https://github.com/edinburgh-genome-foundry/caravagene

🎨 Python library to plot multi-part genetic constructs
https://github.com/edinburgh-genome-foundry/caravagene

dna-assembly molecular-biology sequence-design synthetic-biology

Last synced: 29 days ago
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🎨 Python library to plot multi-part genetic constructs

• Host: GitHub
• URL: https://github.com/edinburgh-genome-foundry/caravagene
• Owner: Edinburgh-Genome-Foundry
• License: mit
• Created: 2017-08-25T17:26:16.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2023-07-21T23:15:30.000Z (over 1 year ago)
• Last Synced: 2024-11-06T18:52:45.551Z (about 2 months ago)
• Topics: dna-assembly, molecular-biology, sequence-design, synthetic-biology
• Language: Python
• Homepage: https://edinburgh-genome-foundry.github.io/Caravagene/
• Size: 7.48 MB
• Stars: 25
• Watchers: 6
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

Awesome Lists containing this project

README

        
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.. image:: https://github.com/Edinburgh-Genome-Foundry/Caravagene/actions/workflows/build.yml/badge.svg

    :target: https://github.com/Edinburgh-Genome-Foundry/Caravagene/actions/workflows/build.yml

    :alt: GitHub CI build status

.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/Caravagene/badge.svg?branch=master

    :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/Caravagene?branch=master

Caravagene (full documentation `here `_) is a Python library to plot schemas of DNA constructs from a list of parts:

.. code:: python

    from caravagene import Part, Construct, ConstructList

    constructs = ConstructList([Construct([

        Part('promoter', label='my promoter'),

        Part('CDS', label='gene with a very very long name'),

        Part('terminator', label='PolyA'),

        Part('insulator', label='I1')

    ])])

    constructs.to_image('construct.jpeg')

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Here is another example producing `this PDF `_

showing multiple constructs:

.. code:: python

    from caravagene import Part, Construct, ConstructList

    my_constructs = ConstructList(

        title="My constructs",

        constructs=[

            Construct(name="ASM1", parts=[

                Part(label='HA1', category='homology-arm'),

                Part(label='rc1', category='recombinase-recognition-sequence'),

                Part(label='my promoter', category='promoter'),

                Part(label='RNA stability', category='rna-stability-sequence'),

                Part(label='acs', category='CDS'),

                Part(label='PolyA', category='terminator'),

                Part(label='I1', category='insulator'),

            ]),

            Construct(name="ASM2", parts=[

                Part(label='my promoter', category='promoter'),

                Part(label='gene with a very very long name', category='CDS'),

                Part(label='PolyA', category='terminator'),

                Part(label='I1', category='insulator')

            ])

        ]

    )

    my_constructs.to_pdf('multiconstruct.pdf')

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Note that ``ConstructList`` can be supplied with a font. It is also possible to extend Caravagene to support other categories/symbols, as follows:

.. code:: python

     from caravagene import SYMBOL_FILES

     SYMBOL_FILES['my-new-category'] = 'path/to/some/symbol.svg'

Finally, here is an example using an Excel spreadsheet:

**Spreadsheet:**

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**Python code:**

.. code:: python

    from caravagene import ConstructList

    my_constructs = ConstructList("my_spreadsheet.xlsx")

    my_constructs.to_pdf('my_schemas.pdf')

or **command-line (one-time use):**

.. code:: shell

    caravagene my_spreadsheet.xlsx my_schemas.pdf

or **command-line (re-render when the spreadsheet changes on disk):**

.. code:: shell

    caravagene my_spreadsheet.xlsx my_schemas.pdf --watch

**Output:**

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Installation

-------------

Caravagene requires `WkHTMLtoPDF `_ to be installed. On Ubuntu, install it with:

.. code:: shell

    (sudo) apt-get install wkhtmltopdf

You can install caravagene through PIP:

.. code:: shell

    pip install caravagene

Alternatively, you can unzip the source code in a folder and type:

.. code:: shell

    sudo python setup.py install

Licence

-------

Caravagene is an open-source software originally written at the `Edinburgh Genome Foundry

`_ by `Zulko `_

and `released on Github `_ under the MIT licence (Copyright 2017 Edinburgh Genome Foundry).

Everyone is welcome to contribute!