.. _cli::p3-gto-dna:


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p3-gto-dna
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Extract DNA from a GTO
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.. code-block:: perl

     p3-gto-dna.pl [options] gtoFile


This script reads one or more locations from the standard input and outputs the corresponding DNA from the input `GenomeTypeObject <GenomeTypeObject>`_ file.

Parameters
==========


The positional parameter should be the name of the `GenomeTypeObject <GenomeTypeObject>`_ file in JSON format.

The standard input can be overridden using the options in :ref:`cli-input-options`. The standard input should contain location
strings in the key column (specified using :ref:`cli-column-options`) and the region name in the column identified by the
\ ``--label``\  parameter.

Location strings are of the form \ *contigID*\ \ ``_``\ \ *start*\ \ ``+``\ \ *len*\  for the forward strand and \ *contigID*\ \ ``_``\ \ *start*\ \ ``-``\ \ *len*\  for
the backward strand.

Additional command-line options are as follows.


- fasta
 
 Output should be in FASTA format, with the region name as the ID.
 


- label
 
 Index (1-based) or name of the column containing the region names. The default is the first column (\ ``1``\ ).