Biopython upgrade on Mac OSX 10.6

One slightly frustrating thing about the Macintosh is that although it comes with Python installed, the versions are out of date. It is possible to install Python from python.org, which replaces the command line one, and also has the idle IDE. However I was finding it difficult to install python packages into that newer version. I would find commands like:

$ easy_install -f http://biopython.org/DIST/ biopython

$ pip install numpy

$ pip install nose

But those would install things to the older versions. By searching around, here's what I found. The provided pythons install into /Library/Python/2.6/site-packages/ or related directories, while the python.org version wants to install into /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages. The easy_install command that my system used was in /usr/bin/easy_install. I managed to get the python.org version to install easy_install (setuptools) with the following command:

$ curl https://bootstrap.pypa.io/ez_setup.py -o - | python

And then upgraded biopython with the following:

$ python -m easy_install --upgrade biopython

That tells the command line version of python, which is the 2.7/python.org version to use its own easy_install command, I am not sure that was strictly necessary because the 'which' command now showed that would be the default:

$ which easy_install

/Library/Frameworks/Python.framework/Versions/2.7/bin/easy_install

# and biopython looks ok, though there were some compilation warnings

$ python

Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)

[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import Bio

>>> Bio.__version__

'1.63'

# used to be 1.57

Research news - Fusobacterium and colon cancer

Two recent papers (Castellarin et al and Kostic et al) have come out in Genome Research showing an association between bacteria of the genus Fusobacterium and colon carcinoma. This is of interest to oral microbiologists as Fusobacterium, especially the species F. nucleatum, is one of the most common bugs in the mouth, but is not particularly prevalent in the gut normally.
Both groups took somewhat similar approaches. Castellarin and co-workers used Illumina deep sequencing of cDNA from tumors compared to control samples from the same patients, while Kostic and co-workers did similar sequencing of genomic DNA. In either case they subtracted human sequences and looked for the remaining sequences that were similar to bacterial DNA. This was doubtless made easier by the extensive sequencing of bacterial genomes that has been done by the Human Microbiome Project. In both studies, the sequences that were most overrepresented in tumors mapped to Fusobacterium. Both sets of workers confirmed their findings by looking at larger patient groups. Castellarin et al did this by qPCR with Fusobacterium specific primers, while Kostic used pyrosequencing of 16S rRNA genes.
Kostic et al demonstrated the presence of the bacteria in tumors by FISH, while Castellarin et al was able to grow a single culture of the bacterium from a frozen tumor, and then sequenced the genome. The organism they cultured was relatively similar to a cultured un-named strain called Fusobacterium sp. 3_1_36A2. They further showed that their cultured bacterium would invade Caco-2 colon carcinoma cells in culture. Fusobacterium has been known to be invasive to human cells in the mouth and in culture for a while, so this is not totally unexpected.
Overall, this is an intriguing finding, and of course 2 labs publishing at the same time shows it must be real. Its not clear yet whether the presence of the bacteria is causing the tumors, though. It may just be preferentially infecting the tumor cells. Helicobacter pylori is thought to contribute to stomach cancer by stimulating inflammation and it is possible that Fusobacterium does something similar in the gut. In our studies, we have not seen a clear relationship between Fusobacterium and the inflammatory disease chronic periodontitis, but perhaps it is a gut-specific phenomenon. The availability of the cultured organism is exciting, suggesting that animal models might be possible.

Why this blog

I am a long time molecular biologist who has been getting into bioinformatics, studying the  human oral microbiome. I have found that a lot of solutions to various problems in this field can be found by Google searches, on other people's blogs. I have been collecting my own bioinformatics notes using TiddlyWiki, and thought there might be one or two things in there that others might find useful, so here it is.