Dear Peter and Guy,
I guess I just cling to the familiar. The output formats given by
emboss are fine,
One more obscure question:
As far as I can see, the output from "seqret -feature" and "entret"
are the same.
Are there any differences?
Thanks and best wishes,
Rich
On Jul 13, 2011, at 5:37 PM, Peter Rice wrote:
Dear Richard,
On 13/07/2011 21:56, Richard Friedman wrote:
I am learning to use Emboss after being a long-time GCG user.
The fetch command in GCG returns a file with the sequence in GCG
format
plus annotation.
In EMBOSS I know how to get just sequence in GCG format with seqret.
In EMBOSS I also know how to get the sequence plus annotation default
format.
What I would like to know is how using EMBOSS to get sequence plus
annotation in GCG format
like in GCG.
Hmmm ... by "annotation in GCG format" you mean the EMBL or Uniprot
entry with gaps in the ". ." feaure records?
The obvious question is why you need GCG format. GCG was not very
clever in handling the annotation.
You can get the sequence plus annotation in one file with:
seqret -feature somedb:someid outfile.seq -osformat embl (or swiss)
That gives you one file with "sequence plus annotation"... and you
can use the annotation.
You can also get the whole entry text with entret somedb:someid
Hope that helps - and if not, please do ask again!
Peter Rice
EMBOSS Team
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