In article <0097C37B.32C6EB80 at vms.csd.mu.edu>, 6566friedman at vms.csd.mu.edu writes:
>> I am looking for some technical assistance in converting the genbank
> database available from the NLM archive into a VMS GCG usable format.
> The LZ decompression file from ncbi.nlm.nih.gov bombed. I understand
> that LVDCMP.EXE from net.bio.net works better. However our systems
> analyst doesn't know what to do with the many files that output when we
> run "Genbank to GCG". Any suggestions???
Make them into a GCG library, as follows. Put the files (.seq, .ref, .names
etc) in a subdirectory. All these files have the same part before the
period, say COWS. Say your username is friedman, you could put
them in [FRIEDMAN.LIBS]. If you named the retrieved file GENBANK.COWS,
you would now have the file [FRIEDMAN.LIBS]GENBANK.COWS.
Then define a logical name for the library, for example:
$ assign [friedman.libs]cows cows
Now run genbanktogcg:
$ GenbankToGCG/dir=[friedman.libs]/ln=cows/out=cows [friedman.libs]genbank.cows
/dir=[friedman.libs] tells the program where to put the .seq etc. files,
/ln=cows is the library name (the logical name, officially), /out=cows
makes sure that the files are called cows.seq etc.
You can now access the sequences as you do from any other library, say
vir:
names cows:*
will show you all the names in te cows library.
If you want to add new files to the library, just append the new file
you retrieved from genbank to the original, and run the whole thing
through genbanktogcg again. (you don't need to redefine the logical
name).
----
Gerard Stafleu
email: gerard at uwo.ca
ITS, University of Western Ontario,
London, Ontario, Canada N6A 5B7
(519)661-2151
