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Running Examples
Paul Lott edited this page Jul 29, 2013
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#Running StochHMM Examples
##Dice Model Examples Each example provides the command used and the output from StochHMM
####Print PATH_LABEL using Viterbi algorithm
#Print Viterbi traceback as State Path Label
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -viterbi -label
>>Eddy Dice TRACK_NAME:TRACK1 Score: -539.062
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
L L L L L L L L L L L L L L L L L L F F F F F F F F F F F F L L L L L L L L L L L L L L L L L L
L L L L L L L L L L L L L L L L F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L L L L L L
L F F F F F F F F F F F
####Print GFF using Viterbi algorithm
#Print Viterbi traceback as GFF (Only states with GFF_DESC will be output)
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -viterbi -gff
#Score: -539.062
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 1 48 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 49 66 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 67 78 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 79 112 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 113 179 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 180 192 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 193 270 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 271 289 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 290 300 . + .
####Print state number using Viterbi algorithm
#Print Viterbi traceback as state position in model
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -viterbi -path
>>Eddy Dice TRACK_NAME:TRACK1 Score: -539.062
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 0 0 0 0 0 0 0 0 0 0 0
####Print Posterior scores
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -posterior
Posterior Probabilities Table
Model: CASINO DICE MODEL
Sequence: >Eddy Dice TRACK_NAME:TRACK1
Probability of Sequence from Forward: Natural Log'd -516.544812
Probability of Sequence from Backward:Natural Log'd -516.544812
Position FAIR LOADED
1 0.812 0.188
2 0.849 0.151
3 0.861 0.139
4 0.850 0.150
5 0.814 0.186
6 0.738 0.262
...(output truncated)
####Print Posterior decoding as GFF
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -posterior -gff
#Score: 0
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 1 47 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 48 66 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 67 78 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 79 95 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 96 104 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 105 112 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 113 129 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 130 138 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 139 179 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 180 192 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 193 201 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 202 207 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 208 269 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 270 289 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 290 300 . + .
####Print GFF using Stochastic Viterbi algorithm 10 samples Reports the number of times the specific traceback path has occurred during the sampling
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic viterbi -rep 10 -gff
Traceback occurred: 1
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 1 50 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 51 68 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 69 89 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 90 112 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 113 131 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 132 143 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 144 154 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 155 155 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 156 183 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 184 196 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 197 203 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 204 210 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 211 275 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 276 288 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 289 300 . + .
Traceback occurred: 1
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 1 48 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 49 63 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 64 65 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 66 66 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 67 81 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 82 85 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 86 86 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 87 117 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 118 131 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 132 142 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 143 167 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 168 168 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 169 179 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 180 209 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 210 230 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 231 231 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 232 270 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM LOADED 271 288 . + .
Eddy Dice TRACK_NAME:TRACK1 StochHMM FAIR 289 300 . + .
...(output truncated)
####Print Hits table for Stochastic Viterbi sampling
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic viterbi -rep 10 -hits
Position FAIR LOADED
1 10 0
2 10 0
3 10 0
4 10 0
5 10 0
6 8 2
7 6 4
... (truncated output)
$ stochhmm -model ../examples/3_16Eddy.hmm -seq ../example/3_16Eddy.fa -viterbi -gff
$ stochhmm -model ../examples/3_16Eddy.hmm -seq ../example/3_17Eddy.fa -posterior
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic viterbi -rep 10 -label
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic posterior -rep 10 -label
#Example Viterbi Decoding Viterbi scores are returned as natural log-values.
##Example 1 Path output Perform viterbi decoding on Dice.fa using model Dice.hmm. Output defaults to path. (Note: Path is the state, represented as a number. ie. First state in model gets assigned value "0", Second->"1"....)
###Command
$ ./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -viterbi
###Output
Viterbi Score: -539.062
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 0 0 0 0 0 0 0 0 0 0 0
##Example 2 Label Output Perform viterbi decoding on Dice.fa using model Dice.hmm. Output the traceback as the state Labels.
###Command
$ ./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -viterbi -label
###Output
Viterbi Score: -539.062
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
L L L L L L L L L L L L L L L L L L F F F F F F F F F F F F L L L L L L L L L L L L L L L L L L
L L L L L L L L L L L L L L L L F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L L L L L L
L F F F F F F F F F F F
##Example 3 GFF Output
###Command
$ ./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -viterbi -gff
###Output
>Dice StochHMM Fair 1 48 . +
>Dice StochHMM Loaded 49 66 . +
>Dice StochHMM Fair 67 78 . +
>Dice StochHMM Loaded 79 112 . +
>Dice StochHMM Fair 113 179 . +
>Dice StochHMM Loaded 180 192 . +
>Dice StochHMM Fair 193 270 . +
>Dice StochHMM Loaded 271 289 . +
>Dice StochHMM Fair 290 300 . +
#Example Calculating Posterior Probability
###Command
./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -posterior
###Output
Posterior Probabilities Table
Model: CASINO DICE MODEL
Sequence: >Dice
Probability of Sequence from Forward: Natural Log'd -516.545
Probability of Sequence from Backward:Natural Log'd -516.545
Position FAIR LOADED
1 0.81184 0.18816
2 0.849421 0.150579
3 0.860841 0.139159
4 0.85016 0.14984
5 0.81358 0.18642
6 0.738095 0.261905
7 0.748312 0.251688
8 0.725866 0.274134
9 0.662776 0.337224
10 0.68518 0.31482
11 0.670831 0.329169
12 0.614627 0.385373
13 0.643782 0.356218
14 0.793853 0.206147
15 0.877151 0.122849
16 0.923291 0.0767085
17 0.948679 0.051321
18 0.96234 0.0376598
19 0.969132 0.0308685
20 0.971468 0.0285323
21 0.970179 0.0298205
22 0.964809 0.0351913
23 0.953446 0.0465541
24 0.932051 0.0679488
25 0.893018 0.106982
26 0.915672 0.0843277
...
#Example Posterior Decoding
##Example 1 Posterior Traceback with Path Output
###Command
./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -posterior -path
###Output
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0
0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 0 0 0 0 0 0 0 0 0 0 0
##Example 2 Posterior Traceback with Label Output
###Command
./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -posterior -label
###Output
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L
L L L L L L L L L L L L L L L L L L F F F F F F F F F F F F L L L L L L L L L L L L L L L L L F
F F F F F F F F L L L L L L L L F F F F F F F F F F F F F F F F F L L L L L L L L L F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L
F F F F F F F F F L L L L L L F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F F
F F F F F F F F F F F F F F F F F F F F F F F F F F F F F L L L L L L L L L L L L L L L L L L L
L F F F F F F F F F F F
##Example 3 Posterior Traceback with GFF Output
###Command
./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -posterior -gff
###Output
>Dice StochHMM Fair 1 47 . +
>Dice StochHMM Loaded 48 66 . +
>Dice StochHMM Fair 67 78 . +
>Dice StochHMM Loaded 79 95 . +
>Dice StochHMM Fair 96 104 . +
>Dice StochHMM Loaded 105 112 . +
>Dice StochHMM Fair 113 129 . +
>Dice StochHMM Loaded 130 138 . +
>Dice StochHMM Fair 139 179 . +
>Dice StochHMM Loaded 180 192 . +
>Dice StochHMM Fair 193 201 . +
>Dice StochHMM Loaded 202 207 . +
>Dice StochHMM Fair 208 269 . +
>Dice StochHMM Loaded 270 289 . +
>Dice StochHMM Fair 290 300 . +
#Example of Stochastic Viterbi Decoding ##Example 1 Stochastic Viterbi Traceback with GFF Output
###Command
./stochHMM -model ./examples/Dice.hmm -seq ./examples/Dice.fa -stochastic posterior -rep 3 -gff
Tracebacks are performed three times and each traceback is stored. The number of times each unique traceback is kept track of and returned.
###Output
Traceback occurred: 1
>Dice StochHMM Fair 1 8 . +
>Dice StochHMM Loaded 9 15 . +
>Dice StochHMM Fair 16 45 . +
>Dice StochHMM Loaded 46 67 . +
>Dice StochHMM Fair 68 81 . +
>Dice StochHMM Loaded 82 100 . +
>Dice StochHMM Fair 101 101 . +
>Dice StochHMM Loaded 102 114 . +
>Dice StochHMM Fair 115 130 . +
>Dice StochHMM Loaded 131 145 . +
>Dice StochHMM Fair 146 178 . +
>Dice StochHMM Loaded 179 192 . +
>Dice StochHMM Fair 193 202 . +
>Dice StochHMM Loaded 203 208 . +
>Dice StochHMM Fair 209 258 . +
>Dice StochHMM Loaded 259 260 . +
>Dice StochHMM Fair 261 277 . +
>Dice StochHMM Loaded 278 290 . +
>Dice StochHMM Fair 291 300 . +
Traceback occurred: 1
>Dice StochHMM Fair 1 48 . +
>Dice StochHMM Loaded 49 75 . +
>Dice StochHMM Fair 76 81 . +
>Dice StochHMM Loaded 82 91 . +
>Dice StochHMM Fair 92 105 . +
>Dice StochHMM Loaded 106 114 . +
>Dice StochHMM Fair 115 118 . +
>Dice StochHMM Loaded 119 119 . +
>Dice StochHMM Fair 120 130 . +
>Dice StochHMM Loaded 131 147 . +
>Dice StochHMM Fair 148 190 . +
>Dice StochHMM Loaded 191 194 . +
>Dice StochHMM Fair 195 216 . +
>Dice StochHMM Loaded 217 220 . +
>Dice StochHMM Fair 221 276 . +
>Dice StochHMM Loaded 277 290 . +
>Dice StochHMM Fair 291 300 . +
Traceback occurred: 1
>Dice StochHMM Fair 1 50 . +
>Dice StochHMM Loaded 51 69 . +
>Dice StochHMM Fair 70 81 . +
>Dice StochHMM Loaded 82 113 . +
>Dice StochHMM Fair 114 130 . +
>Dice StochHMM Loaded 131 141 . +
>Dice StochHMM Fair 142 181 . +
>Dice StochHMM Loaded 182 194 . +
>Dice StochHMM Fair 195 201 . +
>Dice StochHMM Loaded 202 212 . +
>Dice StochHMM Fair 213 274 . +
>Dice StochHMM Loaded 275 291 . +
>Dice StochHMM Fair 292 300 . +