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Project description
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')
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')
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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