J.A.C. Rullmann, Ton wrote:
>> As a newcomer to SRS I ran into problems building the indices for
> GenBank (GCG format).
> I'm using SRS 5.1.0 on IRIX 6.4. The GenBank release is 104 (12/97), as
> obtained from GCG.
>> I tried to modify genbank.i to switch from EMBL to GCG format.
> srsbuild -info genbank seems to work fine.
> srsbuild -w genbank gives the following:
>> > ...processing GENBANK
> > ...processing /u04/gcggenbank/gb_ba.ref
> > ...processing /u04/gcggenbank/gb_ba.seq
> > Entry name mismatch: ref=A16SRRNA, seq=
> >
>
I've seen this also and the fix was changing the line
('ORIGIN' {$Not} lnT {$App})+ lnT)?
to
('ORIGIN' {$Not} lnT {$App})+ lnT lnT?)?
in the entry production in genbank.is. Check
http://www.seqnet.dl.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageIcarusFile+-l+GENBANK+-ifile+is
for a genbank.is which works with gcg genbank. It also handles the
citation field, and does the hyperlinks in the db_xref fields in
the feature tables correctly.
Cheers,
Martin
PS - release 104 ??? - the latest release is 105 !
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