cds go_test bug fixed
Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
This commit is contained in:
alain viari
@@ -1,6 +1,6 @@
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#!/bin/csh -f
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setenv Verbose 1
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setenv Verbose 0
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setenv ORG_HOME `dirname $0`/../../..
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source $ORG_HOME/scripts/csh_init.sh
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@@ -20,7 +20,7 @@ set stat = $status
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if ($stat == 0) then
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echo "+ $VTC[3]CDS test Ok$VTC[1]"
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\rm -r test.bak test.tmp test.db/*.fst.p??
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\rm -r test.bak test.tmp test.db/core/*.fst.p??
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else
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echo "* $VTC[2]CDS test Failure$VTC[1]"
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endif
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29
detectors/cds/test/test.db/models/blosum62.mat
Normal file
29
detectors/cds/test/test.db/models/blosum62.mat
Normal file
@@ -0,0 +1,29 @@
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#
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# blosum62 substitution matrix
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# with larger penalty for stops
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#
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A R N D C Q E G H I L K M F P S T W Y V B Z X *
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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* -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 1
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6
detectors/cds/test/test.db/models/splice.none.frq
Normal file
6
detectors/cds/test/test.db/models/splice.none.frq
Normal file
@@ -0,0 +1,6 @@
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# 3'/5' splice null model
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# A C G T
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25 25 25 25
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splice
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25 25 25 25
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# end of 3'/5' splice null model
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13
detectors/cds/test/test.db/models/splice3.default.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.default.frq
Normal file
@@ -0,0 +1,13 @@
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# 3' splice model : default
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# A C G T
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19 18 27 36
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36 5 34 25
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20 7 51 23
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29 13 14 44
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splice
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5 2 78 15
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3 7 15 75
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4 1 83 12
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5 51 13 31
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5 7 79 9
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53 10 27 11
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13
detectors/cds/test/test.db/models/splice3.ndha.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.ndha.frq
Normal file
@@ -0,0 +1,13 @@
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# 3' splice model : ndha
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# A C G T
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1 43 1 56
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0 57 0 42
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41 1 2 56
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57 42 0 1
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splice
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1 55 42 2
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0 1 57 42
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1 1 43 56
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2 11 56 31
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1 29 42 28
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41 1 57 1
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13
detectors/cds/test/test.db/models/splice3.psba.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.psba.frq
Normal file
@@ -0,0 +1,13 @@
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# 3' splice model : psba
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# A C G T
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26 14 40 21
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13 44 35 9
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41 3 33 23
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1 13 5 81
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splice
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37 5 27 31
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62 5 9 24
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56 13 23 8
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32 28 6 33
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35 21 17 28
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53 12 10 26
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13
detectors/cds/test/test.db/models/splice5.default.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.default.frq
Normal file
@@ -0,0 +1,13 @@
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# 5' splice model : default
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# A C G T
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15 42 3 40
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15 46 6 33
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13 32 2 53
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45 17 21 16
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70 13 6 11
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21 39 8 32
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splice
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37 27 9 26
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31 35 17 17
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29 23 26 22
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30 25 28 17
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13
detectors/cds/test/test.db/models/splice5.ndha.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.ndha.frq
Normal file
@@ -0,0 +1,13 @@
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# 5' splice model : ndha
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# A C G T
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0 54 2 44
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43 1 1 56
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57 1 7 35
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8 1 39 52
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56 2 40 2
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55 1 0 44
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splice
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1 0 2 97
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40 1 1 58
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55 0 1 44
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1 41 1 58
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13
detectors/cds/test/test.db/models/splice5.psba.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.psba.frq
Normal file
@@ -0,0 +1,13 @@
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# 5' splice model : psba
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# A C G T
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38 15 9 37
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40 5 13 42
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41 15 6 37
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32 9 15 44
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22 8 10 60
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0 9 83 8
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splice
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33 15 27 24
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31 6 26 37
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17 28 6 49
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13 15 23 49
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8
detectors/cds/test/test.db/models/start.default.frq
Normal file
8
detectors/cds/test/test.db/models/start.default.frq
Normal file
@@ -0,0 +1,8 @@
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# start model : default
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atg 0.9692592 36165
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acg 0.01173885 438
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gtg 0.007504288 280
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ata 0.003886149 145
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atc 0.00337693 126
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att 0.002840909 106
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ttg 0.001393654 52
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7
detectors/cds/test/test.db/models/start.ndhd.frq
Normal file
7
detectors/cds/test/test.db/models/start.ndhd.frq
Normal file
@@ -0,0 +1,7 @@
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# start model : ndhd
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acg 0.5066667 190
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atg 0.3493333 131
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atc 0.05066667 19
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ata 0.03466667 13
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acc 0.02933333 11
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gtg 0.02933333 11
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3
detectors/cds/test/test.db/models/start.rps19.frq
Normal file
3
detectors/cds/test/test.db/models/start.rps19.frq
Normal file
@@ -0,0 +1,3 @@
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# start model : rps19
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gtg 0.6261023 355
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atg 0.3738977 212
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4
detectors/cds/test/test.db/models/stop.default.frq
Normal file
4
detectors/cds/test/test.db/models/stop.default.frq
Normal file
@@ -0,0 +1,4 @@
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# stop model : default (freq. ignored)
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taa 0.5742367 21968
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tag 0.2351265 8995
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tga 0.1906368 7293
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@@ -8,6 +8,7 @@ FT /gene="ccsA"
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FT /locus_tag=""
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FT /product="cytochrome c biogenesis protein"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp084"
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FT /inference="detect pass:pass1:core"
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FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI
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FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP
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FT SAILTQGFATSGILTEIHQSGILVPALQSEWLIMHVSMMILGYAALLCGSLLSVALLVI
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@@ -24,6 +25,7 @@ FT /gene="ndhA_1"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 1"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
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FT /inference="detect pass:pass1:core"
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FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL
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FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV
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FT PDIFGINKGGKVFGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPI
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@@ -38,6 +40,7 @@ FT /gene="ndhA_2"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 1"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
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FT /inference="detect pass:pass1:core"
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FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL
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FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI
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FT AVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGYGSNNKYSFLGGLR
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@@ -52,6 +55,7 @@ FT /gene="ndhB"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 2"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp066"
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FT /inference="detect pass:pass1:core"
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FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
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FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
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FT LLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCS
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@@ -79,6 +83,7 @@ FT /gene="ndhD"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 4"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp081"
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FT /inference="detect pass:pass1:core"
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FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
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FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
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FT WPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYLLLAMWGGKKRLYS
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@@ -98,6 +103,7 @@ FT /gene="ndhE"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 4L"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp080"
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FT /inference="detect pass:pass1:core"
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FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
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FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
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FT gene complement(11509..13722)
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@@ -110,6 +116,7 @@ FT /gene="ndhF"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 5"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp073"
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FT /inference="detect pass:pass1:core"
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FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV
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FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG
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FT IMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIFWELVGLCSYLLIG
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@@ -133,6 +140,7 @@ FT /gene="ndhG"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 6"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp077"
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FT /inference="detect pass:pass1:core"
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FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC
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FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC
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FT ISLFISLITTISDTSWYGIIWTTRSNQIIEQDFLSNSQQIGIHLSTDFFLPFELISIIL
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@@ -147,6 +155,7 @@ FT /gene="ndhH"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit 7"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp078"
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FT /inference="detect pass:pass1:core"
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FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG
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FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI
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FT MLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATGMRMMHNYFRIGGV
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@@ -164,6 +173,7 @@ FT /gene="ndhI"
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FT /locus_tag=""
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FT /product="NADH dehydrogenase subunit I"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp076"
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FT /inference="detect pass:pass1:core"
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FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE
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FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC
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FT IFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVIDDYTIRTISNLPQ
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@@ -178,6 +188,7 @@ FT /gene="psaC"
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FT /locus_tag=""
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FT /product="photosystem I subunit VII"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp065"
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FT /inference="detect pass:pass1:core"
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FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
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FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
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FT gene 53817..55307
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@@ -190,6 +201,7 @@ FT /gene="rpl2"
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FT /locus_tag=""
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FT /product="ribosomal protein L2"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp030"
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FT /inference="detect pass:pass1:core"
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FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
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FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
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FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
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@@ -213,6 +225,7 @@ FT /gene="rpl23"
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FT /locus_tag=""
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FT /product="ribosomal protein L23"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp026"
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FT /inference="detect pass:pass1:core"
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FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
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FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
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FT gene 14505..14672
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@@ -225,6 +238,7 @@ FT /gene="rpl32"
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FT /locus_tag=""
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FT /product="ribosomal protein L32"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp036"
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FT /inference="detect pass:pass1:core"
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FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS
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FT FFVRQTKINK"
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FT gene complement(24633..24896)
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@@ -237,6 +251,7 @@ FT /gene="rps15"
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FT /locus_tag=""
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FT /product="ribosomal protein S15"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp029"
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FT /inference="detect pass:pass1:core"
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FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL
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FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR"
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FT gene 42157..42624
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@@ -249,6 +264,7 @@ FT /gene="rps7"
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FT /locus_tag=""
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FT /product="ribosomal protein S7"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp008"
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FT /inference="detect pass:pass1:core"
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FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
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FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
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FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"
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@@ -262,6 +278,7 @@ FT /gene="ycf1"
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FT /locus_tag=""
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FT /product="hypothetical chloroplast RF1"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp019"
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FT /inference="detect pass:pass1:core"
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FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL
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FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW
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FT NNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSMLARLVNIYLFRCNNK
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@@ -305,6 +322,7 @@ FT /gene="ycf2"
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FT /locus_tag=""
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FT /product="Ycf2"
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FT /inference="similar to DNA sequence:AC_000188:LyesCp004"
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FT /inference="detect pass:pass1:core"
|
||||
FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH
|
||||
FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY
|
||||
FT LIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISESCFLNPKESTWVL
|
||||
|
||||
Reference in New Issue
Block a user