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Caravagene is a Python library to plot schemas of DNA constructs from a list of parts:

from caravagene import Part, Construct, ConstructList

constructs = ConstructList([Construct([
    Part('my promoter', category='promoter'),
    Part('gene with a very very long name', category='CDS'),
    Part('PolyA', category='terminator'),
    Part('I1', category='insulator')
])])

constructs.to_image('construct.jpeg')
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Here is another example producing this PDF showing multiple constructs:

from caravagene import Part, Construct, ConstructList

my_constructs = ConstructList(
    title="My constructs",
    constructs=[
        Construct(name="ASM1", parts=[
            Part('HA1', category='homology-arm'),
            Part('rc1', category='recombinase-recognition-sequence'),
            Part('my promoter', category='promoter'),
            Part('RNA stability', category='rna-stability-sequence'),
            Part('<i>acs</i>', category='CDS'),
            Part('PolyA', category='terminator'),
            Part('I1', category='insulator'),
        ]),
        Construct(name="ASM2", parts=[
            Part('my promoter', category='promoter'),
            Part('gene with a very very long name', category='CDS'),
            Part('PolyA', category='terminator'),
            Part('I1', category='insulator')
        ])
    ]
)
my_constructs.to_pdf('multiconstruct.pdf')
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It is also possible to add support for other categories/symbols, as follows:

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

Installation

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

(sudo) apt-get install wkhtmltopdf

You can install caravagene through PIP

sudo pip install caravagene

Alternatively, you can unzip the sources in a folder and type

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 Edinburgh Genome Foundry). Everyone is welcome to contribute !

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caravagene-0.1.1.tar.gz (11.4 kB view hashes)

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