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PRESCOTT
Commit eb8c519b by Mustafa Tekpinar
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Separated data from code by putting all data into data/ folder.

parent facba872
Showing with 301 additions and 9 deletions
computePred.R
......@@ -12,7 +12,7 @@ source(paste(Sys.getenv("ESGEMME_PATH"),"/pred.R",sep=""))
aa = c("a","c","d","e","f","g","h","i","k","l","m","n","p","q","r","s","t","v","w","y")
# BLOSUM62 matrix
blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/blosum62p.txt"),row.names=1))
blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
bg = apply(bgp,1,sum)
......
data/BLAT_jet.res 0 → 100644
AA pos chain axs cv pc tr freq trace clusters clusnumber ssjetormax
MET 1 A 1.0 0.1798 0.6606 0.0 0.0 0.0 0.0 0.0 0.0
SER 2 A 1.0 0.4007 0.3574 0.0 0.0 0.0 0.0 0.0 0.0
ILE 3 A 1.0 0.4642 0.638 0.0 0.0 0.0 0.0 0.0 0.0
GLN 4 A 1.0 0.5616 0.4343 0.0971 0.18 0.0174 0.0 0.0 0.0174
HIS 5 A 1.0 0.6781 0.5972 0.1113 0.06 0.0066 0.0 0.0 0.0066
PHE 6 A 1.0 0.645 1.0 0.0928 0.12 0.0111 0.0 0.0 0.0111
ARG 7 A 1.0 0.6488 0.5067 0.1249 0.34 0.0424 0.0 0.0 0.0424
VAL 8 A 1.0 0.7859 0.5656 0.1094 0.54 0.059 0.0 0.0 0.059
ALA 9 A 1.0 0.8354 0.3846 0.1142 0.52 0.0594 0.0 0.0 0.0594
LEU 10 A 1.0 0.7349 0.7058 0.1591 0.14 0.0222 0.0 0.0 0.0222
ILE 11 A 1.0 0.7358 0.638 0.1536 0.4 0.0614 0.0 0.0 0.0614
PRO 12 A 1.0 0.7525 0.466 0.1143 0.38 0.0434 0.0 0.0 0.0434
PHE 13 A 1.0 0.7142 1.0 0.1342 0.78 0.1047 0.0 0.0 0.1047
PHE 14 A 1.0 0.686 1.0 0.1743 0.3 0.0522 0.0 0.0 0.0522
ALA 15 A 1.0 0.8723 0.3846 0.21 0.7 0.147 0.0 0.0 0.147
ALA 16 A 1.0 0.8165 0.3846 0.3606 0.34 0.1226 0.0 0.0 0.1226
PHE 17 A 1.0 0.7198 1.0 0.2187 0.76 0.1662 0.0 0.0 0.1662
CYS 18 A 1.0 0.7581 0.6425 0.2452 0.7 0.1716 0.0 0.0 0.1716
LEU 19 A 1.0 0.7318 0.7058 0.2104 0.94 0.1978 0.0 0.0 0.1978
PRO 20 A 1.0 0.6357 0.466 0.2601 0.74 0.1925 0.0 0.0 0.1925
VAL 21 A 1.0 0.6017 0.5656 0.2712 0.54 0.1464 0.0 0.0 0.1464
PHE 22 A 1.0 0.491 1.0 0.2798 0.52 0.1455 0.0 0.0 0.1455
ALA 23 A 1.0 0.4599 0.3846 0.3037 0.92 0.2794 0.0 0.0 0.2794
HIS 24 A 1.0 0.4471 0.5972 0.2954 0.68 0.2009 0.0 0.0 0.2009
PRO 25 A 1.0 0.4918 0.466 0.2696 0.9 0.2426 0.0 0.0 0.2426
GLU 26 A 1.0 0.4252 0.3348 0.3842 0.66 0.2536 0.0 0.0 0.38
THR 27 A 1.0 0.5993 0.3257 0.5596 1.0 0.5596 0.0 0.0 0.5794
LEU 28 A 1.0 0.5513 0.7058 0.3062 0.86 0.2633 0.0 0.0 0.6285
VAL 29 A 1.0 0.443 0.5656 0.2447 0.82 0.2006 0.0 0.0 0.5043
LYS 30 A 1.0 0.5102 0.2488 0.3921 0.9 0.3528 0.0 0.0 0.4315
VAL 31 A 0.5 0.6384 0.5656 0.6009 0.98 0.5889 0.0 0.0 0.6136
LYS 32 A 1.0 0.4541 0.2488 0.4482 0.88 0.3944 0.0 0.0 0.4242
ASP 33 A 1.0 0.4253 0.3212 0.4874 0.72 0.3509 0.0 0.0 0.3881
ALA 34 A 0.8 0.5623 0.3846 0.6821 1.0 0.6821 0.0 0.0 0.6222
GLU 35 A 1.0 0.4961 0.3348 0.7952 1.0 0.7952 0.0 0.0 0.6457
ASP 36 A 1.0 0.3478 0.3212 0.3964 0.82 0.325 0.0 0.0 0.3364
GLN 37 A 1.0 0.357 0.4343 0.3527 0.92 0.3244 0.0 0.0 0.3956
LEU 38 A 0.8 0.5159 0.7058 0.5341 1.0 0.5341 0.0 0.0 0.62
GLY 39 A 1.0 0.3705 0.4117 0.6772 0.94 0.6365 0.0 0.0 0.5241
ALA 40 A 1.0 0.489 0.3846 0.8016 1.0 0.8016 0.0 0.0 0.6453
ARG 41 A 1.0 0.5109 0.5067 0.7641 1.0 0.7641 0.0 0.0 0.6375
VAL 42 A 0.8 0.6763 0.5656 0.7475 1.0 0.7475 0.0 0.0 0.7119
GLY 43 A 0.5 0.7337 0.4117 0.8915 1.0 0.8915 0.0 0.0 0.8126
TYR 44 A 0.5 0.7363 0.7963 0.7625 1.0 0.7625 0.0 0.0 0.7794
ILE 45 A 0.8 0.7024 0.638 0.557 0.98 0.5459 0.0 0.0 0.6702
GLU 46 A 1.0 0.6608 0.3348 0.6645 1.0 0.6645 0.0 0.0 0.6626
LEU 47 A 0.8 0.6131 0.7058 0.5707 1.0 0.5707 0.0 0.0 0.6594
ASP 48 A 1.0 0.4773 0.3212 0.6963 1.0 0.6963 0.0 0.0 0.5868
LEU 49 A 1.0 0.5763 0.7058 0.6209 1.0 0.6209 0.0 0.0 0.6634
ASN 50 A 1.0 0.3649 0.3936 0.4828 0.96 0.4635 0.0 0.0 0.4286
SER 51 A 1.0 0.3455 0.3574 0.4897 0.96 0.4702 0.0 0.0 0.4138
GLY 52 A 1.0 0.4463 0.4117 0.7399 0.98 0.7251 0.0 0.0 0.5857
LYS 53 A 1.0 0.3604 0.2488 0.3841 0.94 0.3611 0.0 0.0 0.3608
ILE 54 A 1.0 0.4851 0.638 0.3776 0.92 0.3473 0.0 0.0 0.5616
LEU 55 A 1.0 0.4936 0.7058 0.4812 0.98 0.4716 0.0 0.0 0.5997
GLU 56 A 1.0 0.558 0.3348 0.2356 0.54 0.1272 0.0 0.0 0.4464
SER 57 A 1.0 0.5527 0.3574 0.4512 0.86 0.388 0.0 0.0 0.4704
PHE 58 A 1.0 0.5465 1.0 0.4883 1.0 0.4883 0.0 0.0 0.7732
ARG 59 A 1.0 0.4849 0.5067 0.7882 1.0 0.7882 0.0 0.0 0.6475
PRO 60 A 1.0 0.5275 0.466 0.5851 0.98 0.5734 0.0 0.0 0.5504
GLU 61 A 1.0 0.4332 0.3348 0.5789 0.96 0.5557 0.0 0.0 0.4944
GLU 62 A 1.0 0.4866 0.3348 0.772 1.0 0.772 0.0 0.0 0.6293
ARG 63 A 1.0 0.5151 0.5067 0.7803 1.0 0.7803 0.0 0.0 0.6477
PHE 64 A 0.8 0.699 1.0 0.8392 1.0 0.8392 0.0 0.0 0.9196
PRO 65 A 0.8 0.7157 0.466 0.7796 1.0 0.7796 0.0 0.0 0.7476
MET 66 A 0.8 0.8332 0.6606 0.7335 1.0 0.7335 0.0 0.0 0.7834
MET 67 A 0.8 0.8131 0.6606 0.7926 1.0 0.7926 0.0 0.0 0.8029
SER 68 A 1.0 0.8463 0.3574 0.9572 1.0 0.9572 0.6355 1.0 0.9018
THR 69 A 0.5 0.9843 0.3257 0.8622 1.0 0.8622 0.0 0.0 0.9232
PHE 70 A 0.8 0.8894 1.0 0.7921 1.0 0.7921 0.0 0.0 0.9447
LYS 71 A 0.5 0.8959 0.2488 0.9589 1.0 0.9589 0.0 0.0 0.9274
VAL 72 A 0.5 0.9561 0.5656 0.6351 1.0 0.6351 0.0 0.0 0.7956
LEU 73 A 0.8 0.8761 0.7058 0.7186 1.0 0.7186 0.0 0.0 0.7974
LEU 74 A 0.5 0.858 0.7058 0.7184 1.0 0.7184 0.0 0.0 0.7882
CYS 75 A 0.5 0.8582 0.6425 0.7897 1.0 0.7897 0.0 0.0 0.824
GLY 76 A 0.5 0.7779 0.4117 0.6851 1.0 0.6851 0.0 0.0 0.7315
ALA 77 A 0.8 0.6935 0.3846 0.693 1.0 0.693 0.0 0.0 0.6932
VAL 78 A 0.5 0.7046 0.5656 0.6326 1.0 0.6326 0.0 0.0 0.6686
LEU 79 A 0.8 0.6453 0.7058 0.9168 1.0 0.9168 0.0 0.0 0.8113
SER 80 A 1.0 0.5395 0.3574 0.5117 0.98 0.5015 0.0 0.0 0.5205
ARG 81 A 1.0 0.4735 0.5067 0.6856 1.0 0.6856 0.0 0.0 0.5962
VAL 82 A 1.0 0.4813 0.5656 0.7089 1.0 0.7089 0.0 0.0 0.6372
ASP 83 A 1.0 0.4098 0.3212 0.8243 1.0 0.8243 0.0 0.0 0.617
ALA 84 A 1.0 0.3341 0.3846 0.371 1.0 0.371 0.0 0.0 0.3778
GLY 85 A 1.0 0.2913 0.4117 0.833 1.0 0.833 0.0 0.0 0.6224
GLN 86 A 1.0 0.3254 0.4343 0.3336 0.96 0.3202 0.0 0.0 0.3798
GLU 87 A 0.8 0.4682 0.3348 0.7056 1.0 0.7056 0.0 0.0 0.5869
GLN 88 A 1.0 0.3582 0.4343 0.4124 1.0 0.4124 0.0 0.0 0.4234
LEU 89 A 1.0 0.5127 0.7058 0.8865 1.0 0.8865 0.0 0.0 0.7961
GLY 90 A 1.0 0.3832 0.4117 0.5267 0.9 0.4741 0.0 0.0 0.4429
ARG 91 A 1.0 0.416 0.5067 0.6849 1.0 0.6849 0.0 0.0 0.5958
ARG 92 A 1.0 0.3542 0.5067 0.6188 1.0 0.6188 0.0 0.0 0.5628
ILE 93 A 1.0 0.5106 0.638 0.5855 0.98 0.5738 0.0 0.0 0.6059
HIS 94 A 1.0 0.3345 0.5972 0.3589 0.8 0.2871 0.0 0.0 0.4658
TYR 95 A 1.0 0.4788 0.7963 0.5885 1.0 0.5885 0.0 0.0 0.6924
SER 96 A 1.0 0.3264 0.3574 0.3839 1.0 0.3839 0.0 0.0 0.3707
GLN 97 A 1.0 0.2683 0.4343 0.3573 0.92 0.3287 0.0 0.0 0.3815
ASN 98 A 1.0 0.2567 0.3936 0.3483 0.94 0.3274 0.0 0.0 0.3605
ASP 99 A 1.0 0.4286 0.3212 0.7201 1.0 0.7201 0.0 0.0 0.5743
LEU 100 A 1.0 0.4296 0.7058 0.7247 1.0 0.7247 0.6192 1.0 0.7152
VAL 101 A 1.0 0.5086 0.5656 0.6393 1.0 0.6393 0.0 0.0 0.6024
GLU 102 A 1.0 0.4648 0.3348 0.413 0.86 0.3552 0.0 0.0 0.41
TYR 103 A 1.0 0.5424 0.7963 0.6543 1.0 0.6543 0.6695 1.0 0.7253
SER 104 A 1.0 0.5235 0.3574 0.7693 1.0 0.7693 0.564 1.0 0.6464
PRO 105 A 1.0 0.4902 0.466 0.8633 1.0 0.8633 0.6236 1.0 0.6768
VAL 106 A 1.0 0.5153 0.5656 0.6077 1.0 0.6077 0.0 0.0 0.5866
THR 107 A 0.5 0.5797 0.3257 0.7372 1.0 0.7372 0.0 0.0 0.6584
GLU 108 A 1.0 0.3832 0.3348 0.5514 1.0 0.5514 0.0 0.0 0.4673
LYS 109 A 1.0 0.33 0.2488 0.472 1.0 0.472 0.0 0.0 0.401
HIS 110 A 1.0 0.4044 0.5972 0.597 1.0 0.597 0.0 0.0 0.5971
LEU 111 A 1.0 0.3431 0.7058 0.5623 1.0 0.5623 0.0 0.0 0.634
THR 112 A 1.0 0.2267 0.3257 0.6024 1.0 0.6024 0.0 0.0 0.464
ASP 113 A 1.0 0.296 0.3212 0.4415 1.0 0.4415 0.0 0.0 0.3813
GLY 114 A 0.8 0.4171 0.4117 0.7344 1.0 0.7344 0.0 0.0 0.5758
MET 115 A 0.8 0.5403 0.6606 0.668 1.0 0.668 0.0 0.0 0.6643
THR 116 A 1.0 0.4768 0.3257 0.6601 1.0 0.6601 0.0 0.0 0.5684
VAL 117 A 0.5 0.6126 0.5656 0.5921 1.0 0.5921 0.0 0.0 0.6023
ARG 118 A 1.0 0.4881 0.5067 0.4469 1.0 0.4469 0.0 0.0 0.4974
GLU 119 A 1.0 0.5229 0.3348 0.6054 1.0 0.6054 0.0 0.0 0.5642
LEU 120 A 0.5 0.7037 0.7058 0.8074 1.0 0.8074 0.0 0.0 0.7566
CYS 121 A 0.5 0.7749 0.6425 0.8041 1.0 0.8041 0.0 0.0 0.7895
SER 122 A 1.0 0.6332 0.3574 0.5345 0.98 0.5238 0.0 0.0 0.5785
ALA 123 A 0.8 0.6798 0.3846 0.8645 1.0 0.8645 0.0 0.0 0.7722
ALA 124 A 0.5 0.8333 0.3846 0.7104 1.0 0.7104 0.0 0.0 0.7718
ILE 125 A 0.5 0.815 0.638 0.6368 1.0 0.6368 0.0 0.0 0.7265
THR 126 A 1.0 0.6349 0.3257 0.667 1.0 0.667 0.0 0.0 0.651
MET 127 A 1.0 0.5665 0.6606 0.5067 0.98 0.4966 0.0 0.0 0.6136
SER 128 A 1.0 0.7294 0.3574 0.9486 1.0 0.9486 0.6312 1.0 0.839
ASP 129 A 0.5 0.694 0.3212 0.9405 1.0 0.9405 0.0 0.0 0.8172
ASN 130 A 1.0 0.674 0.3936 0.8905 1.0 0.8905 0.6312 1.0 0.7822
THR 131 A 0.8 0.6281 0.3257 0.6701 1.0 0.6701 0.0 0.0 0.6491
ALA 132 A 0.5 0.7599 0.3846 0.902 1.0 0.902 0.0 0.0 0.831
ALA 133 A 0.5 0.8236 0.3846 0.7275 1.0 0.7275 0.0 0.0 0.7756
ASN 134 A 1.0 0.6487 0.3936 0.9255 1.0 0.9255 0.6217 1.0 0.7871
LEU 135 A 1.0 0.6292 0.7058 0.7598 1.0 0.7598 0.0 0.0 0.7328
LEU 136 A 0.5 0.7834 0.7058 0.8068 1.0 0.8068 0.0 0.0 0.7951
LEU 137 A 0.5 0.6911 0.7058 0.7842 1.0 0.7842 0.0 0.0 0.745
THR 138 A 1.0 0.505 0.3257 0.4486 0.88 0.3948 0.0 0.0 0.4499
THR 139 A 1.0 0.5607 0.3257 0.5776 0.92 0.5313 0.0 0.0 0.546
ILE 140 A 1.0 0.593 0.638 0.58 0.98 0.5684 0.0 0.0 0.6155
GLY 141 A 1.0 0.4358 0.4117 0.9101 1.0 0.9101 0.0 0.0 0.673
GLY 142 A 0.8 0.5189 0.4117 0.92 1.0 0.92 0.0 0.0 0.7194
PRO 143 A 1.0 0.5518 0.466 0.8312 1.0 0.8312 0.0 0.0 0.6915
LYS 144 A 1.0 0.354 0.2488 0.4453 0.94 0.4186 0.0 0.0 0.3863
GLU 145 A 1.0 0.4377 0.3348 0.5495 1.0 0.5495 0.0 0.0 0.4936
LEU 146 A 0.8 0.6906 0.7058 0.6933 1.0 0.6933 0.0 0.0 0.6996
THR 147 A 1.0 0.52 0.3257 0.788 1.0 0.788 0.0 0.0 0.654
ALA 148 A 1.0 0.4216 0.3846 0.5145 1.0 0.5145 0.0 0.0 0.468
PHE 149 A 1.0 0.5765 1.0 0.7179 1.0 0.7179 0.0 0.0 0.859
LEU 150 A 0.5 0.636 0.7058 0.6156 1.0 0.6156 0.0 0.0 0.6709
HIS 151 A 1.0 0.3909 0.5972 0.7796 1.0 0.7796 0.0 0.0 0.6884
ASN 152 A 1.0 0.3704 0.3936 0.4439 0.96 0.4262 0.0 0.0 0.4099
MET 153 A 1.0 0.522 0.6606 0.562 0.96 0.5395 0.0 0.0 0.6
GLY 154 A 1.0 0.4098 0.4117 0.901 1.0 0.901 0.0 0.0 0.6564
ASP 155 A 0.8 0.5428 0.3212 0.8998 1.0 0.8998 0.0 0.0 0.7213
HIS 156 A 1.0 0.3581 0.5972 0.3194 0.98 0.3131 0.0 0.0 0.4776
VAL 157 A 1.0 0.4988 0.5656 0.4669 0.98 0.4576 0.0 0.0 0.5322
THR 158 A 0.8 0.6713 0.3257 0.7055 1.0 0.7055 0.0 0.0 0.7055
ARG 159 A 1.0 0.5047 0.5067 0.8208 1.0 0.8208 0.0 0.0 0.8208
LEU 160 A 0.8 0.6849 0.7058 0.7638 1.0 0.7638 0.0 0.0 0.7638
ASP 161 A 1.0 0.5004 0.3212 0.8324 1.0 0.8324 0.0 0.0 0.8324
ARG 162 A 1.0 0.4994 0.5067 0.8001 1.0 0.8001 0.0 0.0 0.8001
TRP 163 A 1.0 0.5305 0.9909 0.4471 0.96 0.4292 0.6565 1.0 0.4292
GLU 164 A 0.8 0.675 0.3348 0.8706 1.0 0.8706 0.0 0.0 0.7728
PRO 165 A 1.0 0.5174 0.466 0.681 1.0 0.681 0.0 0.0 0.5992
GLU 166 A 1.0 0.4656 0.3348 0.472 0.9 0.4248 0.0 0.0 0.4452
LEU 167 A 0.8 0.6894 0.7058 0.8229 1.0 0.8229 0.0 0.0 0.7644
ASN 168 A 1.0 0.6465 0.3936 0.8211 1.0 0.8211 0.5738 1.0 0.7338
GLU 169 A 1.0 0.4575 0.3348 0.5883 1.0 0.5883 0.0 0.0 0.5229
ALA 170 A 1.0 0.5691 0.3846 0.674 1.0 0.674 0.0 0.0 0.6216
ILE 171 A 1.0 0.3772 0.638 0.3896 0.98 0.3818 0.0 0.0 0.5099
PRO 172 A 1.0 0.3669 0.466 0.7768 1.0 0.7768 0.0 0.0 0.6214
ASN 173 A 1.0 0.336 0.3936 0.6994 1.0 0.6994 0.0 0.0 0.5465
ASP 174 A 1.0 0.4217 0.3212 0.8039 1.0 0.8039 0.0 0.0 0.6128
GLU 175 A 1.0 0.4207 0.3348 0.579 0.96 0.5559 0.0 0.0 0.4883
ARG 176 A 1.0 0.423 0.5067 0.7876 1.0 0.7876 0.0 0.0 0.6472
ASP 177 A 0.8 0.6535 0.3212 0.918 1.0 0.918 0.0 0.0 0.7857
THR 178 A 1.0 0.6457 0.3257 0.8561 1.0 0.8561 0.0 0.0 0.7509
THR 179 A 0.5 0.7536 0.3257 0.8062 1.0 0.8062 0.0 0.0 0.7799
MET 180 A 1.0 0.5708 0.6606 0.7298 1.0 0.7298 0.0 0.0 0.6952
PRO 181 A 0.5 0.723 0.466 0.8848 1.0 0.8848 0.0 0.0 0.8039
ALA 182 A 1.0 0.598 0.3846 0.4338 0.96 0.4164 0.0 0.0 0.5072
ALA 183 A 1.0 0.6268 0.3846 0.809 1.0 0.809 0.0 0.0 0.7179
MET 184 A 0.5 0.8376 0.6606 0.7792 1.0 0.7792 0.0 0.0 0.8084
ALA 185 A 0.5 0.7466 0.3846 0.5576 1.0 0.5576 0.0 0.0 0.6521
THR 186 A 1.0 0.584 0.3257 0.4016 0.84 0.3373 0.0 0.0 0.4606
THR 187 A 0.8 0.7083 0.3257 0.735 1.0 0.735 0.0 0.0 0.7216
LEU 188 A 0.5 0.846 0.7058 0.8024 1.0 0.8024 0.0 0.0 0.8242
ARG 189 A 1.0 0.5527 0.5067 0.4245 0.96 0.4075 0.0 0.0 0.5297
LYS 190 A 1.0 0.5328 0.2488 0.392 1.0 0.392 0.0 0.0 0.4624
LEU 191 A 0.5 0.7328 0.7058 0.7264 1.0 0.7264 0.0 0.0 0.7296
LEU 192 A 0.8 0.7139 0.7058 0.629 1.0 0.629 0.0 0.0 0.7098
THR 193 A 1.0 0.5278 0.3257 0.5915 1.0 0.5915 0.0 0.0 0.5596
GLY 194 A 1.0 0.478 0.4117 0.8133 1.0 0.8133 0.0 0.0 0.6457
GLU 195 A 1.0 0.3446 0.3348 0.4892 0.9 0.4403 0.0 0.0 0.3924
LEU 196 A 1.0 0.5054 0.7058 0.4992 0.92 0.4593 0.0 0.0 0.6056
LEU 197 A 0.8 0.5703 0.7058 0.9434 1.0 0.9434 0.0 0.0 0.8246
THR 198 A 1.0 0.3877 0.3257 0.5824 1.0 0.5824 0.0 0.0 0.485
LEU 199 A 1.0 0.3445 0.7058 0.3969 0.8 0.3175 0.0 0.0 0.5252
ALA 200 A 1.0 0.386 0.3846 0.4251 0.98 0.4166 0.0 0.0 0.4013
SER 201 A 0.8 0.5245 0.3574 0.8076 1.0 0.8076 0.0 0.0 0.666
ARG 202 A 1.0 0.4966 0.5067 0.7406 1.0 0.7406 0.0 0.0 0.6236
GLN 203 A 1.0 0.4657 0.4343 0.3721 0.8 0.2977 0.0 0.0 0.45
GLN 204 A 1.0 0.5485 0.4343 0.5601 1.0 0.5601 0.0 0.0 0.5543
LEU 205 A 0.5 0.7577 0.7058 0.8828 1.0 0.8828 0.0 0.0 0.8202
ILE 206 A 1.0 0.6366 0.638 0.4625 0.92 0.4255 0.0 0.0 0.6373
ASP 207 A 1.0 0.5326 0.3212 0.4118 0.94 0.3871 0.0 0.0 0.4598
TRP 208 A 0.8 0.6672 0.9909 0.8299 1.0 0.8299 0.0 0.0 0.9104
MET 209 A 0.5 0.7957 0.6606 0.7864 1.0 0.7864 0.0 0.0 0.791
GLU 210 A 1.0 0.5437 0.3348 0.3948 1.0 0.3948 0.0 0.0 0.4692
ALA 211 A 1.0 0.5428 0.3846 0.5405 0.96 0.5189 0.0 0.0 0.5308
ASP 212 A 1.0 0.6481 0.3212 0.6863 1.0 0.6863 0.0 0.0 0.6672
LYS 213 A 1.0 0.474 0.2488 0.4409 0.96 0.4233 0.0 0.0 0.4486
VAL 214 A 1.0 0.6057 0.5656 0.8586 1.0 0.8586 0.6338 1.0 0.7322
ALA 215 A 0.5 0.6521 0.3846 0.848 1.0 0.848 0.0 0.0 0.75
GLY 216 A 1.0 0.5019 0.4117 0.556 1.0 0.556 0.0 0.0 0.529
PRO 217 A 1.0 0.4821 0.466 0.4396 1.0 0.4396 0.0 0.0 0.474
LEU 218 A 0.5 0.6631 0.7058 0.7855 1.0 0.7855 0.0 0.0 0.7456
LEU 219 A 0.8 0.7409 0.7058 0.7473 1.0 0.7473 0.0 0.0 0.7441
ARG 220 A 1.0 0.5678 0.5067 0.8248 1.0 0.8248 0.0 0.0 0.6963
SER 221 A 1.0 0.4591 0.3574 0.7973 1.0 0.7973 0.0 0.0 0.6282
ALA 222 A 1.0 0.4909 0.3846 0.7543 1.0 0.7543 0.0 0.0 0.6226
LEU 223 A 1.0 0.5015 0.7058 0.7806 0.98 0.765 0.0 0.0 0.7354
PRO 224 A 1.0 0.3538 0.466 0.8972 1.0 0.8972 0.0 0.0 0.6816
ALA 225 A 1.0 0.2464 0.3846 0.3912 0.88 0.3442 0.0 0.0 0.3644
GLY 226 A 1.0 0.2821 0.4117 0.5641 1.0 0.5641 0.0 0.0 0.4879
TRP 227 A 1.0 0.4327 0.9909 0.8583 1.0 0.8583 0.0 0.0 0.9246
PHE 228 A 1.0 0.5177 1.0 0.4604 0.96 0.442 0.0 0.0 0.7588
ILE 229 A 1.0 0.628 0.638 0.7273 1.0 0.7273 0.0 0.0 0.6826
ALA 230 A 0.5 0.7157 0.3846 0.7834 1.0 0.7834 0.0 0.0 0.7495
ASP 231 A 0.5 0.78 0.3212 0.8777 1.0 0.8777 0.0 0.0 0.8288
LYS 232 A 0.5 0.8575 0.2488 0.8946 1.0 0.8946 0.0 0.0 0.876
SER 233 A 0.8 0.793 0.3574 0.8829 1.0 0.8829 0.0 0.0 0.838
GLY 234 A 0.8 0.8195 0.4117 0.9476 1.0 0.9476 0.0 0.0 0.8836
ALA 235 A 1.0 0.6882 0.3846 0.6626 1.0 0.6626 0.0 0.0 0.6754
GLY 236 A 1.0 0.6274 0.4117 0.7509 1.0 0.7509 0.5643 1.0 0.6891
GLU 237 A 1.0 0.482 0.3348 0.4952 0.94 0.4654 0.0 0.0 0.4737
ARG 238 A 1.0 0.4196 0.5067 0.585 1.0 0.585 0.0 0.0 0.5458
GLY 239 A 1.0 0.5384 0.4117 0.7475 1.0 0.7475 0.0 0.0 0.643
SER 240 A 0.8 0.6602 0.3574 0.6542 1.0 0.6542 0.0 0.0 0.6572
ARG 241 A 1.0 0.7045 0.5067 0.5641 1.0 0.5641 0.0 0.0 0.6343
GLY 242 A 0.5 0.8695 0.4117 0.8193 1.0 0.8193 0.0 0.0 0.8444
ILE 243 A 0.5 0.8867 0.638 0.8821 1.0 0.8821 0.0 0.0 0.8844
ILE 244 A 0.5 1.0 0.638 0.6077 1.0 0.6077 0.0 0.0 0.819
ALA 245 A 0.5 0.8736 0.3846 0.832 1.0 0.832 0.0 0.0 0.8528
ALA 246 A 0.5 0.7637 0.3846 0.5933 1.0 0.5933 0.0 0.0 0.6785
LEU 247 A 0.8 0.6955 0.7058 0.522 0.98 0.5116 0.0 0.0 0.7006
GLY 248 A 0.5 0.5269 0.4117 0.7481 1.0 0.7481 0.0 0.0 0.6375
PRO 249 A 1.0 0.3818 0.466 0.8488 1.0 0.8488 0.0 0.0 0.6574
ASP 250 A 1.0 0.2685 0.3212 0.7141 0.98 0.6998 0.0 0.0 0.5105
GLY 251 A 1.0 0.3519 0.4117 0.7147 0.96 0.6861 0.0 0.0 0.5489
LYS 252 A 1.0 0.3777 0.2488 0.557 0.96 0.5347 0.0 0.0 0.4562
PRO 253 A 1.0 0.5517 0.466 0.4431 0.94 0.4165 0.0 0.0 0.5088
SER 254 A 1.0 0.5022 0.3574 0.7783 1.0 0.7783 0.0 0.0 0.6402
ARG 255 A 1.0 0.5697 0.5067 0.5295 1.0 0.5295 0.0 0.0 0.5496
ILE 256 A 0.5 0.7646 0.638 0.6104 1.0 0.6104 0.0 0.0 0.7013
VAL 257 A 0.5 0.8492 0.5656 0.5592 1.0 0.5592 0.0 0.0 0.7074
VAL 258 A 0.5 0.9025 0.5656 0.5984 1.0 0.5984 0.0 0.0 0.7505
ILE 259 A 0.5 0.8927 0.638 0.6416 1.0 0.6416 0.0 0.0 0.7672
TYR 260 A 0.8 0.8772 0.7963 0.7728 1.0 0.7728 0.0 0.0 0.8368
THR 261 A 0.8 0.7217 0.3257 0.6266 1.0 0.6266 0.0 0.0 0.6742
THR 262 A 1.0 0.6203 0.3257 0.595 1.0 0.595 0.0 0.0 0.6076
GLY 263 A 1.0 0.4815 0.4117 0.5253 0.94 0.4938 0.0 0.0 0.4876
SER 264 A 0.8 0.4788 0.3574 0.5525 0.98 0.5414 0.0 0.0 0.5101
GLN 265 A 1.0 0.3055 0.4343 0.3663 0.58 0.2124 0.0 0.0 0.3699
ALA 266 A 1.0 0.3944 0.3846 0.5192 1.0 0.5192 0.0 0.0 0.4568
THR 267 A 1.0 0.322 0.3257 0.4979 0.9 0.4481 0.0 0.0 0.3869
MET 268 A 1.0 0.4751 0.6606 0.5062 1.0 0.5062 0.5384 1.0 0.5834
ASP 269 A 1.0 0.3583 0.3212 0.401 0.96 0.3849 0.0 0.0 0.3716
GLU 270 A 1.0 0.3681 0.3348 0.4038 0.96 0.3876 0.0 0.0 0.3778
ARG 271 A 1.0 0.5589 0.5067 0.6372 1.0 0.6372 0.0 0.0 0.598
ASN 272 A 1.0 0.5374 0.3936 0.5862 1.0 0.5862 0.0 0.0 0.5618
ARG 273 A 1.0 0.3798 0.5067 0.5628 0.98 0.5516 0.0 0.0 0.5292
GLN 274 A 1.0 0.5361 0.4343 0.5753 0.98 0.5638 0.0 0.0 0.5499
ILE 275 A 0.5 0.7372 0.638 0.6805 1.0 0.6805 0.0 0.0 0.7088
ALA 276 A 1.0 0.5733 0.3846 0.7999 1.0 0.7999 0.0 0.0 0.6866
GLU 277 A 1.0 0.4906 0.3348 0.4883 0.84 0.4102 0.0 0.0 0.4504
ILE 278 A 0.8 0.7031 0.638 0.6801 1.0 0.6801 0.0 0.0 0.6916
GLY 279 A 0.5 0.6544 0.4117 0.6752 1.0 0.6752 0.0 0.0 0.6648
ALA 280 A 1.0 0.4945 0.3846 0.6462 1.0 0.6462 0.0 0.0 0.5704
SER 281 A 1.0 0.5238 0.3574 0.5353 0.9 0.4817 0.0 0.0 0.5028
LEU 282 A 0.8 0.6582 0.7058 0.5349 0.98 0.5242 0.0 0.0 0.682
ILE 283 A 1.0 0.508 0.638 0.4816 0.98 0.472 0.0 0.0 0.573
LYS 284 A 1.0 0.3538 0.2488 0.3331 0.68 0.2265 0.0 0.0 0.3013
HIS 285 A 1.0 0.4294 0.5972 0.1371 0.46 0.063 0.0 0.0 0.5133
TRP 286 A 1.0 0.4871 0.9909 0.2251 0.74 0.1666 0.0 0.0 0.739
example/example-esgemme-script.sh → examples/example-esgemme-script.sh
......@@ -17,8 +17,8 @@ then
# In ../tests folder, you can find a sample JET2 file called BLAT_jet.res
echo "Running ESGEMME with a user-provided alignment file."
echo "Using a previously produced prot_jet.res file to check reproducibility!"
cp ../tests/BLAT_jet.res .
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
elif [ "$1" == "withpdb" ]
then
......@@ -26,7 +26,8 @@ then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Entire mutational map of the protein will be calculated!"
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
elif [ "$1" == "withpdb-withmutfile" ]
then
......@@ -34,7 +35,9 @@ then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc -m Stiffler_2015_BLAT_ECOLX.mut
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
elif [ "$1" == "ssjetormax" ]
then
......@@ -42,11 +45,13 @@ then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the secondary structure based calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode ssjetormax -m Stiffler_2015_BLAT_ECOLX.mut
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode ssjetormax \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
else
echo "Running EGEMME with a user-provided alignment file."
echo "Since a pdb file is not provided, only evolutionary information will be used!"
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
fi
pred.R
......@@ -174,7 +174,7 @@ computePSSM2<-function(mat){
}
computeNbSeqsAlph<-function(nbSeqs,alphabet){
path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
facAA = rep(NA,20)
for(Let in AA){
......@@ -210,7 +210,7 @@ readMut<-function(fname){
}
which.class<-function(a,alphabet){
path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
for(Let in AA){
Let = toString(Let)
......
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