[Biopython-dev] support for database of BOLDSYSTEMS?

[Carlos Peña]

Hi all,


I have written an interface to the BOLD database of DNA barcodes. It
accepts FASTA files, sends them to BOLD and gets the specimen
identifications to the species level:

https://github.com/carlosp420/bold_retriever

I was wondering whether it could be included into BioPython? So far the
packages is a bunch of scripts and I want to make it more robust.
The working version is not so efficient as the running time has exponential
growth (n squared).

However, I was able to use asynchronous calls (using Twisted) to make it
faster. The script was able to take (n) seconds for (n) number of
sequences. But I don't fully understand Twisted and the package is unstable.

So, I wanted to ask if this little project of mine has any hope of getting
into BioPython. If that is the case I would need some pointers on using
proper classes for the code and fixing the code so that it can be
integrated. I guess I would need to drop Twisted and use instead a standard
Python library for multithreading.

I want to improve the package anyways, make it more robust and quick. So I
wanted to ask before giving another chance to Twisted.

Any comments would be appreciated,


carlos


Dr. Carlos Peña
Laboratory of Genetics
Department of Biology
University of Turku
20014 Turku
FINLAND
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