[EMBOSS] SCF files (Staden)

[Fields, Christopher J]

On Nov 29, 2011, at 12:35 PM, Peter Cock wrote:

> On Tue, Nov 29, 2011 at 5:53 PM, Tom Keller <kellert at ohsu.edu> wrote:
>> Greetings,
>> You can use BioPerl for this. EMBOSS and perl work well together.
>> Here is a link: http://www.bioperl.org/wiki/HOWTO:SeqIO
>> 
>> cheers,
>> Tom
> 
> Doesn't BioPerl just use the Staden libraries for this internally?

Yes, and it uses an old version as well (via bioperl-ext).  Much of this effort was to go into the biolib initiative for creating cross-lang bindings using swig, but that seems to be silent at the moment.  I'm surprised Python doesn't have io_lib bindings.

> Either way, Perl and I don't work so well together, so I'm happier
> using Staden's trace_convert directly ;)
> 
> Peter

Heh.

chris