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Assemble metabolic pathways from the command line

Project description

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 to be assembled in FASTA or Genbank format. See documentation for file format.

The ypkpathway creates a subdirectory called generates a sub directory called “ypk_assembly”. This subdirectory will contain a file summary of the DNA assembly project called report.html which can be opened in a web browser.

The report will include:

  • The sequence of the final pathway
  • Sequences of all generated intermediate vectors
  • All PCR primers needed for the amplification of pathway components
  • Diagnostic PCR product fragment lengths indicating correct and incorrect clonings

Ypkpathway depends of the pydna package.

NEWS

version date comment
0.0.6 2013-05-14 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 intalled. 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.

Distribution Structure

README.txt – 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> (Currently empty)

ypkpathway/ – The actual code.

docs/ – Documentation.

tests/ – Testing code and data.

Project details


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1.0.1

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0.0.7

This version
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Filename, size & hash SHA256 hash help File type Python version Upload date
ypkpathway-0.0.6-py2.7.egg (19.0 kB) Copy SHA256 hash SHA256 Egg 2.7 May 14, 2014
ypkpathway-0.0.6-py2-none-any.whl (11.3 kB) Copy SHA256 hash SHA256 Wheel 2.7 May 14, 2014
ypkpathway-0.0.6.tar.gz (1.7 MB) Copy SHA256 hash SHA256 Source None May 14, 2014
ypkpathway-0.0.6.zip (1.8 MB) Copy SHA256 hash SHA256 Source None May 14, 2014

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