Loading GFF files
=================

The first column of a GFF file is the reference sequence ID.
Usually, in order to load a GFF file, it's required to have a reference FASTA file loaded.
But some GFF files already have the reference features such as chromosome or scaffold.
In this case, there are two options:

* Load the GFF directly, without a reference FASTA file
* Load the FASTA file and then load the GFF using the parameter 'ignore' to not load the reference features

The GFF file must be indexed using `tabix <http://www.htslib.org/doc/tabix.html>`_.

Load GFF
----------

.. code-block:: bash

    python manage.py load_gff --file organism_genes_sorted.gff3.gz --organism 'Arabidopsis thaliana'

* Loading this file can be faster if you increase the number of threads (--cpu).

.. code-block:: bash

    python manage.py load_gff --help


==========    ==================================================================================
--file 	      GFF3 genome file indexed with tabix (see http://www.htslib.org/doc/tabix.html) *
--organism 	  Species name (eg. Homo sapiens, Mus musculus) *
--ignore 	  List of feature types to ignore (eg. chromosome scaffold)
--doi 		  DOI of a reference stored using *load_publication* (eg. 10.1111/s12122-012-1313-4)
--qtl 		  Set this flag to handle GFF files from QTLDB
--cpu 		  Number of threads
==========    ==================================================================================

\* required fields


Remove file
-----------

If, by any reason, you need to remove a GFF dataset you should use the command *remove_file*. **If you delete a file, every record that depend on it will be deleted on cascade**.

.. code-block:: bash

    python manage.py remove_file --help

* This command requires the file name (Dbxrefprop.value)