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Commit f73133dc authored by Alain Viari's avatar Alain Viari
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cds go_test bug fixed

parent 639cbbdc
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Showing with 231 additions and 37 deletions
detectors/cds/bin/do_exonerate.sh
View file @ f73133dc
......@@ -15,47 +15,66 @@
#
#========================================================================================
#
# usage: do_exonerate.sh dna.fasta prot.fasta [outdir]
# usage: do_exonerate.sh dna.fasta prot.fasta [model_dir [out_dir]]
#
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
set PARAMS_DIR = $LIB_DIR/../params
set MODELS_DIR = $LIB_DIR/../models
alias Override 'if (-e \!:2) set \!:1 = \!:2'
NeedArg 2
set GenoFile = $Argv[1]
set GenoFile = $Argv[1]; Shift
set GenoName = `basename $GenoFile:r`
set ProtFile = $Argv[2]
set ProtFile = $Argv[1]; Shift
set ProtDir = `dirname $ProtFile`
set ProtName = `basename $ProtFile:r`
set ProtType = `basename $ProtDir`
NeedFile $GenoFile
NeedFile $ProtFile
NeedFile $ProtDir/Annot.lst
set ModelsDir = $PROG_DIR/../models
if ($#Argv > 0) then
set ModelsDir = $Argv[1]; Shift
Notify " exonerate models : $ModelsDir"
else
Warning " using default exonerate models : $ModelsDir"
endif
NeedFile $ModelsDir/start.default.frq
NeedFile $ModelsDir/stop.default.frq
NeedFile $ModelsDir/splice3.default.frq
NeedFile $ModelsDir/splice5.default.frq
set OutDir = .
if ($#Argv >= 3) set OutDir = $3
if ($#Argv > 0) then
set OutDir = $Argv[1]; Shift
endif
if (! -d $OutDir) mkdir $OutDir
set ParamsDir = $PROG_DIR/../params
NeedFile $ParamsDir/default
#
# general parameters
#
source $PARAMS_DIR/default
source $ParamsDir/default
#
# family specific parameters
#
if (-e $PARAMS_DIR/$ProtName) then
source $PARAMS_DIR/$ProtName
if (-e $ParamsDir/$ProtName) then
Notify " override parameters with $ParamsDir/$ProtName"
source $ParamsDir/$ProtName
endif
#
......@@ -63,23 +82,23 @@ endif
#
if ($?STARTMODEL == 0) then
set STARTMODEL = $MODELS_DIR/start.default.frq
Override STARTMODEL $MODELS_DIR/start.$ProtName.frq
set STARTMODEL = $ModelsDir/start.default.frq
Override STARTMODEL $ModelsDir/start.$ProtName.frq
endif
if ($?STOPMODEL == 0) then
set STOPMODEL = $MODELS_DIR/stop.default.frq
Override STOPMODEL $MODELS_DIR/stop.$ProtName.frq
set STOPMODEL = $ModelsDir/stop.default.frq
Override STOPMODEL $ModelsDir/stop.$ProtName.frq
endif
if ($?SPLICE3MODEL == 0) then
set SPLICE3MODEL = $MODELS_DIR/splice3.default.frq
Override SPLICE3MODEL $MODELS_DIR/splice3.$ProtName.frq
set SPLICE3MODEL = $ModelsDir/splice3.default.frq
Override SPLICE3MODEL $ModelsDir/splice3.$ProtName.frq
endif
if ($?SPLICE5MODEL == 0) then
set SPLICE5MODEL = $MODELS_DIR/splice5.default.frq
Override SPLICE5MODEL $MODELS_DIR/splice5.$ProtName.frq
set SPLICE5MODEL = $ModelsDir/splice5.default.frq
Override SPLICE5MODEL $ModelsDir/splice5.$ProtName.frq
endif
#
......@@ -178,8 +197,10 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
# translate
#
echo "c pass pass1 $ProtType" > $base.iff
$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/translate.awk T_$$ > $base.iff
-f $LIB_DIR/translate.awk T_$$ >> $base.iff
#
# convert to embl
......
detectors/cds/bin/go_cds.sh
View file @ f73133dc
......@@ -13,7 +13,7 @@
# Results are printed to the standard output
#
#========================================================================================
# usage: go_cds.sh fasta [db_core]
# usage: go_cds.sh fasta [db_root]
#
unsetenv ORG_SOURCED
......@@ -28,13 +28,16 @@ NeedFile $Fasta
set Genome = `basename $Fasta:r`
set DbCore = $CDS_DATA_DIR/chlorodb/core
set DbRoot = $CDS_DATA_DIR/chlorodb
if ($#Argv > 0) then
set DbCore = $Argv[1]; Shift
set DbRoot = $Argv[1]; Shift
endif
NeedFile $DbCore/Annot.lst
NeedDir $DbRoot/core
NeedFile $DbRoot/core/Annot.lst
NeedDir $DbRoot/models
#
# run everything into temporary place
......@@ -50,15 +53,16 @@ endif
# pass1: run exonerate
#
set fams = `ls $DbCore/*.fst`
Notify "running pass1: exonerate of $Genome on $DbCore"
foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $temp
foreach dir ("core" "shell" "dust")
if (-d $DbRoot/$dir) then
set fams = `ls $DbRoot/$dir/*.fst`
Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
end
endif
end
#
# pass2: transsplicing
#
......
detectors/cds/lib/toEmbl.awk
View file @ f73133dc
......@@ -67,10 +67,20 @@ function QQualifier(qual, val) {
SQualifier(qual, "\"" val "\"")
}
function Unk(s) {
return (s =="" ? "none" : s)
}
#
# rules
#
/^c pass/ {
PassType = $3
PassInfo = $NF
next
}
/^c annot/ {
GeneName = $4
Product = $NF
......@@ -113,6 +123,9 @@ function QQualifier(qual, val) {
/^c end_entry/ {
GeneName = Unk(GeneName)
PassType = Unk(PassType)
gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
locus = ""
......@@ -127,6 +140,7 @@ function QQualifier(qual, val) {
QQualifier("locus_tag", locus)
QQualifier("product", Product)
QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("inference", "detect pass:" PassType ":" PassInfo)
QQualifier("translation", Translat)
if (Nexon > 1) {
......
detectors/cds/params/default
View file @ f73133dc
......@@ -2,9 +2,11 @@
# CDS Searching parameters
#
Notify " using default exonerate parameters"
#
# general parameters
# (may be overriden by enviroment variables)
# may be overriden by enviroment variables (AssignUndef)
#
AssignUndef TMP_CLEANUP 1
......@@ -30,11 +32,11 @@ AssignUndef PASS1_BESTN 10
AssignUndef PASS1_FRAMESHIFT -100
# pass1: exonerate use Blosum62 with larger penalty for Stops
AssignUndef PASS1_SUBMAT $MODELS_DIR/blosum62.mat
AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
# comment next lines to use default or specific splice model
# AssignUndef SPLICE3MODEL $MODELS_DIR/splice.none.frq
# AssignUndef SPLICE5MODEL $MODELS_DIR/splice.none.frq
# AssignUndef SPLICE3MODEL $ModelsDir/splice.none.frq
# AssignUndef SPLICE5MODEL $ModelsDir/splice.none.frq
#
# pass1: cluster selection parameters
......
detectors/cds/test/go_test.sh
View file @ f73133dc
#!/bin/csh -f
setenv Verbose 1
setenv Verbose 0
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
......@@ -20,7 +20,7 @@ set stat = $status
if ($stat == 0) then
echo "+ $VTC[3]CDS test Ok$VTC[1]"
\rm -r test.bak test.tmp test.db/*.fst.p??
\rm -r test.bak test.tmp test.db/core/*.fst.p??
else
echo "* $VTC[2]CDS test Failure$VTC[1]"
endif
......
detectors/cds/test/test.db/models/blosum62.mat 0 → 100644
View file @ f73133dc
#
# blosum62 substitution matrix
# with larger penalty for stops
#
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -50
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -50
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -50
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -50
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -50
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -50
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -50
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -50
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -50
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -50
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -50
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -50
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -50
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -50
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -50
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -50
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -50
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -50
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -50
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -50
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -50
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -50
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -50
* -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 1
detectors/cds/test/test.db/models/splice.none.frq 0 → 100644
View file @ f73133dc
# 3'/5' splice null model
# A C G T
25 25 25 25
splice
25 25 25 25
# end of 3'/5' splice null model
detectors/cds/test/test.db/models/splice3.default.frq 0 → 100644
View file @ f73133dc
# 3' splice model : default
# A C G T
19 18 27 36
36 5 34 25
20 7 51 23
29 13 14 44
splice
5 2 78 15
3 7 15 75
4 1 83 12
5 51 13 31
5 7 79 9
53 10 27 11
detectors/cds/test/test.db/models/splice3.ndha.frq 0 → 100644
View file @ f73133dc
# 3' splice model : ndha
# A C G T
1 43 1 56
0 57 0 42
41 1 2 56
57 42 0 1
splice
1 55 42 2
0 1 57 42
1 1 43 56
2 11 56 31
1 29 42 28
41 1 57 1
detectors/cds/test/test.db/models/splice3.psba.frq 0 → 100644
View file @ f73133dc
# 3' splice model : psba
# A C G T
26 14 40 21
13 44 35 9
41 3 33 23
1 13 5 81
splice
37 5 27 31
62 5 9 24
56 13 23 8
32 28 6 33
35 21 17 28
53 12 10 26
detectors/cds/test/test.db/models/splice5.default.frq 0 → 100644
View file @ f73133dc
# 5' splice model : default
# A C G T
15 42 3 40
15 46 6 33
13 32 2 53
45 17 21 16
70 13 6 11
21 39 8 32
splice
37 27 9 26
31 35 17 17
29 23 26 22
30 25 28 17
detectors/cds/test/test.db/models/splice5.ndha.frq 0 → 100644
View file @ f73133dc
# 5' splice model : ndha
# A C G T
0 54 2 44
43 1 1 56
57 1 7 35
8 1 39 52
56 2 40 2
55 1 0 44
splice
1 0 2 97
40 1 1 58
55 0 1 44
1 41 1 58
detectors/cds/test/test.db/models/splice5.psba.frq 0 → 100644
View file @ f73133dc
# 5' splice model : psba
# A C G T
38 15 9 37
40 5 13 42
41 15 6 37
32 9 15 44
22 8 10 60
0 9 83 8
splice
33 15 27 24
31 6 26 37
17 28 6 49
13 15 23 49
detectors/cds/test/test.db/models/start.default.frq 0 → 100644
View file @ f73133dc
# start model : default
atg 0.9692592 36165
acg 0.01173885 438
gtg 0.007504288 280
ata 0.003886149 145
atc 0.00337693 126
att 0.002840909 106
ttg 0.001393654 52
detectors/cds/test/test.db/models/start.ndhd.frq 0 → 100644
View file @ f73133dc
# start model : ndhd
acg 0.5066667 190
atg 0.3493333 131
atc 0.05066667 19
ata 0.03466667 13
acc 0.02933333 11
gtg 0.02933333 11
detectors/cds/test/test.db/models/start.rps19.frq 0 → 100644
View file @ f73133dc
# start model : rps19
gtg 0.6261023 355
atg 0.3738977 212
detectors/cds/test/test.db/models/stop.default.frq 0 → 100644
View file @ f73133dc
# stop model : default (freq. ignored)
taa 0.5742367 21968
tag 0.2351265 8995
tga 0.1906368 7293
detectors/cds/test/test.ref
View file @ f73133dc
......@@ -8,6 +8,7 @@ FT /gene="ccsA"
FT /locus_tag=""
FT /product="cytochrome c biogenesis protein"
FT /inference="similar to DNA sequence:AC_000188:LyesCp084"
FT /inference="detect pass:pass1:core"
FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI
FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP
FT SAILTQGFATSGILTEIHQSGILVPALQSEWLIMHVSMMILGYAALLCGSLLSVALLVI
......@@ -24,6 +25,7 @@ FT /gene="ndhA_1"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 1"
FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /inference="detect pass:pass1:core"
FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL
FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV
FT PDIFGINKGGKVFGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPI
......@@ -38,6 +40,7 @@ FT /gene="ndhA_2"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 1"
FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /inference="detect pass:pass1:core"
FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL
FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI
FT AVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGYGSNNKYSFLGGLR
......@@ -52,6 +55,7 @@ FT /gene="ndhB"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 2"
FT /inference="similar to DNA sequence:AC_000188:LyesCp066"
FT /inference="detect pass:pass1:core"
FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
FT LLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCS
......@@ -79,6 +83,7 @@ FT /gene="ndhD"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 4"
FT /inference="similar to DNA sequence:AC_000188:LyesCp081"
FT /inference="detect pass:pass1:core"
FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
FT WPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYLLLAMWGGKKRLYS
......@@ -98,6 +103,7 @@ FT /gene="ndhE"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 4L"
FT /inference="similar to DNA sequence:AC_000188:LyesCp080"
FT /inference="detect pass:pass1:core"
FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
FT gene complement(11509..13722)
......@@ -110,6 +116,7 @@ FT /gene="ndhF"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 5"
FT /inference="similar to DNA sequence:AC_000188:LyesCp073"
FT /inference="detect pass:pass1:core"
FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV
FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG
FT IMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIFWELVGLCSYLLIG
......@@ -133,6 +140,7 @@ FT /gene="ndhG"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 6"
FT /inference="similar to DNA sequence:AC_000188:LyesCp077"
FT /inference="detect pass:pass1:core"
FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC
FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC
FT ISLFISLITTISDTSWYGIIWTTRSNQIIEQDFLSNSQQIGIHLSTDFFLPFELISIIL
......@@ -147,6 +155,7 @@ FT /gene="ndhH"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit 7"
FT /inference="similar to DNA sequence:AC_000188:LyesCp078"
FT /inference="detect pass:pass1:core"
FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG
FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI
FT MLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATGMRMMHNYFRIGGV
......@@ -164,6 +173,7 @@ FT /gene="ndhI"
FT /locus_tag=""
FT /product="NADH dehydrogenase subunit I"
FT /inference="similar to DNA sequence:AC_000188:LyesCp076"
FT /inference="detect pass:pass1:core"
FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE
FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC
FT IFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVIDDYTIRTISNLPQ
......@@ -178,6 +188,7 @@ FT /gene="psaC"
FT /locus_tag=""
FT /product="photosystem I subunit VII"
FT /inference="similar to DNA sequence:AC_000188:LyesCp065"
FT /inference="detect pass:pass1:core"
FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
FT gene 53817..55307
......@@ -190,6 +201,7 @@ FT /gene="rpl2"
FT /locus_tag=""
FT /product="ribosomal protein L2"
FT /inference="similar to DNA sequence:AC_000188:LyesCp030"
FT /inference="detect pass:pass1:core"
FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
......@@ -213,6 +225,7 @@ FT /gene="rpl23"
FT /locus_tag=""
FT /product="ribosomal protein L23"
FT /inference="similar to DNA sequence:AC_000188:LyesCp026"
FT /inference="detect pass:pass1:core"
FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
FT gene 14505..14672
......@@ -225,6 +238,7 @@ FT /gene="rpl32"
FT /locus_tag=""
FT /product="ribosomal protein L32"
FT /inference="similar to DNA sequence:AC_000188:LyesCp036"
FT /inference="detect pass:pass1:core"
FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS
FT FFVRQTKINK"
FT gene complement(24633..24896)
......@@ -237,6 +251,7 @@ FT /gene="rps15"
FT /locus_tag=""
FT /product="ribosomal protein S15"
FT /inference="similar to DNA sequence:AC_000188:LyesCp029"
FT /inference="detect pass:pass1:core"
FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL
FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR"
FT gene 42157..42624
......@@ -249,6 +264,7 @@ FT /gene="rps7"
FT /locus_tag=""
FT /product="ribosomal protein S7"
FT /inference="similar to DNA sequence:AC_000188:LyesCp008"
FT /inference="detect pass:pass1:core"
FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"
......@@ -262,6 +278,7 @@ FT /gene="ycf1"
FT /locus_tag=""
FT /product="hypothetical chloroplast RF1"
FT /inference="similar to DNA sequence:AC_000188:LyesCp019"
FT /inference="detect pass:pass1:core"
FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL
FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW
FT NNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSMLARLVNIYLFRCNNK
......@@ -305,6 +322,7 @@ FT /gene="ycf2"
FT /locus_tag=""
FT /product="Ycf2"
FT /inference="similar to DNA sequence:AC_000188:LyesCp004"
FT /inference="detect pass:pass1:core"
FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH
FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY
FT LIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISESCFLNPKESTWVL
......
scripts/csh_init.sh
View file @ f73133dc
......@@ -178,4 +178,4 @@ end
# notification for debug
# --------------------------------------
Debug "---> $0"
Debug "---> $0 $argv"
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