ ).
 


- gene_id
 
 The standard gene number.
 


- aa_sequence_md5
 
 The protein sequence MD5 code.
 


- product
 
 The functional assignment of the feature. A standard SOLR-type substring match is used.
 


The standard input can be overridden using the options in :ref:`cli-input-options`.

Additional command-line options are those given in :ref:`cli-data-options` and :ref:`cli-column-options` plus the following.


- keyNames
 
 Rather than processing the input, list the valid key names.
 


Example
-------



.. code-block:: perl

     This command is shown in the tutorial p3_common_tasks.html
 
     p3-echo coaA | p3-find-features --attr patric_id,product --eq genome_id,210007.7 gene
 
     p3-echo coaA | p3-find-features --attr patric_id,product gene
     id  feature.patric_id   feature.product
     coaA    fig|996634.5.peg.916    Pantothenate kinase (EC 2.7.1.33)
     coaA    fig|944560.4.peg.377    Pantothenate kinase (EC 2.7.1.33)
     coaA    fig|992133.3.peg.4201   Pantothenate kinase (EC 2.7.1.33)
     coaA    fig|992141.3.peg.4166   Pantothenate kinase (EC 2.7.1.33)
     ...