Mercurial > repos > mvdbeek > patser
comparison test-data/output.txt @ 0:f9ab3aa3e538 draft
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| author | mvdbeek |
|---|---|
| date | Tue, 07 Apr 2015 12:06:36 -0400 |
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| -1:000000000000 | 0:f9ab3aa3e538 |
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| 1 COMMAND LINE: patser-v3e -A a:t 0.25 c:g 0.25 -m /tmp/tmpE8Kxfh/files/000/dataset_2.dat -b 1 -c -d1 -ls 7.0 -f special.fa -p | |
| 2 | |
| 3 File containing the matrix: /tmp/tmpE8Kxfh/files/000/dataset_2.dat | |
| 4 File containing the sequence information: special.fa | |
| 5 Type of matrix: alignment | |
| 6 Total pseudo-counts added to the elements of the alignment matrix: 1 | |
| 7 | |
| 8 Range for approximating a weight matrix with integers: 10000 | |
| 9 Minimum score for calculating p-values: 0 | |
| 10 Also score the complementary strands | |
| 11 Treat unrecognized symbols as discontinuities in the sequence. | |
| 12 Print scores greater than or equal to 7.00 | |
| 13 | |
| 14 ***** Information for the alphabet from the command line. ***** | |
| 15 letter 1: A (complement: T) prior frequency = 0.250000 | |
| 16 letter 2: C (complement: G) prior frequency = 0.250000 | |
| 17 letter 3: G (complement: C) prior frequency = 0.250000 | |
| 18 letter 4: T (complement: A) prior frequency = 0.250000 | |
| 19 | |
| 20 width of the alignment matrix: 13 | |
| 21 A | 3 0 0 0 0 7 6 0 1 4 7 1 0 | |
| 22 C | 2 0 0 0 7 1 0 1 1 3 3 5 1 | |
| 23 G | 5 8 7 0 2 1 2 1 8 3 0 0 5 | |
| 24 T | 0 2 3 10 1 1 2 8 0 0 0 4 4 | |
| 25 | |
| 26 width of the matrix in file "/tmp/tmpE8Kxfh/files/000/dataset_2.dat": 13 | |
| 27 A C G T | |
| 28 0.17 -0.20 0.65 -2.40 | |
| 29 -2.40 -2.40 1.10 -0.20 | |
| 30 -2.40 -2.40 0.97 0.17 | |
| 31 -2.40 -2.40 -2.40 1.32 | |
| 32 -2.40 0.97 -0.20 -0.79 | |
| 33 0.97 -0.79 -0.79 -0.79 | |
| 34 0.82 -2.40 -0.20 -0.20 | |
| 35 -2.40 -0.79 -0.79 1.10 | |
| 36 -0.79 -0.79 1.10 -2.40 | |
| 37 0.44 0.17 0.17 -2.40 | |
| 38 0.97 0.17 -2.40 -2.40 | |
| 39 -0.79 0.65 -2.40 0.44 | |
| 40 -2.40 -0.79 0.65 0.44 | |
| 41 | |
| 42 Information content (base e): 8.324 | |
| 43 Sample size adjusted information content | |
| 44 (information content minus the average information | |
| 45 expected from an arbitrary alignment of random sequences): 6.101 | |
| 46 Information content after adding pseudo-counts: 6.370 | |
| 47 | |
| 48 maximum score: 11.685 | |
| 49 minimum score: -29.563 | |
| 50 range of scores: 11.685 - -29.563 = 41.248 | |
| 51 | |
| 52 minimum score for calculating p-values: 0.000 | |
| 53 maximum ln(numerically calculated p-value): -3.681 | |
| 54 minimum ln(numerically calculated p-value): -18.022 | |
| 55 | |
| 56 ln(cutoff p-value) based on sample size adjusted information content: -6.101 | |
| 57 numerically calculated cutoff score: 3.835 | |
| 58 ln(numerically calculated cutoff p-value): -6.102 | |
| 59 average score above numerically calculated cutoff: 4.996 | |
| 60 | |
| 61 >3L:3245372,3251371 position= 2004 score= 7.87 ln(p-value)= -10.00 | |
| 62 >3L:3245372,3251371 position= 2062C score= 7.14 ln(p-value)= -9.15 | |
| 63 >3L:3245372,3251371 position= 2535 score= 8.69 ln(p-value)= -11.09 | |
| 64 >3L:3245372,3251371 position= 3092 score= 7.73 ln(p-value)= -9.82 | |
| 65 >3L:3245372,3251371 position= 4690C score= 7.02 ln(p-value)= -9.01 |