PIR/GCG

risler%FRCGM51.earn at uk.ac.earn-relay risler%FRCGM51.earn at uk.ac.earn-relay
Sat Oct 30 18:40:27 EST 1993


 
Hi GCG/VMS fellows,
 
Again a problem with PIR ...
 
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 *
 
Anyway the programs go on, I get the usual .NAMES, .OFFSET, etc...files
whose size seem reasonable.
 
*BUT* I can't FETCH any sequence. If I try to fetch CCHU from PIR1, for
example, I get  * no files in PIR1:CCHU *  .....
 
NOTE 1: I am lazy and I always wait for a certain time before installing the
minor releases, waiting for other people to find the new bugs ... :-)
Hence I'm still under GCG #7.0  Is this the reason?
 
NOTE 2: The files are NOT in CODATA format. They just look like the good
old PIR files. However, the accession number is hidden in a line such as:
c;Accession: xxxxxx
 
Thank you for your help,
 
Jean-Loup
 
 
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  Jean-Loup Risler                      Tel:  (33 1) 69 82 31 34
  CNRS                                  Fax:  (33 1) 69 07 49 73
  Centre de Genetique Moleculaire       Email: risler at cgmvax.cgm.cnrs-gif.fr
  91198 Gif sur Yvette Cedex  France    Email: risler at frcgm51.bitnet
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