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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 on the `pydna <>`_ package.


======= ========== =============================================================
version date comment
======= ========== =============================================================

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 2.7 <>`_.

- `pydna>=0.6.1 <>`_.

- `docutils>=0.11 <>`_.

- `docopt>=0.6.1 <>`_.

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.


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.


Make sure all dependencies are intalled. Open the pydna source code
directory (containing the file) in terminal and type::

sudo python install <enter>

If you need to do additional configuration, e.g. changing the base
directory, please type `python`, or see the documentation for

Distribution Structure

README.txt -- This file.

LICENSE.txt -- What you can do with the code. -- Tells distutils what files to distribute -- Installation file. -- run tests by "python"<enter> (Currently empty)

ypkpathway/ -- The actual code.

docs/ -- Documentation.

tests/ -- Testing code and data.

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Filename, size & hash SHA256 hash help File type Python version Upload date
ypkpathway-0.0.9-py2.7.egg (70.3 kB) Copy SHA256 hash SHA256 Egg 2.7 Jun 16, 2014
ypkpathway-0.0.9-py2-none-any.whl (59.6 kB) Copy SHA256 hash SHA256 Wheel 2.7 Jun 16, 2014
ypkpathway-0.0.9.tar.gz (3.4 MB) Copy SHA256 hash SHA256 Source None Jun 16, 2014
ypkpathway-0.0.9.win32.exe (297.0 kB) Copy SHA256 hash SHA256 Windows Installer 2.7 Jun 16, 2014 (324.7 kB) Copy SHA256 hash SHA256 Windows Installer 2.7 Jun 16, 2014 (3.5 MB) Copy SHA256 hash SHA256 Source None Jun 16, 2014

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