.. _imbiopythonrst:

=========
biopython
=========


.. only:: html

    **Links:** :download:`notebook <im_biopython.ipynb>`, :downloadlink:`html <im_biopython2html.html>`, :download:`PDF <im_biopython.pdf>`, :download:`python <im_biopython.py>`, :downloadlink:`slides <im_biopython.slides.html>`, :githublink:`GitHub|_doc/notebooks/2016/pydata/im_biopython.ipynb|*`


The `Biopython <http://biopython.org/>`__ Project is an international
association of developers of freely available
`Python <http://www.python.org>`__ tools for computational molecular
biology.

`documentation <http://biopython.org/wiki/Documentation>`__
`source <https://github.com/biopython/biopython>`__
`installation <http://biopython.org/wiki/Download>`__
`tutorial <http://biopython.org/DIST/docs/tutorial/Tutorial.html>`__

.. code:: ipython3

    from jyquickhelper import add_notebook_menu
    add_notebook_menu()






.. contents::
    :local:





example
-------

.. code:: ipython3

    from pyquickhelper.filehelper import download
    download("https://raw.githubusercontent.com/biopython/biopython/master/Tests/GenBank/NC_005816.gb",
             outfile="NC_005816.gb")




.. parsed-literal::
    'NC_005816.gb'



.. code:: ipython3

    from reportlab.lib import colors
    from reportlab.lib.units import cm
    from Bio.Graphics import GenomeDiagram
    from Bio import SeqIO
    record = SeqIO.read("NC_005816.gb", "genbank")
    
    gd_diagram = GenomeDiagram.Diagram("Yersinia pestis biovar Microtus plasmid pPCP1")
    gd_track_for_features = gd_diagram.new_track(1, name="Annotated Features")
    gd_feature_set = gd_track_for_features.new_set()
    
    for feature in record.features:
        if feature.type != "gene":
            #Exclude this feature
            continue
        if len(gd_feature_set) % 2 == 0:
            color = colors.blue
        else:
            color = colors.lightblue
        gd_feature_set.add_feature(feature, color=color, label=True)
    
    gd_diagram.draw(format="linear", orientation="landscape", pagesize='A4',
                    fragments=4, start=0, end=len(record))
    gd_diagram.write("plasmid_linear.svg", "svg")

.. code:: ipython3

    from IPython.display import SVG
    SVG("plasmid_linear.svg")




.. image:: im_biopython_6_0.svg



.. code:: ipython3

    gd_diagram.draw(format="circular", circular=True, pagesize=(20*cm,20*cm),
                    start=0, end=len(record), circle_core=0.7)
    gd_diagram.write("plasmid_circular.svg", "svg")
    SVG("plasmid_circular.svg")




.. image:: im_biopython_7_0.svg