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locks; strict; comment @# @; 1.2 date 2005.11.03.19.52.44; author rillig; state Exp; branches; next 1.1; 1.1 date 2003.10.04.19.13.31; author jschauma; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2003.10.04.19.13.31; author jschauma; state Exp; branches; next ; desc @@ 1.2 log @Fixed wrong use of WRKSRC. @ text @$NetBSD: patch-aa,v 1.1.1.1 2003/10/04 19:13:31 jschauma Exp $ --- test/testxylem.csh.orig 2001-08-18 16:31:51.000000000 -0400 +++ test/testxylem.csh 2003-09-28 17:29:21.000000000 -0400 @@@@ -10,13 +10,12 @@@@ # set default parameters ##################################################################### set RM = rm -set BINDIR = ../bin # set $testset to programs to be tested. set NUMARGS = $#argv if ($NUMARGS == 0) then - set TESTSET = (splitdb getloc identify getob reform ribosome shuffle\ + set TESTSET = (splitdb getloc xyl-identify getob reform ribosome shuffle\ dbstat flat2phyl findkey fetch features) else set TESTSET = $1 @@@@ -31,7 +30,7 @@@@ ######### splitdb ####### case splitdb: # run the program - $BINDIR/splitdb sample.gen temp.ano temp.wrp temp.ind + splitdb sample.gen temp.ano temp.wrp temp.ind # if successful, compare sample files with new output set SUCCESS = $status @@@@ -73,7 +72,7 @@@@ ######### getloc ####### case getloc: # run the program - $BINDIR/getloc sample.nam sample.ano sample.wrp sample.ind temp.gen + getloc sample.nam sample.ano sample.wrp sample.ind temp.gen # if successful, compare sample files with new output set SUCCESS = $status @@@@ -95,10 +94,10 @@@@ breaksw ######### identify ####### - case identify: + case xyl-identify: # run the program egrep -n -i LOCUS sample.ano >temp.egrep - $BINDIR/identify temp.egrep sample.ind temp.nam temp.fnd + xyl-identify temp.egrep sample.ind temp.nam temp.fnd # if successful, compare sample files with new output set SUCCESS = $status @@@@ -132,7 +131,7 @@@@ ######### getob ####### case getob: # run the program - $BINDIR/getob sample.inp sample.nam sample.ano sample.wrp sample.ind\ + getob sample.inp sample.nam sample.ano sample.wrp sample.ind\ temp.getob.msg temp.getob.out temp.getob.exp # if successful, compare sample files with new output @@@@ -175,7 +174,7 @@@@ ######### reform ####### case reform: # run the program - $BINDIR/reform -g -p -c -fi temp.ref + reform -g -p -c -fi temp.ref # if successful, compare sample files with new output set SUCCESS = $status @@@@ -199,7 +198,7 @@@@ ######### ribosome ####### case ribosome: # run the program - $BINDIR/ribosome temp.pep + ribosome temp.pep # if successful, compare sample files with new output set SUCCESS = $status @@@@ -223,7 +222,7 @@@@ ######### prot2nuc ####### case prot2nuc: # run the program - $BINDIR/prot2nuc temp.prot2nuc + prot2nuc temp.prot2nuc # if successful, compare sample files with new output set SUCCESS = $status @@@@ -247,7 +246,7 @@@@ ######### dbstat ####### case dbstat: # run the program - $BINDIR/dbstat temp.dbstat + dbstat temp.dbstat # if successful, compare sample files with new output set SUCCESS = $status @@@@ -272,7 +271,7 @@@@ case flat2phyl: # check results for interleaved format - $BINDIR/flat2phyl temp.interleaved.phylip + flat2phyl temp.interleaved.phylip # if successful, compare sample files with new output set SUCCESS = $status @@@@ -295,7 +294,7 @@@@ endif # check results for sequential format - $BINDIR/flat2phyl -s temp.sequential.phylip + flat2phyl -s temp.sequential.phylip # if successful, compare sample files with new output set SUCCESS = $status @@@@ -321,7 +320,7 @@@@ ######### shuffle ####### case shuffle: # run the program - $BINDIR/shuffle -s3456 temp.shuf + shuffle -s3456 temp.shuf # if successful, compare sample files with new output set SUCCESS = $status @@@@ -337,7 +336,7 @@@@ case findkey: # run the program echo "LOCUS" > temp.kw - $BINDIR/findkey -G sample.ano temp.kw temp.nam temp.fnd + findkey -G sample.ano temp.kw temp.nam temp.fnd # if successful, compare sample files with new output set SUCCESS = $status @@@@ -371,7 +370,7 @@@@ ######### fetch ####### case fetch: # run the program - $BINDIR/fetch -G sample sample.nam temp.gen + fetch -G sample sample.nam temp.gen # if successful, compare sample files with new output set SUCCESS = $status @@@@ -396,7 +395,7 @@@@ case features: # run the program cp sample.exp temp.exp - $BINDIR/features -u sample -E temp.exp + features -u sample -E temp.exp # if successful, compare sample files with new output set SUCCESS = $status @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD: $ d3 2 a4 2 --- ../test/testxylem.csh.orig 2001-08-18 16:31:51.000000000 -0400 +++ ../test/testxylem.csh 2003-09-28 17:29:21.000000000 -0400 @ 1.1.1.1 log @Initial import of xylem, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. XYLEM is a package of tools designed to exploit the Unix environment to enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR. @ text @@