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ypkpathway 0.8.4

Assemble metabolic pathways from the command line using the ypkpathway protocol

Ypkpatwhay provides a command line application for planning DNA assembly projects using the Yeast Pathway Kit protocol.

Typical usage at the command line could look like this:

bjorn@bjorn-UL30A:/$ ypkpathway four_gene_xylose_pathway.txt

Where four_gene_xylose_pathway1.txt is a text file containing DNA sequences in FASTA or Genbank format to be assembled. The ypkpathway command above creates a folder with a series of IPython 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.
    -t, --test      Run tests.

The results folder will include:

  • The sequence of the final pathway and all intermediate vectors in Genbank format
  • IPython notebooks file 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.

NEWS

version date comment
0.8.4 2015-05-30 An IPython.display.FileLink object is now returned from the ypkpathway function.
0.8.3 2015-05-29 windows fix for opening final pathway notebook.
0.8.2 2015-05-28 pydna dependency 0.9.2, fix a unicode env variable.
0.8.1 2015-05-26 pydna dependency 0.9.1
0.8.0 2015-05-26 Complete change in functionality. IPython notebook files are generated and executed instead of rst and html files.
0.6.0 2015-04-17 Added nosetests
0.5.0 2014-12-09
Changed to work with new caching version of pydna. Fixed
unicode errors.
0.0.9 2014-06-14 bugfix changed errors in automatically generated pydna source files
0.0.8 2014-05-14 first release

System Requirements

Python 2.x

Versions other than 2.7 has not been tried with this software. Version 2.7.3 was used to build the distribution.

Python 3.x

This code has not been tested with python 3.

Installation

The best way of installing ypkpathway is with pip:

sudo pip install ypkpathway <enter>

Pip will take care of the installation of any missing dependencies.

Source

Make sure all dependencies are installed. 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.

Testing

Nose is needed to run the test suit.

sudo pip install nose <enter>

Then from the source directory do:

python run_tests.py

Distribution Structure

README.rst – This file.

LICENSE.txt – What you can do with the code.

MANIFEST.in – Tells distutils what files to distribute

setup.py – Installation file.

run_tests.py – run tests by “python run_tests.py”<enter>

ypkpathway/ – The actual code.

docs/ – Documentation.

tests/ – Testing code and data.

 
File Type Py Version Uploaded on Size
ypkpathway-0.8.4-py2-none-any.whl (md5) Python Wheel 2.7 2015-06-12 24KB
ypkpathway-0.8.4.tar.gz (md5) Source 2015-06-12 6MB
ypkpathway-0.8.4.zip (md5) Source 2015-06-12 6MB
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