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The Readme — PyCogent 1.9 documentation

http://pycogent.org/README.html

PyCogent 1.9 documentation. Or follow the Quick installation using pip. The toolkit requires Python 2.5.1 or greater, and Numpy 1.3 or greater. Aside from these the dependencies below are optional and the code will work as is. A C compiler, however, will allow external C module’s responsible for the likelihood and matrix exponentiation calculations to be compiled, resulting in significantly improved performance. The language the toolkit is primarily written in, and in which the user writes control scripts.

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Scripting guidelines — PyCogent 1.9 documentation

http://pycogent.org/scripting_guidelines.html

PyCogent 1.9 documentation. Developing command line interfaces for your scripts is a convenient way to create easily reproducible analyses with PyCogent. This document covers the support for developing standardized interfaces in PyCogent. In addition to making your code easier to distribute (or to return to months after it was originally written), several GUI generators that are currently in development make use of the PyCogent. Module – this means that defining your interfaces with PyCogent’s. For PyCog...

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Index — PyCogent 1.9 documentation

http://pycogent.org/genindex.html

PyCogent 1.9 documentation. PyCogent News and Announcements. Quick installation using pip. The data files used in the documentation.

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Integrating news feeds into Sphinx pages | Greg Caporaso

https://gregcaporaso.wordpress.com/2010/01/26/integrating-news-feeds-into-sphinx-pages

Integrating news feeds into Sphinx pages. I’ve worked on a few Sphinx. Based websites for software projects lately. (I’ve found the matplotlib sphinx tutorial. Useful for getting started.) A couple of examples are the PyCogent. One thing I’ve needed to do was integrate a news feed that is easy for developers on the project to update, without having to mess with uploading new html, sharing the site password, etc. The solution I came up with was creating a wordpress blog (e.g., PyCogent. One option you sho...

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PyCogent Cookbook — PyCogent 1.9 documentation

http://pycogent.org/cookbook/index.html

PyCogent 1.9 documentation. Tips for using python. Using the dir() function. Loading nucleotide, protein sequences. DNA and RNA sequences. Getting a genetic code. Translate all six frames. Find out how many stops in a frame. Look up the amino acid corresponding to a single codon. Or get all the codons for one amino acid. For a group of amino acids. Obtaining the codons from a. Species to be queried. What alignment types available. Get genomic alignment for a gene region. Analysis of sequence composition.

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Coding guidelines — PyCogent 1.9 documentation

http://pycogent.org/coding_guidelines.html

PyCogent 1.9 documentation. As project size increases, consistency increases in importance. Unit testing and a consistent style are critical to having trusted code to integrate. Also, guesses about names and interfaces will be correct more often. What should I call my variables? Choose the name that people will most likely guess. Make it descriptive, but not too long:. Current genbank record from database. Good names are hard to find. Use singular names for individual things, plural names for collections.

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Quick installation using pip — PyCogent 1.9 documentation

http://pycogent.org/install.html

PyCogent 1.9 documentation. Quick installation using pip. The following assumes you have. On your system (this comes standard with new Macs for instance), that you have made a virtualenv. Environment and that you’re connected to the internet. The key steps for the minimal install are:. Use pip to download, build and install PyCogent. If the above fails to download PyCogent you can download an archive. To your hard drive and then do. Pip install path/to/pycogent-master.zip. To use the Ensembl querying code.

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For Developers — PyCogent 1.9 documentation

http://pycogent.org/developer_notes.html

PyCogent 1.9 documentation. Anyone can contribute to the development of PyCogent, not just registered developers. If you figure out a solution to something using PyCogent that you’d like to share, or if you have ideas for improving the current documentation, please consider submitting a pull request. To the PyCogent git repository on GitHub. And we’ll look into including it in PyCogent! To grab PyCogent from GitHub, do the following:. Git clone git:/ github.com/pycogent/pycogent.git PyCogent. You can now...

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Licenses and disclaimer — PyCogent 1.9 documentation

http://pycogent.org/licenses.html

PyCogent 1.9 documentation. PyCogent is released under the GPL license, a copy of which is included in the distribution (see PyCogent License. Licenses for other code sources are left in place. PyCogent News and Announcements. Quick installation using pip. The data files used in the documentation.

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The data files used in the documentation — PyCogent 1.9 documentation

http://pycogent.org/data_file_links.html

PyCogent 1.9 documentation. The data files used in the documentation. All data files referred to in the documentation can be download by clicking on the links below. Not all browsers handle the file suffixes well, so you may need to rename the downloaded files in order to use them. Dists for phylo.pickle. Motif example meme results.txt. Primate cdx2 promoter.fasta. PyCogent News and Announcements. Quick installation using pip. The data files used in the documentation.