[mira_talk] Re: new sff_extract
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 31 Oct 2012 09:48:29 +0000
On Wed, Oct 31, 2012 at 9:39 AM, Jose Blanca <jblanca@xxxxxx> wrote:
> Hi:
>
> Sometime ago we discussed in this list the future of sff_extract. We started
> working on it and we have a version that we think is working.
> The sff_extract functionality has been split in two sff_extract and
> split_matepairs that can be linked together with a pipe. We haven't done
> extensive testing so if you use them, please let us know.
> These utilities are bundled with some other little tools that we have
> developed for our day to day work. They are all written in python and they
> use biopython.
> You can take a look at the development site:
>
> https://github.com/JoseBlanca/seq_crumbs
>
> Or our site:
>
> http://bioinf.comav.upv.es/seq_crumbs/
>
> Of course we'd love to have some feedback.
> Best regards,
Hi Jose,
That looks very interesting - I'll forward this to the Biopython
list.
For those not aware of this, the Biopython SFF code was
based on Jose's original work for sff_extract - then reworked
as part of the Biopython parsing framework, made Python 3
compatible etc.
Jose - Is there anything you found missing in the Biopython
SFF code? For example a public API to get at the low-level
information from an SFF file rather than as Biopython objects?
Thanks,
Peter
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