[Biopython-dev] Biopython: question regarding example code

[Brad Chapman]

Hi Jón;

> I have been looking at biopython and reading the tutorial and cookbook.
> There are good examples there about what can be done with it but is there
> some sort of white paper or overview of what is currently implemented with
> biopython. Like for example overview of all the databases that biopython
> can be used to work with.

The documentation you can find at

http://www.biopython.org/wiki/html/BioPython/BiopythonCode.html

is what we've got. I am currently working on a rewrite of the docs as I
know a lot of errors have crept in (but first I have to finish the web
pages -- hard workin' over here :-) since they were written.

I'm not sure exactly what you are looking for, but there are also a
couple of online courses with nice Biopython introductions linked to
from the above page which might be worth checking out.

> Also I tried running the examples that come with the distribution but
> could not run the pubmed_search.py program. The output was:
> 
> [jongud at oracle examples]$ python pubmed_search.py
> Traceback (most recent call last):
>   File "pubmed_search.py", line 6, in ?
>     from Bio.Medline import PubMed
> ImportError: cannot import name PubMed
> 
> I tried changing the import lines in the code to something else that might
> work but nothing worked. I was running it on linux machine and the other
> examples worked. The distribution of biopython that was set up was 1.10.

This is my fault -- an out of date import. You need to change the import
line to:

from Bio import PubMed

and it should work fine. Thanks for reporting this -- I've fixed it in CVS.
I know there are other places in the docs and examples where import
errors may have crept in -- I'm working on tracking them all down.

Sorry about some of the out-of-dateness of the documentation -- I
definitely welcome patches or reports of mistakes as we're trying to get
them cleaned up. Always happy to have people trying out Biopython!

Thanks again for the report!
Brad