.. _checkAnno:

=====================================
Session 7: Take a look at annotations
=====================================

In the last part of the course, you have used the analysis module of the `IMP3 <https://imp3.readthedocs.io/en/latest/>`_ pipeline. In this session, you can explore the annotations a bit further.


Data
----

In this session, you can use a .gff file prepared on crunchomics:

.. code-block:: console

   cd /zfs/omics/projects/metatools/SANDBOX/Metagenomics101/EXAMPLE_DATA/ANNOTATION
   ls



Quick look at the annotations
-----------------------------

Here are a couple of bash tricks you can use to get a quick overview of the annotations.

Take a look at the file:

.. code-block:: console

   head annotation_CDS_RNA_hmms.gff
   tail -n 5 annotation_CDS_RNA_hmms.gff
   less annotation_CDS_RNA_hmms.gff
   
(You exit `less` with `q`)

How many annotated sequences?

.. code-block:: console

   wc -l annotation_CDS_RNA_hmms.gff

How many are CDS?

.. code-block:: console

   grep "   CDS     " -c annotation_CDS_RNA_hmms.gff

What fields are the in column 3?

.. code:: console

   cut -f 3 annotation_CDS_RNA_hmms.gff | sort | uniq -c 

You could have also looked which other fields there are in column 3:

.. code:: console

   grep "   CDS     " -v annotation_CDS_RNA_hmms.gff | cut -f 3 | sort | uniq -c

How many sequences are annotated with a KEGG KO?

.. code:: console

   grep "kegg_ko" -c annotation_CDS_RNA_hmms.gff

Which KO is most common?

.. code:: console

   grep "kegg_ko" annotation_CDS_RNA_hmms.gff | sed 's#.*kegg_ko=\([^;]*\).*#\1#' | tr ',' '\n' | sort | uniq -c | sort -n

.. admonition:: Do it yourself (easy)

   | Try to adapt the code above to the Pfam domains.

.. admonition:: Do it yourself (not so easy)

   | Try to find the cog annotations of the genes are annotated with the most common KO.

.. admonition:: Do it yourself (interesting)

   | Try to find the Pfam annotations of the genes are annotated with the most common KO. Check the Pfam DB and KEGG DB for what these annotations mean. Do they correspond to a similar function? 

End of today's lesson. Next time, we will look at quantifying the functional annotations.