[Biopython] GeneWise in Python

[Eric Talevich]

On Thu, May 27, 2010 at 8:42 AM, Tony Heitkam <Tony.Heitkam at tu-dresden.de>wrote:

> Hello everyone and thanks to all BioPython developpers,
>
> I am new to the mailing list, new to coding and I already have a question
> to ask. I regularly use GeneWise
> http://www.ebi.ac.uk/Tools/Wise2/index.html for the annotation of ORF
> sequences. In the moment, I have approx. 100 sequences that I want to
> compare with a reference sequence and I would love to automatize this
> process.
>
> Does anybody know how to run this algorithm from python? Help would be
> greatly appreciated.
>
>
Hi Tony,

Which algorithm are you referring to, the GeneWise algorithm or the loop to
run it 100 times?

I don't use GeneWise, but it looks like the program does some clever things
beyond simply transcribing a DNA sequence and comparing it to the query
protein sequence. Since GeneWise is available as a stand-alone program, you
could install that and use either a shell script or Python's
subprocess.call() to loop over each sequence:
http://docs.python.org/library/subprocess.html

Regards,
Eric