Mercurial > repos > iuc > last
diff test-data/last_train.txt @ 0:9a7e91fc6562 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
| author | iuc |
|---|---|
| date | Wed, 17 Jun 2020 14:50:21 -0400 |
| parents | |
| children | 3de2195f32c0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/last_train.txt Wed Jun 17 14:50:21 2020 -0400 @@ -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