scripting for getz

Colin Semple Colin.Semple at hgu.mrc.ac.uk
Wed Nov 11 07:28:42 EST 1998

Dear all,

I'm rather new to getz and for some reason can't get scripts
incorporating getz queries to behave properly on the hgmp server. The
script below looks like it should work but generates the error message:

SRSICA:icarus.i:0: error: invalid character, character "'" is not
allowed within parameter "fieldList"

Any help/advice you can give me would be much appreciated, here's the

#!/bin/tcsh -f
#script to make getz queries
set noglob
set name = N22117
set query = "'[libs={embl emblnew}-AllText: $name*]'"
echo query = $query
set bit = "-f 'AccNumber seq' -sf 'fasta'"
echo getz $query $bit
getz $query $bit > jim
#this works from command line:
#getz '[libs={embl emblnew}-AllText: N22117*]' -f 'AccNumber seq' -sf
'fasta' > jim

Colin Semple
MRC Human Genetics Unit
Western General Hospital
Edinburgh EH4 2XU

Tel: + 44 - (0) 131-332-2471 x4001
Fax: + 44 - (0) 131-343-2620
Email: C.Semple at hgu.mrc.ac.uk
Web: http://www.hgu.mrc.ac.uk/Users/colins

More information about the Bio-srs mailing list

Send comments to us at biosci-help [At] net.bio.net