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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://biopython.org/DIST/docs/install/Installation.pdf) and html formats (http://biopython.org/DIST/docs/install/Installation.html).

1.3  FAQ

  1. Why doesn’t Bio.SeqIO work? It imports fine but there is no parse function etc.
    You need Biopython 1.43 or later. Older versions did contain some related code under the Bio.SeqIO name which has since been deprecated - and this is why the import “works”.
  2. Why doesn’t Bio.SeqIO.read() work? The module imports fine but there is no read function!
    You need Biopython 1.45 or later.
  3. Why doesn’t Bio.Blast work with the latest plain text NCBI blast output?
    The NCBI keep tweaking the plain text output from the BLAST tools, and keeping our parser up to date is an ongoing struggle. We recommend you use the XML output instead, which is designed to be read by a computer program.
  4. Why isn’t Bio.AlignIO) present? The module import fails!
    You need Biopython 1.46 or later.
  5. Why doesn’t Bio.Entrez.read() work? The module imports fine but there is no read function!
    You need Biopython 1.46 or later.
  6. 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.

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