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Cannot generate EMBL-pid index files

Peter Rice pmr at sanger.ac.uk
Tue Feb 9 12:25:53 EST 1999


Morten Stig Andersen <mosa at novo.dk> writes:

> Has anyone got a solution to this:
> The "PID" field of coding sequences in EMBL cannot be indexed in SRS.
> The srsupdate script can generate and compress the individual index
> files, but it dumps core when it tries to merge them. There are no
> problems in EMBLNEW, or with generation with any of the other EMBL
> indices. My SRS server runs on a SGI IRIX64, v. 6.4.
> 
> An extract from the log file is given below.
> 
> 
> + srsbuild EMBL -f  pid -xdir SRSINX: -odir SRSINX: -s unix -nn
> ...processing EMBL
> ...processing /usr/databases/embl/est1.dat
> ...processing /usr/databases/embl/est1.dat
> 

As Martin Hilbers pointed out, you must have PIDs in the first file
you index (strictly, in the first 100,000 entries). est1.dat has no
PIDs and has 100,000 entries.

There are index files at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/embl
but you have some work to do to use them for EMBL flat files
(see the README file and watch for filenames in embl.i)

I used this method for the Sanger server, but I modified the indices
later (added NID indices).

-- 
----------------------------------------------------------------------
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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