[Biopython-dev] [Biopython] ngs_backbone

[Jose Blanca]

Hi Peter:

On Tuesday 04 May 2010 11:13:05 Peter wrote:
> On Mon, May 3, 2010 at 11:37 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
> > Hi:
> >
> > As in many other labs we are working with NGS sequences. We work mostly
> > in non model plants and we were repeating the same analyses for different
> > projects: sequence cleaning, mapping to a reference, annotation and SNV
> > calling and filtering. To solve the problem we have developed a software
> > named ngs_backbone. We use this software and we think that it might be of
> > some use to the biopython community. To take a look at it you can go to
> > http://bioinf.comav.upv.es/ngs_backbone/index.html
> >
> > This software is build on top of biopython.
> >
> > If the biopython developers think that some part of this software could
> > be added to biopython we would be glad to do it. We are aware of the
> > different licences used by both projects, but we could relicence the
> > required parts to solve that.
> >
> > Best regards,
>
> Hi Jose,
>
> This sounds very interesting. Are there any bits of low level functionality
> you think would be particularly suitable for including in Biopython?

That I don't know. Most of the package is of higher level, but maybe there's 
something.

> I've just had a quick look at your function  _seqs_in_file_with_bio in
> http://github.com/JoseBlanca/franklin/blob/master/franklin/seq/readers.py
> Would be it be simpler to do FASTA+QUAL parsing using
> Bio.SeqIO.PairedFastaQualIterator?

I going to look into that, it seems a good tip, thanks Peter.

> I see you have a copy of our (private) function Bio.Seq._maketrans() here:
> http://github.com/JoseBlanca/franklin/blob/master/franklin/seq/seqs.py
> Would it be useful to have this as a public API in Biopython?

I dont' think so. We copied the function because of the self.__class__ problem 
that we discussed some time ago. The complement method or our Seq should 
return our class and not the Biopython one, that's why we have duplicated 
this method.

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)