Contains classes and code for representing double stranded DNA and functions for simulating homologous recombination between DNA molecules.
Pydna provide classes and functions for molecular biology using python. Notably, PCR, cut and paste cloning and homologous recombination between linear DNA fragments are supported. Most functionality is implemented as methods for the double stranded DNA sequence record classes Dseq and Dseqrecord, which are subclasses of the Biopython. Seq and SeqRecord classes.
Pydna might be useful to automate the simulation of sub cloning experiments using python. This could be helpful to generate examples for teaching purposes. Read the documentation or the cookbook with example files for further information.
Pydna was designed to semantically imitate how sub cloning experiments are typically documented in Scientific literature. Pydna code describing a sub cloning is reasonably compact and meant to be easily readable.
One use case for Pydna is to create a sort of executable documentation describing a subcloning experiment. The Pydna code unambiguously describe a sub cloning experiment, and can be executed to yield the sequence of the of the resulting DNA molecule.
Please post a message in the google group “pydna” at https://groups.google.com/forum/?fromgroups#!forum/pydna if you have problems, questions or comments.
Feedback is very welcome!
Typical usage at the command line could look like this:
>>> import pydna >>> seq = pydna.Dseq("GGATCCAAA","TTTGGATCC",ovhg=0) >>> seq Dseq(-9) GGATCCAAA CCTAGGTTT >>> from Bio.Restriction import BamHI >>> a,b = seq.cut(BamHI) >>> a Dseq(-5) G CCTAG >>> b Dseq(-8) GATCCAAA GTTT >>> a+b Dseq(-9) GGATCCAAA CCTAGGTTT >>> b+a Dseq(-13) GATCCAAAG GTTTCCTAG >>> b+a+b Dseq(-17) GATCCAAAGGATCCAAA GTTTCCTAGGTTT >>> b+a+a Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217, in __add__ raise TypeError("sticky ends not compatible!") TypeError: sticky ends not compatible! >>>
|0.1.3||2013-04-09||pydna created from Python-dna.|
Versions other than 2.7 has not been tried with this software. Version 2.7.3 was used to build the distribution.
This code has not been tried with python 3.
You need to install the dependencies listed above. If you are using Windows, you need to have a C compiler installed. The free MS visual studio 2008 express can be used.
Open the pydna source code directory (containing the setup.py file) in terminal and type:
sudo python setup.py install <enter>
If you need to do additional configuration, e.g. changing the base directory, please type python setup.py, or see the documentation for Setuptools.
A Binary installer for 32 bit editions of MS Windows XP and 7 are provided.
The installer has been tested on succesfully on both.
The dependencies have to be installed from source or using binary installers for 32 bit windows.
This is a list of locations of binary installers:
- Python <http://www.python.org/download/>
- NumPy <http://sourceforge.net/projects/numpy/files/NumPy/>
- Biopython <http://biopython.org/wiki/Download>
- networkx <http://www.lfd.uci.edu/~gohlke/pythonlibs/#networkx>
Source Code Repository
pydna is hosted by google code:
README.txt – This file.
NEWS.txt – Release notes and news
LICENSE.txt – What you can do with the code.
MANIFEST.in – Tells distutils what files to distribute
setup.py – Installation file.
setup_build.py – Building from Cython source (not needed for install)
distribute_setup.py – Bootstrap distribute installation for version 0.6.34 which will pretend to be setuptools 0.6c11
run_tests.py – run tests by “python run_tests.py”<enter>
pydna/ – The actual code.
docs/ – Documentation.
scripts/ – Miscellaneous perhaps useful scripts
tests/ – Testing code
Release history Release notifications
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|pydna-0.1.3.tar.gz (2.9 MB) Copy SHA256 hash SHA256||Source||None||Apr 9, 2013|
|pydna-0.1.3.win32-py2.7.exe (281.8 kB) Copy SHA256 hash SHA256||Windows Installer||2.7||Apr 9, 2013|
|pydna-0.1.3.win-amd64-py2.7.exe (311.3 kB) Copy SHA256 hash SHA256||Windows Installer||2.7||Apr 9, 2013|
|pydna-0.1.3.zip (3.0 MB) Copy SHA256 hash SHA256||Source||None||Apr 9, 2013|