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|
Author: Michael R. Crusoe <crusoe@debian.org>
Description: disable tests that require external databases
Forwarded: not-needed
--- a/test/test.sh
+++ b/test/test.sh
@@ -7,71 +7,13 @@ if [ ! -d results ]; then
mkdir results
fi
-export FA_DB=$SLIB2/fa_dbs/qfo20.lseg
-
-echo "starting fasta36 - protein" `date`
-../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html
-../bin/fasta36 -S -q -z 11 -O results/test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 $FA_DB
-echo "done"
-echo "starting fastxy36" `date`
-../bin/fastx36 -m 9c -S -q ../seq/mgtt2_x.seq $FA_DB 1 > results/test_t2.xk1
-../bin/fasty36 -S -q ../seq/mgtt2_x.seq $FA_DB > results/test_t2.yk2
-../bin/fastx36 -m 9c -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.xk2z2
-../bin/fasty36 -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.yk2z2
-echo "done"
-echo "starting fastxy36 rev" `date`
-../bin/fastx36 -m 9c -q -m 5 ../seq/mgstm1.rev $FA_DB > results/test_m1.xk2r
-../bin/fasty36 -q -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz2
-../bin/fasty36 -q -m 5 -z 11 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz11
-echo "done"
-echo "starting ssearch36" `date`
-../bin/ssearch36 -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.ssz3
-../bin/ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.ss_p25
-echo "done"
-if [ -e ../bin/ssearch36s ]; then
- echo "starting ssearch36s" `date`
- ../bin/ssearch36s -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.sssz3
- ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
- echo "done"
-fi
echo "starting prss36(ssearch/fastx)" `date`
../bin/ssearch36 -q -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test_m1.rss
../bin/fastx36 -q -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test_m1.rfx
echo "done"
-echo "starting ggsearch36/glsearch36" `date`
-../bin/ggsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gg
-../bin/glsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gl
-../bin/ggsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gg
-../bin/glsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gl
-echo "done"
-echo "starting fasta36 - DNA" `date`
-../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
-../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
-echo "done"
#echo "starting tfasta36" `date`
#tfasta36 -q ../seq/mgstm1.aa %RMB > results/test_m1.tk2
#echo "done"
-echo "starting tfastxy36" `date`
-../bin/tfastx36 -m 9c -q -i -3 -m 6 ../seq/mgstm1.aa %p > results/test_m1.tx2.html
-../bin/tfasty36 -q -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test_m1.ty2
-echo "done"
-echo "starting fastf36" `date`
-../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff
-../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff_s
-echo "done"
-echo "starting tfastf36" `date`
-../bin/tfastf36 -q ../seq/m1r.aa %r > results/test_mf.tfr
-echo "done"
-echo "starting fasts36" `date`
-../bin/fasts36 -q -V '*?@' ../seq/ngts.aa $FA_DB > results/test_m1.fs1
-../bin/fasts36 -q ../seq/ngt.aa $FA_DB > results/test_m1.fs
-../bin/fasts36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfs
-echo "starting fastm36" `date`
-../bin/fastm36 -q ../seq/ngts.aa $FA_DB > results/test_m1.fm
-../bin/fastm36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfm
-echo "done"
-echo "starting tfasts36" `date`
-../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
echo "starting lalign36" `date`
../bin/lalign36 -k 1000 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal
../bin/lalign36 -z 3 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal_z3
--- a/test/test2G.sh
+++ b/test/test2G.sh
@@ -6,69 +6,69 @@ echo ""
if [ ! -d results ]; then
mkdir results
fi
-echo "starting fasta36 - protein" `date`
-../bin/fasta36 -XM2G -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 q > results/test2G_m1.ok2.html
-../bin/fasta36 -q -XM2G -S -z 11 -O results/test2G_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 q
-echo "done"
-echo "starting fastxy36" `date`
-../bin/fastx36 -q -XM2G -m 9c -S ../seq/mgtt2_x.seq q 1 > results/test2G_t2.xk1
-../bin/fasty36 -q -XM2G -S ../seq/mgtt2_x.seq q > results/test2G_t2.yk2
-../bin/fastx36 -q -XM2G -m 9c -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.xk2z2
-../bin/fasty36 -q -XM2G -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.yk2z2
-echo "done"
-echo "starting fastxy36 rev" `date`
-../bin/fastx36 -q -XM2G -m 9c -m 5 ../seq/mgstm1.rev q > results/test2G_m1.xk2r
-../bin/fasty36 -q -XM2G -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz2
-../bin/fasty36 -q -XM2G -m 5 -z 11 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz11
-echo "done"
-echo "starting ssearch36" `date`
-../bin/ssearch36 -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.ssz3
-../bin/ssearch36 -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.ss_p25
-echo "done"
-if [ -e ../bin/ssearch36s ]; then
- echo "starting ssearch36s" `date`
- ../bin/ssearch36s -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.sssz3
- ../bin/ssearch36s -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.sss_p25
- echo "done"
-fi
+# echo "starting fasta36 - protein" `date`
+# ../bin/fasta36 -XM2G -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 q > results/test2G_m1.ok2.html
+# ../bin/fasta36 -q -XM2G -S -z 11 -O results/test2G_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 q
+# echo "done"
+# echo "starting fastxy36" `date`
+# ../bin/fastx36 -q -XM2G -m 9c -S ../seq/mgtt2_x.seq q 1 > results/test2G_t2.xk1
+# ../bin/fasty36 -q -XM2G -S ../seq/mgtt2_x.seq q > results/test2G_t2.yk2
+# ../bin/fastx36 -q -XM2G -m 9c -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.xk2z2
+# ../bin/fasty36 -q -XM2G -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.yk2z2
+# echo "done"
+# echo "starting fastxy36 rev" `date`
+# ../bin/fastx36 -q -XM2G -m 9c -m 5 ../seq/mgstm1.rev q > results/test2G_m1.xk2r
+# ../bin/fasty36 -q -XM2G -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz2
+# ../bin/fasty36 -q -XM2G -m 5 -z 11 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz11
+# echo "done"
+# echo "starting ssearch36" `date`
+# ../bin/ssearch36 -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.ssz3
+# ../bin/ssearch36 -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.ss_p25
+# echo "done"
+# if [ -e ../bin/ssearch36s ]; then
+# echo "starting ssearch36s" `date`
+# ../bin/ssearch36s -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.sssz3
+# ../bin/ssearch36s -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.sss_p25
+# echo "done"
+# fi
echo "starting prss36(ssearch/fastx)" `date`
../bin/ssearch36 -q -XM2G -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test2G_m1.rss
../bin/fastx36 -q -XM2G -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test2G_m1.rfx
echo "done"
-echo "starting ggsearch36/glsearch36" `date`
-../bin/ggsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gg
-../bin/glsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gl
-../bin/ggsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gg
-../bin/glsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gl
-echo "done"
-echo "starting fasta36 - DNA" `date`
-../bin/fasta36 -S -q -XM2G ../seq/mgstm1.nt %RMB 4 > results/test2G_m1.ok4
-../bin/fasta36 -S -q -XM2G ../seq/mgstm1.rev %RMB 4 > results/test2G_m1.ok4r
-echo "done"
+# echo "starting ggsearch36/glsearch36" `date`
+# ../bin/ggsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gg
+# ../bin/glsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gl
+# ../bin/ggsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gg
+# ../bin/glsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gl
+# echo "done"
+# echo "starting fasta36 - DNA" `date`
+# ../bin/fasta36 -S -q -XM2G ../seq/mgstm1.nt %RMB 4 > results/test2G_m1.ok4
+# ../bin/fasta36 -S -q -XM2G ../seq/mgstm1.rev %RMB 4 > results/test2G_m1.ok4r
+# echo "done"
#echo "starting tfasta36" `date`
#tfasta36 -q -XM2G ../seq/mgstm1.aa %RMB > results/test2G_m1.tk2
#echo "done"
-echo "starting tfastxy36" `date`
-../bin/tfastx36 -m 9c -q -XM2G -i -3 -m 6 ../seq/mgstm1.aa %p > results/test2G_m1.tx2.html
-../bin/tfasty36 -q -XM2G -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test2G_m1.ty2
-echo "done"
-echo "starting fastf36" `date`
-../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff
-../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff_s
-echo "done"
-echo "starting tfastf36" `date`
-../bin/tfastf36 -q -XM2G ../seq/m1r.aa %r > results/test2G_mf.tfr
-echo "done"
-echo "starting fasts36" `date`
-../bin/fasts36 -q -XM2G -V '*?@' ../seq/ngts.aa q > results/test2G_m1.fs1
-../bin/fasts36 -q -XM2G ../seq/ngt.aa q > results/test2G_m1.fs
-../bin/fasts36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfs
-echo "starting fastm36" `date`
-../bin/fastm36 -q -XM2G ../seq/ngts.aa q > results/test2G_m1.fm
-../bin/fastm36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfm
-echo "done"
-echo "starting tfasts36" `date`
-../bin/tfasts36 -q -XM2G ../seq/n0.aa %r > results/test2G_m1.ts_r
+# echo "starting tfastxy36" `date`
+# ../bin/tfastx36 -m 9c -q -XM2G -i -3 -m 6 ../seq/mgstm1.aa %p > results/test2G_m1.tx2.html
+# ../bin/tfasty36 -q -XM2G -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test2G_m1.ty2
+# echo "done"
+# echo "starting fastf36" `date`
+# ../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff
+# ../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff_s
+# echo "done"
+# echo "starting tfastf36" `date`
+# ../bin/tfastf36 -q -XM2G ../seq/m1r.aa %r > results/test2G_mf.tfr
+# echo "done"
+# echo "starting fasts36" `date`
+# ../bin/fasts36 -q -XM2G -V '*?@' ../seq/ngts.aa q > results/test2G_m1.fs1
+# ../bin/fasts36 -q -XM2G ../seq/ngt.aa q > results/test2G_m1.fs
+# ../bin/fasts36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfs
+# echo "starting fastm36" `date`
+# ../bin/fastm36 -q -XM2G ../seq/ngts.aa q > results/test2G_m1.fm
+# ../bin/fastm36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfm
+# echo "done"
+# echo "starting tfasts36" `date`
+# ../bin/tfasts36 -q -XM2G ../seq/n0.aa %r > results/test2G_m1.ts_r
echo "starting lalign36" `date`
../bin/lalign36 -q -XM2G -k 1000 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal
../bin/lalign36 -q -XM2G -z 3 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal_z3
--- fasta3.orig/scripts/test_py.sh
+++ fasta3/scripts/test_py.sh
@@ -13,18 +13,6 @@
get_protein.py 'P09488'
get_protein.py 'NP_000552'
-echo '################################################################'
-echo 'requires mysql database'
-echo 'get_protein_sql.py'
-get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
-get_protein_sql.py 'P09488'
-get_protein_sql.py 'NP_000552'
-
-echo 'get_protein_sql_www.py'
-get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
-get_protein_sql_www.py 'P09488'
-get_protein_sql_www.py 'NP_000552'
-
echo 'get_refseq.py'
get_refseq.py NP_000552
get_refseq.py NP_0000552
@@ -34,12 +22,6 @@
get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
echo '################################################################'
-echo 'requires mysql database'
-echo 'get_up_prot_iso_sql.py'
-get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
-get_up_prot_iso_sql.py P09488
-
-echo '################################################################'
echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
# (a) produce an appropriate alignment file
fasta36 -q -m 8CBL -V \!ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!ann_exons_up_sql.pl+--gen_coord+--exon_label \!get_protein.py+P30711 \!get_protein.py+P20135 > hum_chk_map_test.m8CBL
|
