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Chapter 1  Introduction

1.1  What is Biopython?

The Biopython Project is an international association of developers of freely available Python (http://www.python.org) tools for computational molecular biology. The web site http://www.biopython.org provides an online resource for modules, scripts, and web links for developers of Python-based software for life science research.

Basically, we just like to program in python and want to make it as easy as possible to use python for bioinformatics by creating high-quality, reusable modules and scripts.

1.1.1  What can I find in the Biopython package

The main Biopython releases have lots of functionality, including: We hope this gives you plenty of reasons to download and start using Biopython!

1.2  Installing Biopython

All of the installation information for Biopython was separated from this document to make it easier to keep updated. The instructions cover installation of python, Biopython dependencies and Biopython itself. It is available in pdf (http://www.biopython.org/docs/install/Installation.pdf) and html formats (http://www.biopython.org/docs/install/Installation.html).

1.3  FAQ

  1. I looked in a directory for code, but I couldn't seem to find the code that does something. Where's it hidden?
    One thing to know is that we put code in __init__.py files. If you are not used to looking for code in this file this can be confusing. The reason we do this is to make the imports easier for users. For instance, instead of having to do a “repetitive” import like from Bio.GenBank import GenBank, you can just import like from Bio import GenBank.

  2. What happened to the br_regrtest.py regression tests? We updated the regression testing framework to use PyUnit, and also to fix newline problems. br_regrtest.py is still there, but almost all of its functionality has been moved (well, copy and pasted) to run_tests.py.

  3. Why do some of the tests fail when running the regression tests with output like:
    Writing: '\012', expected: '\015'
    This shouldn't happen any more! We updated the regression testing suite so that it uses PyUnit and we hopefully have fixed newline problems. Please let us know if any tests fail.

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