[Biopython] ngs_backbone

[Brent Pedersen]

On Tue, May 4, 2010 at 2:13 AM, Peter <biopython at maubp.freeserve.co.uk> 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?
>
> 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?

just out of curiosity (since it's tested and working), is the reason
it's safe to rely on dictionary
order in _maketrans() there because it's simple keys -- letters -- in
the mapping dictionary?



>
> Peter
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