Scripts to auto-update GCG db's?

Nick Staffa, ph 361-9422 ext226 STAFFA at NIEHS.NIH.GOV
Mon Feb 12 09:14:49 EST 1996

>From:	IN%"jquinn at shellx.best.com" 10-FEB-1996 18:06:56.66
>To:	IN%"info-gcg at net.bio.net"
>Subj:	Scripts to auto-update GCG db's?
>Does anyone know of pre-existing scripts that could be run as a cron job  
>and would automatically fetch databases in the early hours of the morning 
>and format them into gcg format? I can and will write some progs/scripts 
>myself, but I thought that this might be something that other people have 
>already developed (and I didn't want to re-invent the wheel here).
>Thanks for any help
>Greg Quinn 

In Unix one can gussy up the get_gbnew script by putting in indeces and 
making a big loop out of it to get all 16 Genbank divisions.
Stuff like
set nn=(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16)
set ftpfiles=(gbbct.seq.Z gbinv.seq.Z gbmam.seq.Z gbpat.seq.Z \
gbphg.seq.Z gbpln.seq.Z gbpri.seq.Z gbrna.seq.Z gbrod.seq.Z gbsts.seq.Z \
gbsyn.seq.Z gbuna.seq.Z gbvrl.seq.Z gbvrt.seq.Z gbest1.seq.Z gbest2.seq.Z)
set uncompfiles=(gbbac_seq gbinv_seq gbom_seq gbpat_seq gbphg_seq \
gbpln_seq gbpri_seq gbstr_seq gbrod_seq gbsts_seq gbsyn_seq gbuna_seq \
gbvi_seq gbov_seq gbest1_seq gbest2_seq)
set gcgnames=(gb_ba gb_in gb_om gb_pat gb_ph gb_pl gb_pr gb_st gb_ro \

et c.
with the following inserted at the appropriat spot:

#  Loop here
foreach i ($nn)
set ftpfile="$ftpfiles[$i]"           # remotZe fil[$
set outfile="${uncompfiles[$i]}.Z"   # local file after transfer
set uncompressedfile="$uncompfiles[$i]"    # local file after decompression
set gcgname="$gcgnames[$i]"          # name of .seq file of data library
set sn="$snames[$i]"
Ask via E-mail direct to me and I will send this script to you.
A similar one does genpept.
I also have a "system" for downloading data bases written for VMS.
I consists of a file of database names and two command files; one submits
the other with appropriate parameters. This is also available on request.

Nick Staffa
National Institute of Environmental Health Sciences
Research Triangle Park, North Carolina.

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