[EMBOSS] SCF files (Staden)
Fields, Christopher J
cjfields at illinois.edu
Tue Nov 29 19:09:42 UTC 2011
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
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