Package: ypkpathway
ypkpathwayYpkpathway is a simulator and documentation generator forin-vivopathway 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.The assembly process is simulated usingpydnainJupyter notebookswhich are automatically generated and executed.See an example of a four gene assemblyhere.
The notebooks in the example are located in the docs folder in this repository and visualized throughnbviewer.
The example above was made with thepth6indata.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.There are five more example indata files that are a part of the automatic test suit:pth1pth2pth3pth4pth5pth7Python wheel and source distributions on Pypi.Conda packages for MacOSX built on TravisCI.Conda packages built on Appveyor-CI.Anaconda download count.Github repository.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 themanualfor details on how to use the software.InstallationThe best way of installing ypkpathway is by first installing the freeAnaconda Python distributionwhich comes with
many packages and dependencies out of the box. Using the conda package manages simply type:bjorn@bjorn-UL30A:/$ conda install ypkpathwayand the app and all dependencies will be installed. Themanualcontains a detailed
walk through of this installation option.Alternatively, ypkpathway can be installed usingpipwhich is thePyPA recommendedtool for installing Python packages.bjorn@bjorn-UL30A:/$ pip install ypkpathwayPip may have trouble to install two dependeciesbiopythonwhich is a dependency of pydna andPyQt4which have binary extensions.
These can be separately installed. Binary installers of PyQt4 can be foundhere. Instructions for how to install Biopython can
be foundhere.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 installDependencies 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.DependenciesThe ypkpathway dependencies are pure Python modules except for PyQt.
Pydna depends onbiopythonwhich has
to be installed using a binary installer or else a C compiler has to be available.pydnaipythonnotedownnbformatPyQt5docoptThere are binary Windows installers for IPython, Bioppython, docopthereGraphical user interfaceThe application is written in PyQt4 and can be started from the command line by typing ypkpathway and pressing :bjorn@bjorn-UL30A:/$ ypkpathwayIt can also be started from the Anaconda Launcher if installed using conda on the Anaconda Python distribution.Command line interfaceTypical usage at the command line could look like this:bjorn@bjorn-UL30A:/$ ypkpathway_cli pth6.txtWhere pth6.txt is a text file containing DNA sequences in FASTA or Genbank format to be assembled as described in themanual.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.ResultsThe 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 inGenbankformatJupyter 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.DevelopmentYpkpathway is open source software and developed on
Github.How it worksYpkpathway generates a series of text documents inmarkdownformat
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 thenotedownpackage.The notebooks are executed using IPython. All files and
raw data are saved in a self contained result folder.