Caravagene (full documentation here) 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('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')
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(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='<i>acs</i>', 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')
Note that ConstructList can be supplied with a font. It is also possible to extend Caravagene to support other categories/symbols, as follows:
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:
Python code:
from caravagene import ConstructList
my_constructs = ConstructList("my_spreadsheet.xlsx")
my_constructs.to_pdf('my_schemas.pdf')or command-line (one-time use):
caravagene my_spreadsheet.xlsx my_schemas.pdfor command-line (re-render when the spreadsheet changes on disk):
caravagene my_spreadsheet.xlsx my_schemas.pdf --watchOutput:
Caravagene requires WkHTMLtoPDF to be installed. On Ubuntu, install it with:
(sudo) apt-get install wkhtmltopdfYou can install caravagene through PIP:
pip install caravageneAlternatively, you can unzip the source code in a folder and type:
sudo python setup.py installCaravagene 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!
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