Simulation and documentation of metabolic pathway assemblies using the Yeast Pathway Kit.
Ypkpathway is a simulator and documentation generator for in-vivo pathway assembly using the Yeast Pathway Kit protocol. It takes as argument a series of sequences in a text file and produces a self contained folder containing assembled sequences of intermediary vectors, final assembly and PCR primers. Other useful information such as PCR conditions and PCR product sizes for construction and confirmation are also included. The documantation of the assembly is given in the narrative Jupyter notebook format which can be executed independently of ypkpathway.
See an example of a four gene assembly here. The notebooks in the example are located in the docs folder in this repository and visualized through nbviewer. The example above was made with the pth6 indata.
Version 3.0.1 runs on Python 3.6 or 3.7 and depends on pyqt5 and pydna 3.0.1 or later. The jupyter notebooks generated by ypkpathway 3.0.1 also need pydna 3.0.1 or later to run.
The ypkpatwhay package provides a graphical point and click interface and a command line application for planning DNA assembly projects using the Yeast Pathway Kit protocol.
Please refer to the manual for details on how to use the software.
The best way of installing ypkpathway is by first installing the free Anaconda Python distribution which comes with many packages and dependencies out of the box. Using the conda package manages simply type:
bjorn@bjorn-UL30A:/$ conda install ypkpathway
and the app and all dependencies will be installed. The manual contains a detailed walk through of this installation option.
bjorn@bjorn-UL30A:/$ pip install ypkpathway
Pip may have trouble to install two dependecies biopython which is a dependency of pydna and PyQt4 which have binary extensions. These can be separately installed. Binary installers of PyQt4 can be found here. Instructions for how to install Biopython can be found here.
Ypkpathway can also be installed from source by downloading one of the source distributions. Unpack the zip or .tar.gz archive and type:
bjorn@bjorn-UL30A:/$ python setup.py install
Dependencies has to be manually installed in this case. There are also .exe installers for ypkpathway that can be installed by double clicking. These do not install the dependencies either.
The ypkpathway dependencies are pure Python modules except for PyQt. Pydna depends on biopython which has to be installed using a binary installer or else a C compiler has to be available.
There are binary Windows installers for IPython, Bioppython, docopt here
Graphical user interface
The application is written in PyQt4 and can be started from the command line by typing ypkpathway and pressing <enter>:
It can also be started from the Anaconda Launcher if installed using conda on the Anaconda Python distribution.
Command line interface
Typical usage at the command line could look like this:
bjorn@bjorn-UL30A:/$ ypkpathway_cli pth6.txt
Where pth6.txt is a text file containing DNA sequences in FASTA or Genbank format to be assembled as described in the manual.
The ypkpathway_cli command above creates a folder with a series of Jupyter notebooks describing the assembly process simulated with pydna. Help is available by the -h option:
bjorn@bjorn-UL30A:/$ ypkpathway -h Usage: ypkpathway <path> [<dir>] ypkpathway -h|--help ypkpathway -v|--version ypkpathway -t|--test Arguments: <path> path to data file containing sequences to be assembled <dir> Directory to put generated sequence files,defaults to <ypk_assembly> in the current working directory. Options: -h, --help Show this screen. -v, --version Show version.
The ypkpathway and ypkpathway_cli both produce the same result, which is a results folder containing a selection of files. The folder will contain:
- The sequence of the final pathway and all intermediate vectors in Genbank format
- Jupyter notebooks files describing the final assembly and intermediate assemblies.
- All PCR primers needed for the amplification of pathway components.
- Expected diagnostic PCR product fragment lengths indicating correct and incorrect clonings.
The Jupyter notebook files in the results folder can be viewed with a web browser with only IPython/Jupyter installed. There are also static html versions of the notebook files that can be viewed on any computer with a web browser.
How it works
Ypkpathway generates a series of text documents in markdown format that are formatted with the given data. There is one document per vector generated in in the assembly process. These documents contain comments and links as well as Python code. The python code describe the cloning and assembly steps using pydna.
The markdown documents are turned into JSON format using the notedown package.
The notebooks are executed using IPython. All files and raw data are saved in a self contained result folder.
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