[Biopython-dev] Reverse complement SeqRecord and features

[Peter]

On Tue, Dec 21, 2010 at 11:17 AM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
> Hi Peter
>
> I see there is experimental code to allow SeqRecords to be
> reverse_complemented, preserving features. That's just what I need for my
> project.
>
> But should I be using branch 'seqrecords' or 'seqrecords-rc' ?
>
> And do you think this will make it to master soon? I realise there are
> (potentially insurmountable) issues with certain types of annotations but
> the basic functionality which can deal with exact locations is all I need.
>
> Cheers
>
> Nick

Oh right - this had dropped off my personal priority list ;)

http://lists.open-bio.org/pipermail/biopython-dev/2009-September/006850.html
http://lists.open-bio.org/pipermail/biopython-dev/2009-October/006851.html
http://lists.open-bio.org/pipermail/biopython-dev/2010-June/007850.html

Based on the above old posts, and a quick check this is most recent branch
(and it looks like I deleted the other branch "seqrecords"):

http://github.com/peterjc/biopython/commits/seqrecord-rc

You can read the reverse_complement method docstring online here:

https://github.com/peterjc/biopython/blob/7f17bbfef9882ef039d02ff04908d01ab400b71b/Bio/SeqRecord.py

I've had a quick look, and to rebase it or merge it requires some manual
merge conflict resolution due to changes in Bio/SeqFeature.py and its
unit tests. However, I'll make time to update the branch if you are willing
to test this, and we should be able to get this into the master shortly -
perhaps even before the new year? If not, certainly in January.

We'll need to add a warning to the docstring about strand specific
annotation in features (the SNP feature problem raised by Jose in
June).

Regards,

Peter