Scripts to auto-update GCG db's?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Mon Feb 12 10:37:03 EST 1996

: Does anyone know of pre-existing scripts that could be run as a cron job  

Two considerations have to be kept in mind: 

1) The update files become very large (100MB) and a considerable scratch
   space is required if you download all at once (.Z is 2/3rd of the original
   flat file, and the flat file must co-exist with the gcg file spacewise).
   Including a save copy of GCG formatted data the currently needed space, 
   therefore, is about 350 MByte by now. Think about the growth and calcu-
   late for 2 Gigabyte at the end of next year. 

2) Incremental updating cannot simply append files because of duplications 
   and deletions. To my knowledge, there is no current GENBANK-compliant 
   procedure which will allow processing of the incremental updates and its 
   quality validation. 

For mirroring in general, you may find it useful to employ the perl script 
solution as it is more flexible and readily available. Lee McLoughlin has 
written this based on the basis of a script by  Alan R. Martello written 
in turn on software by Randal L. Schwartz. Many people were patching the final
(currently, version 2.3) version. It doesn't work reliably on perl5 yet 
as far as I am informed. 


Reinhard Doelz, Basel, Switzerland

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