caravagene 0.1.4

No project description provided

.. raw:: html

<p align="center">
<img alt="caravagene Logo" title="lala Logo" src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/logo.png" width="500">
<br /><br />
</p>

.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/Caravagene.svg?branch=master
:target: https://travis-ci.org/Edinburgh-Genome-Foundry/lala
:alt: Travis 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 <https://edinburgh-genome-foundry.github.io/Caravagene/>`_) 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')

.. raw:: html

<p align="center">
<img src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/examples/construct.jpeg" width="600">
</p>

Here is another example producing `this PDF <https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/examples/multiconstruct.pdf>`_
showing multiple constructs:

.. code:: python

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')

.. raw:: html

<p align="center">
<img src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/examples/multiconstruct_screen_capture.png" width="800">
</p>

Note that ``ConstructsList`` can be supplied with a fontthat 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:**

.. raw:: html

<p align="center">
<img src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/examples/from_spreadsheet_sample.png" width="600">
</p>

**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:**


.. raw:: html

<p align="center">
<img src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Caravagene/master/examples/from_spreadsheet_screen_capture.png" width="700">
</p>


Installation
-------------

Caravagene requires `WkHTMLtoPDF <https://wkhtmltopdf.org/>`_ to be installed. On Ubuntu, install it with

.. code:: shell

(sudo) apt-get install wkhtmltopdf


You can install caravagene through PIP

.. code:: shell

sudo pip install caravagene

Alternatively, you can unzip the sources 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
<http://www.genomefoundry.org>`_ by `Zulko <https://github.com/Zulko>`_
and `released on Github <https://github.com/Edinburgh-Genome-Foundry/Caravagene>`_ under the MIT licence (copyright Edinburgh Genome Foundry).
Everyone is welcome to contribute !