[Biopython-dev] support for database of BOLDSYSTEMS?

Peter Cock p.j.a.cock at googlemail.com
Wed Nov 5 10:45:52 UTC 2014

Hi Carlos,

I've not done anything with Twisted or other asynchronous mechanism
for accessing online resources - services like the NCBI discourage
submitting multiple requests in parallel anyway.

One idea might be to leave that to the library's user, and focus on the
lower level API (building the URLs, parsing the returned values, etc)?


On Tue, Nov 4, 2014 at 8:31 PM, Carlos Peña <mycalesis at gmail.com> wrote:
> 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
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