diff test-data/last_train_E.txt @ 3:3de2195f32c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/last_train_E.txt	Fri Nov 13 09:05:49 2020 +0000
@@ -0,0 +1,504 @@
+# lastal version: 1021
+# maximum percent identity: 100
+# scale of score parameters: 4.5512
+# scale used while training: 91.024
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14901
+# deletes: 694
+# inserts: 834
+# delOpens: 350
+# insOpens: 402
+# alignments: 1
+# mean delete size: 1.98286
+# mean insert size: 2.07463
+# matchProb: 0.951836
+# delOpenProb: 0.0223571
+# insOpenProb: 0.0256787
+# delExtendProb: 0.495677
+# insExtendProb: 0.517986
+
+# substitution percent identity: 71.9408
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3291           532            387            390           
+# C 552            3221           180            685           
+# G 235            102            1561           84.7          
+# T 335            554            146            2651          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.220773       0.0356887      0.0259615      0.0261627     
+# C 0.0370303      0.216077       0.0120751      0.0459525     
+# G 0.0157647      0.00684256     0.104718       0.00568201    
+# T 0.0224731      0.0371645      0.00979425     0.177839      
+
+# delExistCost: 346
+# insExistCost: 342
+# delExtendCost: 62
+# insExtendCost: 58
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     76    -90    -59   -105
+# C    -87     73   -129    -54
+# G    -88   -164    145   -167
+# T   -112    -66   -127     90
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14771
+# deletes: 379.3
+# inserts: 567.1
+# delOpens: 185.2
+# insOpens: 246.1
+# alignments: 2
+# mean delete size: 2.04806
+# mean insert size: 2.30435
+# matchProb: 0.971438
+# delOpenProb: 0.01218
+# insOpenProb: 0.0161851
+# delExtendProb: 0.511732
+# insExtendProb: 0.566038
+
+# substitution percent identity: 70.0105
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3158           583.4          429.9          391.6         
+# C 589            3065           156.8          774           
+# G 252.2          88.64          1571           68.46         
+# T 342.6          630.1          131.09         2566          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.21341        0.0394248      0.0290516      0.0264634     
+# C 0.0398032      0.207126       0.0105962      0.0523051     
+# G 0.0170431      0.00599008     0.106165       0.00462637    
+# T 0.0231521      0.0425807      0.00885876     0.173404      
+
+# delExistCost: 406
+# insExistCost: 400
+# delExtendCost: 60
+# insExtendCost: 51
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -79    -48   -102
+# C    -78     72   -140    -41
+# G    -79   -174    146   -185
+# T   -107    -52   -136     89
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14881
+# deletes: 258.8
+# inserts: 446.1
+# delOpens: 112.91
+# insOpens: 168
+# alignments: 2
+# mean delete size: 2.29209
+# mean insert size: 2.65536
+# matchProb: 0.981278
+# delOpenProb: 0.00744548
+# insOpenProb: 0.0110782
+# delExtendProb: 0.563717
+# insExtendProb: 0.623403
+
+# substitution percent identity: 68.9366
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3126           618.3          445            406.6         
+# C 622.8          3041           159.4          805.4         
+# G 265.2          91.16          1560           68.22         
+# T 357.3          660            133.33         2554          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.209606       0.0414585      0.0298383      0.0272635     
+# C 0.0417602      0.203906       0.0106882      0.054004      
+# G 0.0177823      0.0061125      0.104602       0.00457431    
+# T 0.0239578      0.0442546      0.0089401      0.171252      
+
+# delExistCost: 470
+# insExistCost: 457
+# delExtendCost: 52
+# insExtendCost: 42
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -73    -44    -99
+# C    -73     71   -138    -37
+# G    -73   -171    147   -185
+# T   -103    -48   -134     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 214.8
+# inserts: 402.9
+# delOpens: 82.32
+# insOpens: 131.98
+# alignments: 2
+# mean delete size: 2.60933
+# mean insert size: 3.05274
+# matchProb: 0.985702
+# delOpenProb: 0.0054164
+# insOpenProb: 0.00868387
+# delExtendProb: 0.61676
+# insExtendProb: 0.672425
+
+# substitution percent identity: 68.4035
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3114           635.9          450            416.3         
+# C 640.1          3019           164.9          816.3         
+# G 270.6          93.43          1560           69.38         
+# T 365.7          670            135.53         2543          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.208097       0.0424949      0.0300719      0.0278198     
+# C 0.0427756      0.201749       0.0110197      0.0545504     
+# G 0.0180832      0.00624359     0.104249       0.00463642    
+# T 0.0244384      0.0447737      0.00905699     0.16994       
+
+# delExistCost: 518
+# insExistCost: 498
+# delExtendCost: 44
+# insExtendCost: 36
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -71    -43    -97
+# C    -70     71   -135    -36
+# G    -71   -169    146   -183
+# T   -101    -46   -133     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197.5
+# inserts: 386.4
+# delOpens: 68.51
+# insOpens: 115.71
+# alignments: 2
+# mean delete size: 2.88279
+# mean insert size: 3.33938
+# matchProb: 0.987657
+# delOpenProb: 0.00451668
+# insOpenProb: 0.00762845
+# delExtendProb: 0.653114
+# insExtendProb: 0.700543
+
+# substitution percent identity: 68.1501
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3103           643.6          451.1          422.5         
+# C 649.8          3008           167            819.5         
+# G 272.7          94.59          1560           70.43         
+# T 369.8          675.4          136.61         2542          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.20706        0.0429467      0.0301014      0.0281929     
+# C 0.0433604      0.20072        0.0111437      0.0546843     
+# G 0.0181969      0.00631188     0.104097       0.00469971    
+# T 0.0246763      0.0450686      0.00911582     0.169625      
+
+# delExistCost: 549
+# insExistCost: 522
+# delExtendCost: 39
+# insExtendCost: 32
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -43    -95
+# C    -68     70   -134    -35
+# G    -71   -168    146   -182
+# T   -100    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 192.1
+# inserts: 380.9
+# delOpens: 62.34
+# insOpens: 108.21
+# alignments: 2
+# mean delete size: 3.08149
+# mean insert size: 3.52001
+# matchProb: 0.988548
+# delOpenProb: 0.00411362
+# insOpenProb: 0.00714043
+# delExtendProb: 0.675482
+# insExtendProb: 0.71591
+
+# substitution percent identity: 67.9883
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648            451.1          425.7         
+# C 654.2          3008           169            821.5         
+# G 272.8          95.26          1550           71.05         
+# T 371.8          677.5          136.66         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206509       0.0432647      0.0301184      0.0284225     
+# C 0.0436786      0.200834       0.0112835      0.0548487     
+# G 0.0182139      0.00636018     0.103488       0.00474376    
+# T 0.0248238      0.0452343      0.00912431     0.169053      
+
+# delExistCost: 566
+# insExistCost: 534
+# delExtendCost: 36
+# insExtendCost: 30
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -133    -35
+# G    -70   -167    147   -181
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 194.5
+# inserts: 383.3
+# delOpens: 60.42
+# insOpens: 106.36
+# alignments: 2
+# mean delete size: 3.21913
+# mean insert size: 3.6038
+# matchProb: 0.988794
+# delOpenProb: 0.00398791
+# insOpenProb: 0.0070201
+# delExtendProb: 0.689357
+# insExtendProb: 0.722515
+
+# substitution percent identity: 67.9593
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.9          451.2          426.7         
+# C 655.2          3008           169            821.4         
+# G 273.8          95.46          1550           71.26         
+# T 372.8          678.6          136.64         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206421       0.0433063      0.0301122      0.0284771     
+# C 0.0437268      0.200748       0.0112787      0.0548186     
+# G 0.0182729      0.00637081     0.103444       0.00475575    
+# T 0.0248799      0.0452884      0.00911908     0.168981      
+
+# delExistCost: 575
+# insExistCost: 539
+# delExtendCost: 34
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -167    147   -180
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 196.9
+# inserts: 385.7
+# delOpens: 59.47
+# insOpens: 105.68
+# alignments: 2
+# mean delete size: 3.31091
+# mean insert size: 3.6497
+# matchProb: 0.9889
+# delOpenProb: 0.00392563
+# insOpenProb: 0.00697597
+# delExtendProb: 0.697969
+# insExtendProb: 0.726005
+
+# substitution percent identity: 67.9572
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          426.6         
+# C 655.1          3008           169.9          821.4         
+# G 273.8          95.45          1550           71.26         
+# T 372.7          678.6          136.63         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206414       0.0432982      0.0301112      0.0284695     
+# C 0.0437187      0.200742       0.0113384      0.0548169     
+# G 0.0182723      0.00636994     0.103441       0.0047556     
+# T 0.0248725      0.045287       0.00911813     0.168975      
+
+# delExistCost: 580
+# insExistCost: 541
+# delExtendCost: 33
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -167    147   -180
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197
+# inserts: 385.7
+# delOpens: 58.72
+# insOpens: 105.14
+# alignments: 2
+# mean delete size: 3.3549
+# mean insert size: 3.66844
+# matchProb: 0.988985
+# delOpenProb: 0.00387646
+# insOpenProb: 0.00694091
+# delExtendProb: 0.701929
+# insExtendProb: 0.727405
+
+# substitution percent identity: 67.9308
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          426.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.55          1550           71.36         
+# T 372.7          678.6          136.62         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206537       0.043324       0.0301292      0.0284865     
+# C 0.0438048      0.200193       0.0113452      0.0548495     
+# G 0.0182832      0.00638041     0.103502       0.00476511    
+# T 0.0248873      0.0453139      0.00912288     0.169076      
+
+# delExistCost: 584
+# insExistCost: 542
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    146   -180
+# T    -99    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197
+# inserts: 384.7
+# delOpens: 57.97
+# insOpens: 104.51
+# alignments: 2
+# mean delete size: 3.39831
+# mean insert size: 3.68099
+# matchProb: 0.989075
+# delOpenProb: 0.00382729
+# insOpenProb: 0.00689995
+# delExtendProb: 0.705736
+# insExtendProb: 0.728334
+
+# substitution percent identity: 67.93
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          427.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.75          1550           71.36         
+# T 372.7          678.6          135.61         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206534       0.0433235      0.0301288      0.0285529     
+# C 0.0438042      0.200191       0.011345       0.0548488     
+# G 0.0182829      0.00639368     0.103501       0.00476505    
+# T 0.024887       0.0453133      0.00905532     0.169074      
+
+# delExistCost: 586
+# insExistCost: 543
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    147   -180
+# T    -99    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 196
+# inserts: 384.7
+# delOpens: 57.87
+# insOpens: 104.51
+# alignments: 2
+# mean delete size: 3.3869
+# mean insert size: 3.68099
+# matchProb: 0.989081
+# delOpenProb: 0.00382071
+# insOpenProb: 0.0069
+# delExtendProb: 0.704745
+# insExtendProb: 0.728334
+
+# substitution percent identity: 67.93
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          427.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.75          1550           71.36         
+# T 372.7          678.6          135.61         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206534       0.0433235      0.0301288      0.0285529     
+# C 0.0438042      0.200191       0.011345       0.0548488     
+# G 0.0182829      0.00639368     0.103501       0.00476505    
+# T 0.024887       0.0453133      0.00905532     0.169074      
+
+# delExistCost: 586
+# insExistCost: 543
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    147   -180
+# T    -99    -45   -132     88
+
+#last -X 0
+#last -Q 0
+#last -t4.80115
+#last -a 29
+#last -A 28
+#last -b 2
+#last -B 1
+#last -s 1
+#last -S 1
+# score matrix (query letters = columns, reference letters = rows):
+       A      C      G      T
+A      4     -3     -2     -5
+C     -3      4     -7     -2
+G     -3     -8      7     -9
+T     -5     -2     -7      4