[Biopython-dev] a tool which doesn't exist but could be useful

Peter Cock p.j.a.cock at googlemail.com
Sun Nov 2 18:21:36 UTC 2014

On Sun, Nov 2, 2014 at 4:46 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
> Welcome, and thanks for your willingness to contribute!

Yes indeed, welcome.

> There are a bunch of parsers that need writing.

Bioinformatics is in no danger of running out of file formats,
as a group we keep inventing new ones :(

Was there a particular topic you're interested in?

e.g. I gather proteomics file formats tend to be binary and poorly
documented (there is work in that area happening, although
not necessarily in Python - not my area), or we don't have much
for microarrays but on the other hand this is an area somewhat
in decline with high throughput sequencing.

> I believe that a GFF parser/
> writer and GenBank <--> GFF converter are high on the list.

Actually that is kind-of covered with Brad's work, we just need to
sit down and integrate it.

> Please look to
> the wiki for what we have, what is neede, and the biopython "coding
> culture". Also, wait for a few others to chime in with suggestions before
> you start.

e.g. http://biopython.org/wiki/Active_projects
and http://biopython.org/wiki/Contributing

Also have a look at our open issues,
https://github.com/biopython/biopython/issues - new
https://redmine.open-bio.org/projects/biopython - old
(currently broken, it needs some love from a Ruby expert
following an OS update forced by bash shellshock).

On the other hand, although I appreciate you said you'd
looking for a more biological focus - you might be a good
person to help with things like compiling from source on
Windows 64bit, or know about technical stuff like unicode
and XML, or ...?

> Thanks again!
> Iddo Friedberg
> http://iddo-friedberg.net
> Sent from a device that promotes typos



> On Nov 2, 2014 11:34 AM, "integral susy" <integral299792458 at gmail.com>
> wrote:
>> hello everyone,
>> I'm transforming myself from pure programming into bioinformatic and I
>> want to contribute to biopython by writing e.g. a parser that doesn't exist
>> - let's say that's a part of my "learn by doing" strategy. Due to my lack of
>> biology and biopython knowledge I'd like to ask you for a helpful hand in
>> creating a goal for me.
>> Thus, does anyone of more experienced biopython users could give
>> me a good task?
>> Thank you in advance

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