PIR/GCG

Peter Rice rice at embl-heidelberg.de
Mon Nov 1 14:12:35 EST 1993


In article <1993Oct30.184049.4664 at gserv1.dl.ac.uk>, risler%FRCGM51.earn at uk.ac.earn-relay writes:
> Up to now I received the PIR database from MIPS on a magtape. Like many many
> others, I had troubles with the GCG files provided on the tape, which were
> fixed by re-running DBINDEX.
>  
> Now I receive PIR on their CD-ROM. Since I want to use GCG, I have to copy
> the files onto my VAX/VMS. *NOTE* this was a pain in the neck, a CD_MOUNT
> followed by a COPY doesn't work because the resulting file are "undefined".
> The CD_ACCESS program from P. Stockwell, available from the EMBL server,
> doesn't work either on these CD-ROMs (it's the only case I know of).
>  
> You MUST mount the CD-ROM with the following command:
>  
> CD_MOUNT/media=cdrom/UNDEFINED=(STREAM_LF:512)
>  
> It was rather hard to be aware of the UNDEFINED switch ... this may be
> useful to other people...
>  
> Well, finally it worked. The .REF and .SEQ files seem to be OK. Now, if I
> run PIRTOGCG or DBINDEX, I get the following message for *ALL* the
> sequences:
>  
> * no accession number for sequence XXXX *

A wild guess, but perhaps you still have stray characters in the files,
probably carriage returns or line feeds, from not having exactly the right
/undefined definition (which should define the record type to VMS as
the CD-ROM is lacking the necessary information). Try looking at the
REF files with DUMP /BLOCK=END=5 and see what characters appear. You then
have to change the /undefined qualifier on the mount until they look OK.

I have seen similar problems with other CD-ROM copies, but don't have the PIR
one around to check the exact command you need.

It's not their fault - most CD-ROMS suffer from the problem. PIR should
be able to tell you the correct syntax.

 -----------------------------------------------------------------------------
 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice at EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       69012 Heidelberg
 Fax:     +49-6221-387306                     |       Germany




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