PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

added test for chlorodb

Browse Source 
Former-commit-id: 639cbbdc91a6c7f11544dbbe1fa0c47e1e28eaad
Former-commit-id: 59f6ff3f727d01f3ed4d553a554b322b24119b06
This commit is contained in:
alain viari
2015-11-13 18:53:47 +01:00
parent 13b03062d5
commit 42707c281c
17 changed files with 433 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
detectors/cds/tools/chlorodb/go_chlorodb.sh
View File

@ -35,6 +35,7 @@ cd $DB_BASE/info
#
if (! -e $DB_BASE/parameters.sh) then
Notify "no $DB_BASE/parameters.sh found : creating one for you"
@ n = `find $DB_BASE/download -depth 1 -type f -print | wc -l`
@ cor_cutoff = $n / 2
@ atg_cutoff = $n / 10
@ -70,7 +71,9 @@ if (! -e $DB_BASE/parameters.sh) then
echo "set DUST_PMAX = 1e-6" >> $DB_BASE/parameters.sh
echo "set DUST_IDMIN = 30" >> $DB_BASE/parameters.sh
echo "set DUST_SIZMIN = 10" >> $DB_BASE/parameters.sh
Cat $DB_BASE/parameters.sh
else
Notify "DB parameters : $DB_BASE/parameters.sh"
endif
source $DB_BASE/parameters.sh
@ -198,12 +201,34 @@ if (-e db.core.pat.txt) then
Notify "Making core DB (take some time... please wait)"
$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.core.pat.txt \
$CORE_DELTA $CORE_COVMIN $CORE_PMAX $CORE_IDMIN $CORE_SIZMIN
# add discarded entries into shell
if (-e db.core.pat.db/Annot.lst) then
sort db.core.pat.txt > A_$$
sort db.core.pat.db/Annot.lst > B_$$
join -a1 A_$$ B_$$ | awk '(NF==3) {print $0}' > C_$$
set n = `cat C_$$ | wc -l`
Notify "transfering $n discarded entries to shell"
cat C_$$ >> db.shell.pat.txt
\rm -f ?_$$
endif
endif
if (-e db.shell.pat.txt) then
Notify "Making shell DB (take some time... please wait)"
$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.shell.pat.txt \
$SHEL_DELTA $SHEL_COVMIN $SHEL_PMAX $SHEL_IDMIN $SHEL_SIZMIN
# add discarded entries into dust
if (-e db.shell.pat.db/Annot.lst) then
sort db.shell.pat.txt > A_$$
sort db.shell.pat.db/Annot.lst > B_$$
join -a1 A_$$ B_$$ | awk '(NF==3) {print $0}' >> C_$$
set n = `cat C_$$ | wc -l`
Notify "transfering $n discarded entries to dust"
cat C_$$ >> db.dust.pat.txt
\rm -f ?_$$
endif
endif
if (-e db.dust.pat.txt) then

37
detectors/cds/tools/chlorodb/subdb/go_subdb.sh
View File

@ -27,7 +27,7 @@ set Delta = 0.5
set Covmin = 30
set Pmax = 1e-6
set Idmin = 30
set Sizmin = 5
set Sizmin = 10
if ($#Argv > 0) then
set Delta = $Argv[1]; Shift
@ -91,14 +91,17 @@ set noms = `awk '{print $1}' $PatFile`
foreach nom ($noms)
set pat = `egrep "^$nom " $PatFile | awk '{print $2}'`
$AwkCmd -f $LIB_DIR/db.filter.pat.awk -v PAT="$pat" P_$$ > D_$$/$nom.fst
Report D_$$/$nom.fst "pattern_filter"
set n = `egrep '^>' D_$$/$nom.fst | wc -l`
Notify " pattern : $nom : $n"
Report D_$$/$nom.fst "pattern_filter"
if ($n <= $Sizmin) \rm -f D_$$/$nom.fst
if ($n < $Sizmin) \rm -f D_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
if ($ok == 0) then
Warning "no entries found after pattern selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# select by length
@ -115,12 +118,14 @@ foreach f (D_$$/*.fst)
Report E_$$/$nom.fst "length_filter"
set n = `egrep '^>' E_$$/$nom.fst | wc -l`
Notify " length filter : $nom : $n"
if ($n <= $Sizmin) \rm -f E_$$/$nom.fst
if ($n < $Sizmin) \rm -f E_$$/$nom.fst
end
set ok = `ls E_$$ | wc -l`
if ($ok == 0) goto fin
if ($ok == 0) then
Warning "no entries found after length selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# select by similarity
@ -152,12 +157,15 @@ foreach f (E_$$/*.fst)
set n = `egrep '^>' F_$$/$nom.fst | wc -l`
Notify " blast filter : $nom : $n"
if ($n <= $Sizmin) \rm -f F_$$/$nom.fst
if ($n < $Sizmin) \rm -f F_$$/$nom.fst
end
set ok = `ls D_$$ | wc -l`
if ($ok == 0) goto fin
set ok = `ls F_$$ | wc -l`
if ($ok == 0) then
Warning "no entries found after similarity selection (increase Sizmin = $Sizmin)"
goto fin
endif
#
# annotations
@ -187,7 +195,14 @@ Notify "copy $n files to $OutDir"
#
fin:
Notify "output directory : $OutDir"
set n = `find $OutDir -name \*.fst -print | wc -l`
if ($n == 0) then
Warning "no entries found : removing $OutDir"
\rm -r $OutDir
else
Notify "output directory : $OutDir : $n entries"
endif
\rm -r ?_$$

25
detectors/cds/tools/chlorodb/test/go_test.sh Executable file
View File

@ -0,0 +1,25 @@
#!/bin/csh -f
setenv ORG_HOME `dirname $0`/../../../../..
source $ORG_HOME/scripts/csh_init.sh
echo "+ testing go_chlorodb.sh"
\cp -r test.db TMP
`dirname $0`/../go_chlorodb.sh TMP
find TMP -name \*.fst -print | sort > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo "+ $VTC[3]test Ok$VTC[1]"
\rm -r TMP test.bak
else
echo "* $VTC[2]test Failure$VTC[1]"
endif
exit $stat

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_000925.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_000926.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_000927.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_000932.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001319.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001320.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001568.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001603.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001631.gbk.gz Executable file
View File

Binary file not shown.

BIN
detectors/cds/tools/chlorodb/test/test.db/download/NC_001666.gbk.gz Executable file
View File

Binary file not shown.

33
detectors/cds/tools/chlorodb/test/test.db/parameters.sh Normal file
View File

@ -0,0 +1,33 @@
# sourced file
#
# warning : these parameters are just for speeding up test
# (SIZMIN is way too high)
#
set CORE_NCDS_CUTOFF = 10
set CORE_START_ATG_CUTOFF = 5
set CORE_START_DFT_CUTOFF = 5
set CORE_START_OTH_CUTOFF = 5
set CORE_STOP_CUTOFF = 5
set CORE_SPLICE_CUTOFF = 5
set SHEL_NCDS_CUTOFF = 9
set CORE_DELTA = Inf
set CORE_COVMIN = 30
set CORE_PMAX = 1e-6
set CORE_IDMIN = 30
set CORE_SIZMIN = 11
set SHEL_DELTA = 0.5
set SHEL_COVMIN = 30
set SHEL_PMAX = 1e-6
set SHEL_IDMIN = 30
set SHEL_SIZMIN = 10
set DUST_DELTA = 0.5
set DUST_COVMIN = 30
set DUST_PMAX = 1e-6
set DUST_IDMIN = 30
set DUST_SIZMIN = 9

274
detectors/cds/tools/chlorodb/test/test.log Normal file
View File

@ -0,0 +1,274 @@
2015-11-13 18:01:14 [OA INFO ] uncompressing 10 entries
2015-11-13 18:01:14 [OA INFO ] convert 10 gbk/embl entries to fasta
2015-11-13 18:01:14 [OA INFO ] get gbk/embl info for 10 entries
2015-11-13 18:01:15 [OA INFO ] get gbk/embl cds for 10 entries
2015-11-13 18:01:15 [OA INFO ] get prots
2015-11-13 18:01:15 [OA INFO ] get gbk/embl introns for 10 entries
2015-11-13 18:01:16 [OA INFO ] Making models
2015-11-13 18:01:16 [OA FILE ] + loading info table
2015-11-13 18:01:16 [OA FILE ] + loading cds table
2015-11-13 18:01:16 [OA FILE ] + writing patterns for core : db.core.pat.txt
2015-11-13 18:01:16 [OA FILE ] + writing patterns for dust : db.dust.pat.txt
2015-11-13 18:01:16 [OA FILE ] + writing patterns for shell : db.shell.pat.txt
2015-11-13 18:01:16 [OA FILE ] + writing start model: models/start.default.frq
2015-11-13 18:01:16 [OA FILE ] + writing stop model: models/stop.default.frq
2015-11-13 18:01:16 [OA FILE ] + loading intron table
2015-11-13 18:01:16 [OA FILE ] + writing splice3 model: models/splice3.default.frq
2015-11-13 18:01:16 [OA FILE ] + writing splice5 model: models/splice5.default.frq
2015-11-13 18:01:16 [OA FILE ] + writing uniform splice model: models/splice.none.frq
2015-11-13 18:01:16 [OA FILE ] + saving db.data.Rdata
2015-11-13 18:01:16 [OA INFO ] Making core DB (take some time... please wait)
2015-11-13 18:01:16 [OA INFO ] cleanup db.prot.fst
2015-11-13 18:01:16 [OA INFO ] select by patterns
2015-11-13 18:01:17 [OA INFO ] pattern : rpl2 : 14
2015-11-13 18:01:17 [OA INFO ] pattern : rps7 : 14
2015-11-13 18:01:17 [OA INFO ] pattern : rpl23 : 12
2015-11-13 18:01:17 [OA INFO ] pattern : rps19 : 11
2015-11-13 18:01:17 [OA INFO ] pattern : rbcl : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rpl16 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rpl20 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rpl36 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps11 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps12 : 13
2015-11-13 18:01:17 [OA INFO ] pattern : rps14 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps18 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps2 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps3 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps4 : 10
2015-11-13 18:01:17 [OA INFO ] pattern : rps8 : 10
2015-11-13 18:01:17 [OA INFO ] output directory : db.core.pat.db
2015-11-13 18:01:17 [OA INFO ] Making shell DB (take some time... please wait)
2015-11-13 18:01:17 [OA INFO ] cleanup db.prot.fst
2015-11-13 18:01:17 [OA INFO ] select by patterns
2015-11-13 18:01:17 [OA INFO ] pattern : atpa : 9
2015-11-13 18:01:17 [OA INFO ] pattern : atpb : 9
2015-11-13 18:01:17 [OA INFO ] pattern : atpe : 9
2015-11-13 18:01:17 [OA INFO ] pattern : atpf : 9
2015-11-13 18:01:17 [OA INFO ] pattern : atph : 9
2015-11-13 18:01:17 [OA INFO ] pattern : atpi : 9
2015-11-13 18:01:17 [OA INFO ] pattern : ccsa : 9
2015-11-13 18:01:17 [OA INFO ] pattern : petb : 9
2015-11-13 18:01:17 [OA INFO ] pattern : petg : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psaa : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psab : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psac : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psba : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbb : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbc : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbd : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbe : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbf : 9
2015-11-13 18:01:17 [OA INFO ] pattern : psbh : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbi : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbj : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbk : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbl : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbn : 9
2015-11-13 18:01:18 [OA INFO ] pattern : psbt : 9
2015-11-13 18:01:18 [OA INFO ] pattern : rpl14 : 9
2015-11-13 18:01:18 [OA INFO ] pattern : rpl32 : 9
2015-11-13 18:01:18 [OA INFO ] pattern : rpob : 9
2015-11-13 18:01:18 [OA INFO ] pattern : rpoc1 : 9
2015-11-13 18:01:18 [OA INFO ] pattern : rpoc2 : 9
2015-11-13 18:01:18 [OA INFO ] pattern : ycf4 : 9
2015-11-13 18:01:18 [OA INFO ] pattern : cema : 8
2015-11-13 18:01:18 [OA INFO ] pattern : ndhb : 8
2015-11-13 18:01:18 [OA INFO ] pattern : peta : 8
2015-11-13 18:01:18 [OA INFO ] pattern : petd : 8
2015-11-13 18:01:18 [OA INFO ] pattern : psai : 8
2015-11-13 18:01:18 [OA INFO ] pattern : psaj : 8
2015-11-13 18:01:18 [OA INFO ] pattern : psbz : 8
2015-11-13 18:01:18 [OA INFO ] pattern : rpl22 : 8
2015-11-13 18:01:18 [OA INFO ] pattern : rpl33 : 8
2015-11-13 18:01:18 [OA INFO ] pattern : rpoa : 8
2015-11-13 18:01:18 [OA INFO ] pattern : clpp : 7
2015-11-13 18:01:18 [OA INFO ] pattern : rps15 : 7
2015-11-13 18:01:18 [OA INFO ] pattern : ycf3 : 7
2015-11-13 18:01:18 [OA INFO ] pattern : accd : 6
2015-11-13 18:01:18 [OA INFO ] pattern : infa : 6
2015-11-13 18:01:18 [OA INFO ] pattern : petl : 6
2015-11-13 18:01:18 [OA INFO ] pattern : petn : 6
2015-11-13 18:01:18 [OA INFO ] pattern : psbm : 6
2015-11-13 18:01:18 [OA INFO ] pattern : ycf12 : 6
2015-11-13 18:01:18 [OA INFO ] pattern : chlb : 5
2015-11-13 18:01:18 [OA INFO ] pattern : chll : 5
2015-11-13 18:01:18 [OA INFO ] pattern : matk : 5
2015-11-13 18:01:18 [OA INFO ] pattern : ndha : 5
2015-11-13 18:01:18 [OA INFO ] pattern : ndhc : 5
2015-11-13 18:01:18 [OA INFO ] pattern : ndhd : 5
2015-11-13 18:01:18 [OA INFO ] pattern : ndhe : 5
2015-11-13 18:01:18 [OA INFO ] pattern : ndhf : 5
2015-11-13 18:01:19 [OA INFO ] pattern : ndhg : 5
2015-11-13 18:01:19 [OA INFO ] pattern : ndhh : 5
2015-11-13 18:01:19 [OA INFO ] pattern : ndhi : 5
2015-11-13 18:01:19 [OA INFO ] pattern : ndhk : 5
2015-11-13 18:01:19 [OA INFO ] pattern : psam : 5
2015-11-13 18:01:19 [OA INFO ] pattern : rps16 : 5
2015-11-13 18:01:19 [OA INFO ] pattern : chli : 4
2015-11-13 18:01:19 [OA INFO ] pattern : chln : 4
2015-11-13 18:01:19 [OA INFO ] pattern : ndhj : 4
2015-11-13 18:01:19 [OA INFO ] pattern : rpl12 : 4
2015-11-13 18:01:19 [OA INFO ] pattern : rpl5 : 4
2015-11-13 18:01:19 [OA INFO ] pattern : rps9 : 4
2015-11-13 18:01:19 [OA INFO ] pattern : tufa : 4
2015-11-13 18:01:19 [OA INFO ] pattern : ycf2 : 5
2015-11-13 18:01:19 [OA INFO ] output directory : db.shell.pat.db
2015-11-13 18:01:19 [OA INFO ] Making dust DB (take some time... please wait)
2015-11-13 18:01:19 [OA INFO ] cleanup db.prot.fst
2015-11-13 18:01:19 [OA INFO ] select by patterns
2015-11-13 18:01:19 [OA INFO ] pattern : mind : 3
2015-11-13 18:01:19 [OA INFO ] pattern : rne : 3
2015-11-13 18:01:19 [OA INFO ] pattern : rpl19 : 3
2015-11-13 18:01:19 [OA INFO ] pattern : rpl21 : 3
2015-11-13 18:01:19 [OA INFO ] pattern : ycf1 : 3
2015-11-13 18:01:19 [OA INFO ] pattern : acpp : 2
2015-11-13 18:01:19 [OA INFO ] pattern : atpd : 2
2015-11-13 18:01:19 [OA INFO ] pattern : atpg : 2
2015-11-13 18:01:19 [OA INFO ] pattern : cbbx : 2
2015-11-13 18:01:19 [OA INFO ] pattern : ccs1 : 2
2015-11-13 18:01:19 [OA INFO ] pattern : clpc : 2
2015-11-13 18:01:19 [OA INFO ] pattern : cpeb : 2
2015-11-13 18:01:19 [OA INFO ] pattern : cyst : 2
2015-11-13 18:01:19 [OA INFO ] pattern : dnab : 2
2015-11-13 18:01:19 [OA INFO ] pattern : dnak : 2
2015-11-13 18:01:19 [OA INFO ] pattern : ftrb : 2
2015-11-13 18:01:19 [OA INFO ] pattern : ftsh : 2
2015-11-13 18:01:19 [OA INFO ] pattern : ftsw : 2
2015-11-13 18:01:19 [OA INFO ] pattern : groel : 2
2015-11-13 18:01:19 [OA INFO ] pattern : ilvb : 2
2015-11-13 18:01:20 [OA INFO ] pattern : ilvh : 2
2015-11-13 18:01:20 [OA INFO ] pattern : infb : 2
2015-11-13 18:01:20 [OA INFO ] pattern : orf27 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : pbsa : 2
2015-11-13 18:01:20 [OA INFO ] pattern : petf : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psad : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psae : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psaf : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psak : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psal : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psbv : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psbw : 2
2015-11-13 18:01:20 [OA INFO ] pattern : psbx : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rbcr : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rbcs : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl1 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl11 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl13 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl18 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl24 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl27 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl29 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl3 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl31 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl34 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl35 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl4 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rpl6 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps10 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps13 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps17 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps20 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps5 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : rps6 : 2
2015-11-13 18:01:20 [OA INFO ] pattern : seca : 2
2015-11-13 18:01:20 [OA INFO ] pattern : secy : 2
2015-11-13 18:01:20 [OA INFO ] pattern : tatc : 2
2015-11-13 18:01:20 [OA INFO ] pattern : tsf : 2
2015-11-13 18:01:20 [OA INFO ] pattern : ycf16 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf17 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf19 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf20 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf24 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf29 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf31 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf33 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf35 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf36 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf37 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf39 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf46 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf61 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf62 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : ycf65 : 2
2015-11-13 18:01:21 [OA INFO ] pattern : acca : 1
2015-11-13 18:01:21 [OA INFO ] pattern : accb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : apca : 1
2015-11-13 18:01:21 [OA INFO ] pattern : apcb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : apcd : 1
2015-11-13 18:01:21 [OA INFO ] pattern : apce : 1
2015-11-13 18:01:21 [OA INFO ] pattern : apcf : 1
2015-11-13 18:01:21 [OA INFO ] pattern : argb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cara : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cpca : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cpcb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cpcg : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cpea : 1
2015-11-13 18:01:21 [OA INFO ] pattern : cysa : 1
2015-11-13 18:01:21 [OA INFO ] pattern : fabh : 1
2015-11-13 18:01:21 [OA INFO ] pattern : ftsi : 1
2015-11-13 18:01:21 [OA INFO ] pattern : glnb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : gltb : 1
2015-11-13 18:01:21 [OA INFO ] pattern : hlp : 1
2015-11-13 18:01:21 [OA INFO ] pattern : infc : 1
2015-11-13 18:01:21 [OA INFO ] pattern : mbpx : 1
2015-11-13 18:01:21 [OA INFO ] pattern : mine : 1
2015-11-13 18:01:21 [OA INFO ] pattern : odpa : 1
2015-11-13 18:01:21 [OA INFO ] pattern : odpb : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf107 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf108 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf111 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf114 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf121 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf148 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf149 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf1738 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf174 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf198 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf199 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf203 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf238 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf240 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf263 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf287 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf320 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf327 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf382 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf450 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf58 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf62 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf621 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf635 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf71 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : orf75 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : petj : 1
2015-11-13 18:01:22 [OA INFO ] pattern : pgma : 1
2015-11-13 18:01:22 [OA INFO ] pattern : prea : 1
2015-11-13 18:01:22 [OA INFO ] pattern : psby : 1
2015-11-13 18:01:22 [OA INFO ] pattern : rpl28 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : rpl9 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : rps1 : 1
2015-11-13 18:01:22 [OA INFO ] pattern : syfb : 1
2015-11-13 18:01:22 [OA INFO ] pattern : syh : 1
2015-11-13 18:01:22 [OA INFO ] pattern : thig : 1
2015-11-13 18:01:22 [OA INFO ] pattern : trpa : 1
2015-11-13 18:01:22 [OA INFO ] pattern : trpg : 1
2015-11-13 18:01:22 [OA INFO ] pattern : trxa : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf13 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf18 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf21 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf22 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf23 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf26 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf28 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf32 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf34 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf38 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf47 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf59 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf6 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf7 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf81 : 1
2015-11-13 18:01:23 [OA INFO ] pattern : ycf9 : 1
2015-11-13 18:01:23 [OA INFO ] output directory : db.dust.pat.db
2015-11-13 18:01:23 [OA INFO ] recompressing 10 entries
2015-11-13 18:01:23 [OA INFO ] compressing 10 fasta entries

47
detectors/cds/tools/chlorodb/test/test.ref Normal file
View File

@ -0,0 +1,47 @@
TMP/core/rpl2.fst
TMP/core/rpl23.fst
TMP/core/rps12.fst
TMP/core/rps19.fst
TMP/core/rps7.fst
TMP/dust/atpa.fst
TMP/dust/atpb.fst
TMP/dust/atpe.fst
TMP/dust/atpf.fst
TMP/dust/atph.fst
TMP/dust/atpi.fst
TMP/dust/ccsa.fst
TMP/dust/petb.fst
TMP/dust/petg.fst
TMP/dust/psaa.fst
TMP/dust/psab.fst
TMP/dust/psac.fst
TMP/dust/psba.fst
TMP/dust/psbb.fst
TMP/dust/psbc.fst
TMP/dust/psbd.fst
TMP/dust/psbe.fst
TMP/dust/psbf.fst
TMP/dust/psbh.fst
TMP/dust/psbi.fst
TMP/dust/psbj.fst
TMP/dust/psbk.fst
TMP/dust/psbl.fst
TMP/dust/psbn.fst
TMP/dust/psbt.fst
TMP/dust/rpl14.fst
TMP/dust/rpl32.fst
TMP/dust/rpob.fst
TMP/dust/rpoc1.fst
TMP/dust/rpoc2.fst
TMP/dust/ycf4.fst
TMP/info/db.prot.fst
TMP/shell/rbcl.fst
TMP/shell/rpl16.fst
TMP/shell/rpl20.fst
TMP/shell/rpl36.fst
TMP/shell/rps11.fst
TMP/shell/rps14.fst
TMP/shell/rps2.fst
TMP/shell/rps3.fst
TMP/shell/rps4.fst
TMP/shell/rps8.fst

2
scripts/csh_init.sh
View File

@ -98,6 +98,8 @@ alias Cat 'awk -v D="`date '"'"'+%Y-%m-%d %H:%M:%S'"'"'`" '"'"'{print D " [OA FI
alias Notify 'Cout "INFO " \!:*'
alias Warning 'Cout "WARN " \!:*'
alias Error 'Cout ERROR \!:2-*; Exit \!:1'
alias Exit 'set Stat = \!:1; Debug "<--- $0 [$Stat]"; exit \!:1'