How to get around changing .i files while indexing offline

Peter Rice pmr at sanger.ac.uk
Wed Sep 22 04:20:38 EST 1999


tdeboer at hgmp.mrc.ac.uk writes:
> How do I get around changing and recompiling the .i files when I want=20
> to both index the new database offline and still be able to retrieve=20
> entries from the former release, without having to revert to using two=20
> completely seperate macines ?

In general it is a problem, but for EMBL there is a solution.

The SRS index files are on the FTP server at the EBI. You can simply
FTP them over and make them live with the new embl.i. The instructions
are a little out of date (these are the index files for the flat file
version, but it still has a reference to 'GCG formatted files').

The README says they cannot be reallocated for GCG formatted databases.
Not sure why - the EBI files used to be for GCG databases and I could
reallocate them for flat files with "srsbuild -r embl" given a little
care in updating the file names in embl.i.

The accession number index has a long-standing bug that misses
secondary accession numbers. I have a fixed embl.is file at Sanger but
you would need to be careful about rebuilding the links if you reindex
the accession numbers. srscheck misses the change and I had to relink
by hand.



-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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