[Biopython-dev] Introduction from a newbie; Tiny contribution

Peter Cock p.j.a.cock at googlemail.com
Mon Dec 9 16:42:43 UTC 2013

On Mon, Dec 9, 2013 at 4:29 PM, Kashyap Chhatbar <kashyap.cc at gmail.com> wrote:
> Hi,
> I am happy to join the dev mailing list for Biopython. I would be
> definitely interested in learning more and hopefully at some point
> contributing to the biopython source.

Thank you and welcome :)

> A few days ago, I created an issue on
> the official github repository of biopython
> (#267<https://github.com/biopython/biopython/issues/267>).

Yes, thank for for raising this - it is something we can improve.

> I think I have come up with a noobish contribution to convert the file name
> (if relative path is given) to absolute paths when creating sqlite3
> database using Bio.SeqIO.index_db() function. (commit
> de9ba35<https://github.com/kashyapchhatbar/biopython/commit/de9ba359b668b1880edb12f4d9df3e9424515745>).
> I have not looked up too much of the biopython code so as to conclude
> whether introducing the absolute path for filenames is as such a good idea
> or not but I thought of this because Peter J Cock hinted of improving the
> code for relative paths.

I don't think storing the absolute path is the best plan - I have
tried to better explain what I meant by using relative filenames on
the GitHub issue,


Is that clearer?



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