[Biopython] Lightweight version of Biopython?

[Erick Matsen]

Hello Peter--


Thanks for the quick response.

Perhaps "heavy" isn't the right word, but it definitely seems overkill
when all we want to do is convert between three file formats (FASTA,
phylip, and Stockholm). Furthermore, something little we can include
directly in the project (with credit given where it is due) would be
ideal. An installation script could look for Biopython and use it if
it's there, or use the lite version if not.


Thanks,

Erick

On Wed, Nov 3, 2010 at 5:10 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Nov 3, 2010 at 12:06 PM, Erick Matsen <matsen at fhcrc.org> wrote:
>> Hello there Biopython community--
>>
>> We're writing some python code to use SCons for reproducible
>> bioinformatics research with intelligent dependencies. As part of the
>> project, we often need to do very simple bioinformatics tasks, such as
>> reading in various formats and spitting out others. We could use
>> Biopython for such things, but it's a very heavy dependency for such
>> trivial tasks.
>>
>> I'm curious if there exists a Biopython "lite". The ideal situation
>> would be a tiny module that we could include directly in our project.
>> I have searched the Biopython mailing list and have yet to find
>> anything.
>>
>> Thanks in advance,
>>
>> Erick
>
> Hi Erick,
>
> Why do you consider Biopython a heavy dependency? It can
> be installed with no 3rd party libraries (although we do strongly
> recommend NumPy, if you are not using anything numerical
> you don't need it).
>
> Peter
>