[Biopython] ngs_backbone

[Peter]

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?

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 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?

Peter