[Biopython-dev] providing python code on tandem repeat detectors to Biopython?

[Peter Cock]

Elke Schaper wrote:
>> We've been working on sequence tandem repeat detectors during the past
>> couple of months in my research lab. A couple of parsers for commonly
>> used detectors, and a repeat class (basically an extension to sequence
>> alignments) have come up along the way.
>>
>> Would there principally be any interest in introducing the code to
>> Biopython?


On Fri, Mar 23, 2012 at 12:00 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Elke;
> Welcome and thanks for the e-mail. This sounds like useful
> functionality. The first step would be to generalize it and make the
> code available on GitHub. This should give folks something concrete to
> provide feedback on.
>
> Thanks again,
> Brad

Hi Elke,

We're starting to do more and more annotation where I work, so this
does sound very useful directly (as well as to the Biopython community).

Which commonly used tandem repeat detectors do you have parsers
for? I'm curious about their file formats - are they tool specific text
files, XML, or something more general, e.g. GFF3?

Brad's right that it would be great to see your current code - assuming
you're happy to post it online - and that would make it much easier to
give guidance on how best it might be integrated into Biopython.

Assuming it is all your own work, and you are happy with the Biopython
licensee (MIT/BSD style), there will be no problems. However, if you're
using any GPL or LGPL code for example, that may complicate things.

Thanks,

Peter