Biopython

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3. The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. [Read More]

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website. This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2. [Read More]

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). Python support This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported. We still fully support Python 2. [Read More]

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online ( PDF). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). [Read More]

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported. Most functionality is also working under Python 3. [Read More]

I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. You can now control the start and end points of individual tracks, and you can add cross-links between regions of different tracks, as shown here: This example attempts a simplified reproduction of Figure 6 in Proux et al. (2002), and shows three related phage genomes one above the other. Different classes of genes have been given different colors, while the strength of the red shaded cross-links indicates the percentage identity of the linked genes. [Read More]

Source distributions and Windows installers for Biopython 1.59 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4 Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy), and under PyPy (excluding our NumPy dependencies). [Read More]

One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. I’ve just been updating the Biopython Tutorial (current version here, PDF) to include an example drawing this: Here’s a PDF version too. This example just parses the Arabidopsis thaliana GenBank files to get the chromosome lengths and the tRNA gene placements. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. [Read More]

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI). A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module. Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. [Read More]

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index. Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary. [Read More]