[EMBOSS] Getting headers from Seqret

[Peter Rice]

"simon andrews (BI)" wrote:
> The database formatted OK, and I can fetch sequences back from it, but
> at some point I will need to retrieve the entire header from the
> original file to get at some of the extra information in there
> (feature tables, cross references, authors etc).
>
> I've tried several different output USAs with
> seqret, but the most I can seem to get back is the name, accession number
> and description.

It all depends on how much information we store in the internal data
structures. As standard, we keep the ID, Accession, Description and
sequence so we can write a FASTA format file easily.

We also keep the complete feature table, but only optionally. seqret
ignores it, but seqretallfeat reads and writes it. Most programs only need
the sequence data and parsing feature information wastes time and space on
large sequences.

We can also read the entire text of an entry with entret, assuming you want
the original flatfile format.

>I can't believe that this information is thrown away by seqret
> (it's still there in the flat file after all),

Yes, it is (but we can easily read more fields - the problem is whether we
can convert them to other file formats easily)

> so how can I retrieve it?

Using entret - which sounds like the solution you need.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723