149 lines
4.9 KiB
Text
149 lines
4.9 KiB
Text
$NetBSD: patch-aa,v 1.2 2005/11/03 19:52:44 rillig Exp $
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--- test/testxylem.csh.orig 2001-08-18 16:31:51.000000000 -0400
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+++ test/testxylem.csh 2003-09-28 17:29:21.000000000 -0400
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@@ -10,13 +10,12 @@
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# set default parameters
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#####################################################################
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set RM = rm
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-set BINDIR = ../bin
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# set $testset to programs to be tested.
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set NUMARGS = $#argv
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if ($NUMARGS == 0) then
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- set TESTSET = (splitdb getloc identify getob reform ribosome shuffle\
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+ set TESTSET = (splitdb getloc xyl-identify getob reform ribosome shuffle\
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dbstat flat2phyl findkey fetch features)
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else
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set TESTSET = $1
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@@ -31,7 +30,7 @@
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######### splitdb #######
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case splitdb:
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# run the program
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- $BINDIR/splitdb sample.gen temp.ano temp.wrp temp.ind
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+ splitdb sample.gen temp.ano temp.wrp temp.ind
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -73,7 +72,7 @@
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######### getloc #######
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case getloc:
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# run the program
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- $BINDIR/getloc sample.nam sample.ano sample.wrp sample.ind temp.gen
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+ getloc sample.nam sample.ano sample.wrp sample.ind temp.gen
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -95,10 +94,10 @@
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breaksw
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######### identify #######
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- case identify:
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+ case xyl-identify:
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# run the program
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egrep -n -i LOCUS sample.ano >temp.egrep
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- $BINDIR/identify temp.egrep sample.ind temp.nam temp.fnd
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+ xyl-identify temp.egrep sample.ind temp.nam temp.fnd
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -132,7 +131,7 @@
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######### getob #######
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case getob:
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# run the program
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- $BINDIR/getob sample.inp sample.nam sample.ano sample.wrp sample.ind\
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+ getob sample.inp sample.nam sample.ano sample.wrp sample.ind\
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temp.getob.msg temp.getob.out temp.getob.exp
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# if successful, compare sample files with new output
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@@ -175,7 +174,7 @@
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######### reform #######
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case reform:
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# run the program
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- $BINDIR/reform -g -p -c -fi <sample.aln > temp.ref
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+ reform -g -p -c -fi <sample.aln > temp.ref
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -199,7 +198,7 @@
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######### ribosome #######
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case ribosome:
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# run the program
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- $BINDIR/ribosome <sample.out > temp.pep
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+ ribosome <sample.out > temp.pep
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -223,7 +222,7 @@
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######### prot2nuc #######
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case prot2nuc:
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# run the program
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- $BINDIR/prot2nuc <sample.pro > temp.prot2nuc
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+ prot2nuc <sample.pro > temp.prot2nuc
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -247,7 +246,7 @@
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######### dbstat #######
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case dbstat:
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# run the program
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- $BINDIR/dbstat <sample.pep > temp.dbstat
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+ dbstat <sample.pep > temp.dbstat
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -272,7 +271,7 @@
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case flat2phyl:
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# check results for interleaved format
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- $BINDIR/flat2phyl <sample.flat > temp.interleaved.phylip
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+ flat2phyl <sample.flat > temp.interleaved.phylip
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -295,7 +294,7 @@
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endif
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# check results for sequential format
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- $BINDIR/flat2phyl -s <sample.flat > temp.sequential.phylip
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+ flat2phyl -s <sample.flat > temp.sequential.phylip
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -321,7 +320,7 @@
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######### shuffle #######
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case shuffle:
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# run the program
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- $BINDIR/shuffle -s3456 <sample.out > temp.shuf
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+ shuffle -s3456 <sample.out > temp.shuf
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -337,7 +336,7 @@
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case findkey:
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# run the program
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echo "LOCUS" > temp.kw
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- $BINDIR/findkey -G sample.ano temp.kw temp.nam temp.fnd
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+ findkey -G sample.ano temp.kw temp.nam temp.fnd
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -371,7 +370,7 @@
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######### fetch #######
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case fetch:
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# run the program
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- $BINDIR/fetch -G sample sample.nam temp.gen
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+ fetch -G sample sample.nam temp.gen
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# if successful, compare sample files with new output
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set SUCCESS = $status
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@@ -396,7 +395,7 @@
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case features:
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# run the program
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cp sample.exp temp.exp
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- $BINDIR/features -u sample -E temp.exp
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+ features -u sample -E temp.exp
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# if successful, compare sample files with new output
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set SUCCESS = $status
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