From f9a7732b80aa91dcbd250fcdbad74ead7036f0c6 Mon Sep 17 00:00:00 2001 From: Marcin Magnus Date: Tue, 25 May 2021 12:21:43 +0200 Subject: [PATCH] rt: make it lighter, branch out with splix --- rna_tools/tools/splix/clarna/yCs_5MPS.clarna | 612 ------------------ rna_tools/tools/splix/db/inters_of_A25.csv | 18 - rna_tools/tools/splix/docs/Network.png | Bin 25189 -> 0 bytes rna_tools/tools/splix/literature.tsv | 7 - rna_tools/tools/splix/readme.md | 37 -- rna_tools/tools/splix/splix.py | 98 --- rna_tools/tools/splix/splix_math.py | 64 -- rna_tools/tools/splix/splix_trx.py | 59 -- rna_tools/tools/splix/test.sh | 9 - rna_tools/tools/splix/yeast-in-monte-carlo.py | 51 -- 10 files changed, 955 deletions(-) delete mode 100644 rna_tools/tools/splix/clarna/yCs_5MPS.clarna delete mode 100644 rna_tools/tools/splix/db/inters_of_A25.csv delete mode 100644 rna_tools/tools/splix/docs/Network.png delete mode 100644 rna_tools/tools/splix/literature.tsv delete mode 100644 rna_tools/tools/splix/readme.md delete mode 100755 rna_tools/tools/splix/splix.py delete mode 100644 rna_tools/tools/splix/splix_math.py delete mode 100755 rna_tools/tools/splix/splix_trx.py delete mode 100755 rna_tools/tools/splix/test.sh delete mode 100644 rna_tools/tools/splix/yeast-in-monte-carlo.py diff --git a/rna_tools/tools/splix/clarna/yCs_5MPS.clarna b/rna_tools/tools/splix/clarna/yCs_5MPS.clarna deleted file mode 100644 index f07933932..000000000 --- a/rna_tools/tools/splix/clarna/yCs_5MPS.clarna +++ /dev/null @@ -1,612 +0,0 @@ -Cs -------------------------------------------------------------------- -chains: 2 1 49 5 4 173 6 1 1005 -2 1 2 2 bp A C >> 0.9685 -2 1 6 104 bp A U WW_cis 0.9462 -6 1 6 2 bp G U >> 0.9838 -6 1 6 25 bp G C WW_cis 0.9260 -2 2 2 3 bp C G >> 0.6486 -2 2 6 103 bp C A WW_cis 0.6498 -6 2 6 3 bp U U >> 0.9536 -6 2 6 24 bp U A WW_cis 0.9433 -2 3 2 4 bp G A >> 0.9760 -2 3 6 102 bp G U WW_cis 0.8733 -2 3 6 103 bp G A <> 0.9161 -6 3 6 23 bp U G WW_cis 0.8741 -2 4 2 5 bp A A >> 0.9671 -2 4 6 101 bp A U WW_cis 0.9341 -5 4 5 144 bp C G WW_cis 0.9570 -6 4 6 22 bp C G WW_cis 0.9119 -2 4 6 102 bp A U <> 0.6504 -2 5 6 100 bp A U WW_cis 0.9483 -2 5 2 6 bp A U >> 0.9577 -5 5 5 6 bp A G >> 0.9728 -5 5 5 143 bp A U WW_cis 0.9424 -5 5 5 144 bp A G <> 0.9657 -6 5 6 6 bp G C >> 0.9441 -6 5 6 21 bp G U WW_cis 0.8536 -6 5 6 22 bp G G <> 0.9761 -2 5 6 101 bp A U <> 0.7332 -2 6 2 7 bp U C >> 0.9603 -2 6 6 99 bp U A WW_cis 0.9187 -5 6 5 142 bp G C WW_cis 0.9191 -5 6 5 7 bp G C >> 0.9777 -6 6 6 20 bp C G WW_cis 0.9149 -2 7 2 8 bp C U >> 0.9393 -2 7 6 98 bp C G WW_cis 0.9348 -5 7 5 141 bp C G WW_cis 0.9172 -5 7 5 8 bp C U >> 0.9686 -6 7 6 19 bp G C WW_cis 0.9142 -6 7 6 8 bp G A >> 0.9746 -6 7 6 20 bp G G <> 0.9695 -2 8 2 9 bp U C >> 0.9674 -2 8 6 97 bp U A WW_cis 0.9589 -5 8 5 140 bp U A WW_cis 0.9283 -5 8 5 9 bp U U >> 0.9754 -6 8 6 18 bp A U WW_cis 0.9406 -6 8 6 9 bp A A >> 0.9616 -2 9 6 96 bp C G WW_cis 0.9144 -5 9 5 139 bp U A WW_cis 0.9464 -5 9 5 10 bp U U >> 0.9522 -6 9 6 10 bp A G >> 0.9437 -6 9 6 17 bp A U WW_cis 0.9353 -6 9 6 18 bp A U <> 0.8006 -2 10 6 95 bp U A WW_cis 0.9508 -2 10 6 96 bp U G <> 0.7165 -5 10 5 138 bp U A WW_cis 0.9200 -5 10 5 139 bp U A <> 0.8373 -6 10 6 16 bp G C WW_cis 0.9404 -6 10 6 17 bp G U <> 0.9609 -2 11 6 94 bp U A WW_cis 0.9289 -2 11 2 12 bp U U >> 0.9781 -5 11 5 138 bp A A <> 0.9180 -5 11 5 12 bp A C >> 0.9711 -5 11 5 137 bp A U WW_cis 0.9635 -2 12 2 13 bp U G >> 0.8789 -2 12 6 93 bp U A WW_cis 0.9289 -5 12 5 136 bp C G WW_cis 0.9210 -2 13 2 14 bp G C >> 0.9886 -2 13 6 93 bp G A <> 0.9800 -5 13 5 14 bp A G >> 0.9682 -5 13 5 136 bp A G <> 0.6456 -5 13 5 135 bp A G WW_cis 0.7654 -5 14 5 15 bp G A >> 0.9496 -5 14 5 134 bp G A WW_cis 0.7658 -5 15 5 134 bp A A <> 0.9192 -2 17 6 88 bp U U << 0.7948 -5 18 5 19 bp A A >> 0.9402 -6 18 6 19 bp U C >> 0.9306 -5 19 5 20 bp A U >> 0.9156 -6 19 6 20 bp C G >> 0.7807 -5 20 5 132 bp U A WW_cis 0.9229 -5 20 5 21 bp U G >> 0.7962 -6 20 6 21 bp G U >> 0.9841 -2 21 2 22 bp G C >> 0.9828 -2 21 6 61 bp G C WW_cis 0.9332 -2 21 6 62 bp G A <> 0.9728 -5 21 5 131 bp G A WW_cis 0.7154 -5 21 5 22 bp G G >> 0.9559 -5 21 5 132 bp G A <> 0.8480 -2 22 6 60 bp C G WW_cis 0.9166 -5 22 5 130 bp G A WW_cis 0.6564 -6 22 6 23 bp G G >> 0.9903 -2 23 6 59 bp U A WW_cis 0.9405 -6 23 6 24 bp G A >> 0.9779 -5 24 5 26 bp G A <> 0.9476 -6 24 6 25 bp A C >> 0.9857 -6 25 6 26 bp C A >> 0.9289 -2 26 2 27 bp G A >> 0.9910 -2 26 6 53 bp G A << 0.8190 -2 26 6 58 bp G C WW_cis 0.9394 -2 26 6 59 bp G A <> 0.9201 -5 26 5 129 bp A G >> 0.8514 -6 26 6 27 bp A U >> 0.8653 -2 27 2 28 bp A U >> 0.9730 -2 27 6 57 bp A U WW_cis 0.9514 -5 27 5 129 bp G G >< 0.7597 -2 28 2 29 bp U C >> 0.9922 -2 28 6 56 bp U A WW_cis 0.9378 -5 28 5 125 bp G C WW_cis 0.9265 -5 28 5 126 bp G A <> 0.9861 -5 28 5 29 bp G G >> 0.9723 -2 29 6 55 bp C G WW_cis 0.9018 -5 29 5 124 bp G C WW_cis 0.9165 -5 29 5 30 bp G A >> 0.9672 -6 29 6 30 bp U G >> 0.9467 -5 30 5 123 bp A U WW_cis 0.9376 -5 30 5 31 bp A G >> 0.9879 -6 30 6 31 bp G G >> 0.9092 -5 31 5 32 bp G G >> 0.9774 -5 31 5 122 bp G C WW_cis 0.8971 -5 31 5 123 bp G U <> 0.6646 -2 32 2 33 bp G U >> 0.9757 -5 32 5 34 bp G C >> 0.9782 -5 32 5 121 bp G U WW_cis 0.8222 -2 33 2 34 bp U G >> 0.8871 -2 34 2 35 bp G U >> 0.9655 -5 34 5 35 bp C A >> 0.7844 -5 34 5 120 bp C G WW_cis 0.9157 -2 35 2 36 bp U A >> 0.9693 -5 35 5 36 bp A A >> 0.9735 -5 35 5 120 bp A G <> 0.9731 -5 35 5 119 bp A U WW_cis 0.9630 -2 36 2 37 bp A G >> 0.9900 -5 36 5 37 bp A C >> 0.9755 -5 36 5 118 bp A U WW_cis 0.9646 -2 37 2 38 bp G U >> 0.9854 -5 37 5 38 bp C A >> 0.7370 -5 37 5 117 bp C G WW_cis 0.9084 -2 38 2 39 bp U A >> 0.9462 -5 38 5 39 bp A U >> 0.9628 -5 38 5 116 bp A U WW_cis 0.9426 -5 38 5 117 bp A G <> 0.9690 -2 39 2 40 bp A U >> 0.9853 -5 39 5 40 bp U C >> 0.9560 -5 39 5 115 bp U G WW_cis 0.8462 -5 40 5 114 bp C G WW_cis 0.9139 -2 41 2 42 bp C U >> 0.9437 -5 41 5 78 bp A A >< 0.9756 -6 41 6 42 bp A A >> 0.9532 -2 42 2 43 bp U G >> 0.8928 -5 42 5 78 bp A A HW_tran 0.7206 -5 42 5 45 bp A A >> 0.9053 -6 42 6 43 bp A C >> 0.9774 -2 43 2 44 bp G U >> 0.9778 -6 43 6 44 bp C A >> 0.7855 -2 44 2 45 bp U U >> 0.9274 -5 44 5 77 bp A A HW_tran 0.6517 -5 44 5 75 bp A A HH_tran 0.6916 -5 44 5 45 bp A A << 0.9649 -6 44 6 45 bp A A >> 0.9593 -2 45 2 46 bp U C >> 0.9559 -6 45 6 46 bp A U >> 0.9502 -2 46 2 47 bp C U >> 0.9151 -5 46 5 69 bp C G WW_cis 0.9082 -6 46 6 47 bp U A >> 0.9632 -2 47 2 48 bp U U >> 0.8342 -5 47 5 69 bp U G <> 0.7427 -5 47 5 68 bp U A WW_cis 0.9536 -5 47 5 48 bp U G >> 0.8610 -6 47 6 48 bp A C >> 0.9829 -2 48 2 49 bp U U >> 0.7527 -5 48 5 68 bp G A <> 0.9676 -5 48 5 49 bp G U >> 0.9788 -5 48 5 67 bp G U WW_cis 0.7357 -6 48 6 49 bp C A >> 0.8410 -5 49 5 50 bp U G >> 0.7635 -5 49 5 66 bp U A WW_cis 0.9346 -6 49 6 50 bp A G >> 0.9799 -5 50 5 51 bp G G >> 0.9822 -5 50 5 65 bp G U WW_cis 0.8432 -5 50 5 66 bp G A <> 0.9625 -5 51 5 64 bp G C WW_cis 0.9110 -5 51 5 52 bp G G >> 0.9698 -5 52 5 63 bp G C WW_cis 0.9191 -5 52 5 53 bp G C >> 0.9837 -6 52 6 53 bp G A >> 0.9407 -6 52 6 60 bp G G WH_tran 0.8005 -6 52 6 80 bp G U <> 0.9591 -5 53 5 62 bp C G WW_cis 0.9334 -6 53 6 59 bp A A WH_tran 0.7953 -6 55 6 56 bp G A >> 0.9770 -6 56 6 57 bp A U >> 0.9860 -6 57 6 58 bp U C >> 0.9848 -6 59 6 60 bp A G >> 0.9703 -6 60 6 61 bp G C >> 0.9865 -6 61 6 62 bp C A >> 0.9046 -6 61 6 80 bp C U HS_cis 0.8383 -5 62 5 63 bp G C >> 0.9819 -6 62 6 63 bp A G >> 0.9446 -5 63 5 64 bp C C >> 0.9528 -6 63 6 64 bp G U >> 0.9826 -6 63 6 84 bp G C WW_cis 0.8846 -5 64 5 65 bp C U >> 0.9626 -6 64 6 83 bp U A WW_cis 0.9243 -6 64 6 65 bp U U >> 0.9812 -5 65 5 66 bp U A >> 0.8431 -6 65 6 82 bp U A WW_cis 0.9350 -5 66 5 67 bp A U >> 0.9705 -5 67 5 68 bp U A >> 0.7283 -6 67 6 82 bp C A <> 0.9293 -6 67 6 81 bp C G WW_cis 0.9291 -6 67 6 68 bp C C >> 0.8865 -5 68 5 69 bp A G >> 0.9845 -6 68 6 78 bp C G WW_cis 0.9112 -6 68 6 81 bp C G <> 0.9077 -5 69 5 70 bp G A >> 0.9621 -6 69 6 70 bp C U >> 0.9225 -6 69 6 78 bp C G <> 0.6694 -6 69 6 77 bp C G WW_cis 0.9250 -6 70 6 71 bp U G >> 0.9799 -6 70 6 76 bp U A WW_cis 0.9183 -6 70 6 77 bp U G <> 0.6981 -5 71 5 72 bp A C >> 0.9833 -6 71 6 75 bp G A SW_tran 0.8324 -5 72 5 73 bp C U >> 0.9083 -6 72 6 73 bp C A >> 0.9683 -5 73 5 74 bp U U >> 0.9246 -6 73 6 75 bp A A >< 0.9765 -5 75 5 77 bp A A <> 0.9418 -6 75 6 76 bp A A <> 0.9515 -6 76 6 77 bp A G >> 0.9695 -5 77 5 78 bp A A >> 0.7359 -6 77 6 78 bp G G >> 0.9704 -6 78 6 81 bp G G >> 0.9497 -5 79 5 113 bp C G WW_cis 0.8617 -5 79 5 114 bp C G <> 0.9597 -5 80 5 112 bp G C WW_cis 0.9225 -5 80 5 82 bp G A >> 0.9182 -5 80 5 113 bp G G <> 0.9614 -6 81 6 82 bp G A >> 0.9625 -5 82 5 83 bp A C >> 0.9687 -6 82 6 83 bp A A >> 0.9640 -6 83 6 84 bp A C >> 0.9745 -5 84 5 85 bp A U >> 0.9783 -5 84 5 110 bp A U WW_cis 0.9343 -5 85 5 109 bp U A WW_cis 0.9147 -5 86 5 87 bp G G >> 0.9765 -5 86 5 108 bp G C WW_cis 0.9270 -5 86 5 109 bp G A <> 0.9740 -6 86 6 87 bp G U >> 0.9929 -5 87 5 88 bp G U >> 0.9775 -5 87 5 107 bp G C WW_cis 0.9096 -6 87 6 88 bp U U >> 0.9880 -5 88 5 89 bp U U >> 0.9708 -5 88 5 106 bp U A WW_cis 0.9418 -5 89 5 90 bp U C >> 0.9707 -5 89 5 105 bp U A WW_cis 0.9219 -5 90 5 104 bp C G WW_cis 0.9240 -5 90 5 91 bp C U >> 0.9502 -5 91 5 92 bp U U >> 0.9531 -5 91 5 103 bp U A WW_cis 0.9366 -5 92 5 93 bp U G >> 0.9113 -5 92 5 102 bp U C WW_cis 0.8307 -5 92 5 103 bp U A <> 0.7692 -5 93 5 94 bp G C >> 0.9830 -5 93 5 101 bp G C WW_cis 0.8731 -5 93 5 102 bp G C <> 0.9716 -6 93 6 94 bp A A >> 0.9690 -6 94 6 95 bp A A >> 0.9801 -5 95 5 96 bp C U >> 0.9603 -6 95 6 96 bp A G >> 0.9752 -6 96 6 97 bp G A >> 0.9752 -6 97 6 98 bp A G >> 0.9778 -5 98 5 99 bp U U >> 0.9685 -6 98 6 99 bp G A >> 0.9823 -5 99 5 100 bp U A >> 0.9534 -6 99 6 100 bp A U >> 0.9638 -5 100 5 101 bp A C >> 0.8726 -6 100 6 101 bp U U >> 0.9632 -5 101 5 102 bp C C >> 0.7208 -6 101 6 102 bp U U >> 0.9661 -5 102 5 103 bp C A >> 0.8540 -6 102 6 103 bp U A >> 0.9563 -5 103 5 104 bp A G >> 0.9528 -6 103 6 104 bp A U >> 0.9724 -5 104 5 105 bp G A >> 0.9756 -5 105 5 106 bp A A >> 0.9626 -5 106 5 107 bp A C >> 0.9823 -5 107 5 108 bp C C >> 0.9261 -5 108 5 109 bp C A >> 0.8540 -5 109 5 110 bp A U >> 0.9351 -5 110 5 111 bp U C >> 0.9583 -5 112 5 113 bp C G >> 0.8854 -5 113 5 114 bp G G >> 0.9448 -5 114 5 115 bp G G >> 0.9761 -5 115 5 116 bp G U >> 0.9876 -5 116 5 117 bp U G >> 0.9073 -5 117 5 118 bp G U >> 0.9887 -5 118 5 119 bp U U >> 0.9807 -5 119 5 120 bp U G >> 0.9596 -5 120 5 121 bp G U >> 0.9768 -5 122 5 123 bp C U >> 0.9474 -5 123 5 124 bp U C >> 0.9761 -5 124 5 125 bp C C >> 0.9611 -5 126 5 127 bp A U >> 0.9473 -5 130 5 131 bp A A >> 0.8178 -5 131 5 132 bp A A >> 0.9123 -5 134 5 135 bp A G >> 0.9799 -5 135 5 136 bp G G >> 0.9838 -5 136 5 137 bp G U >> 0.9887 -5 137 5 138 bp U A >> 0.9322 -5 138 5 139 bp A A >> 0.9665 -5 139 5 140 bp A A >> 0.9538 -5 140 5 141 bp A G >> 0.9713 -5 141 5 142 bp G C >> 0.9402 -5 142 5 143 bp C U >> 0.9480 -5 143 5 144 bp U G >> 0.8141 -5 144 5 145 bp G U >> 0.9542 -5EXON_Cs -------------------------------------------------------------- -# problem with -16 -15 etc -U2_Cs ----------------------------------------------------------------- -chains: 2 1 49 -2 1 2 2 bp A C >> 0.9685 -2 2 2 3 bp C G >> 0.6486 -2 3 2 4 bp G A >> 0.9760 -2 4 2 5 bp A A >> 0.9671 -2 5 2 6 bp A U >> 0.9577 -2 6 2 7 bp U C >> 0.9603 -2 7 2 8 bp C U >> 0.9393 -2 8 2 9 bp U C >> 0.9674 -2 11 2 12 bp U U >> 0.9781 -2 12 2 13 bp U G >> 0.8789 -2 13 2 14 bp G C >> 0.9886 -2 21 2 22 bp G C >> 0.9828 -2 26 2 27 bp G A >> 0.9910 -2 27 2 28 bp A U >> 0.9730 -2 28 2 29 bp U C >> 0.9922 -2 32 2 33 bp G U >> 0.9757 -2 33 2 34 bp U G >> 0.8871 -2 34 2 35 bp G U >> 0.9655 -2 35 2 36 bp U A >> 0.9693 -2 36 2 37 bp A G >> 0.9900 -2 37 2 38 bp G U >> 0.9854 -2 38 2 39 bp U A >> 0.9462 -2 39 2 40 bp A U >> 0.9853 -2 41 2 42 bp C U >> 0.9437 -2 42 2 43 bp U G >> 0.8928 -2 43 2 44 bp G U >> 0.9778 -2 44 2 45 bp U U >> 0.9274 -2 45 2 46 bp U C >> 0.9559 -2 46 2 47 bp C U >> 0.9151 -2 47 2 48 bp U U >> 0.8342 -2 48 2 49 bp U U >> 0.7527 -U5_Cs ----------------------------------------------------------------- -chains: 5 4 173 -5 4 5 144 bp C G WW_cis 0.9570 -5 5 5 6 bp A G >> 0.9728 -5 5 5 143 bp A U WW_cis 0.9424 -5 5 5 144 bp A G <> 0.9657 -5 6 5 7 bp G C >> 0.9777 -5 6 5 142 bp G C WW_cis 0.9191 -5 7 5 8 bp C U >> 0.9686 -5 7 5 141 bp C G WW_cis 0.9172 -5 8 5 9 bp U U >> 0.9754 -5 8 5 140 bp U A WW_cis 0.9283 -5 9 5 10 bp U U >> 0.9522 -5 9 5 139 bp U A WW_cis 0.9464 -5 10 5 138 bp U A WW_cis 0.9200 -5 10 5 139 bp U A <> 0.8373 -5 11 5 12 bp A C >> 0.9711 -5 11 5 137 bp A U WW_cis 0.9635 -5 11 5 138 bp A A <> 0.9180 -5 12 5 136 bp C G WW_cis 0.9210 -5 13 5 14 bp A G >> 0.9682 -5 13 5 135 bp A G WW_cis 0.7654 -5 13 5 136 bp A G <> 0.6456 -5 14 5 15 bp G A >> 0.9496 -5 14 5 134 bp G A WW_cis 0.7658 -5 15 5 134 bp A A <> 0.9192 -5 18 5 19 bp A A >> 0.9402 -5 19 5 20 bp A U >> 0.9156 -5 20 5 132 bp U A WW_cis 0.9229 -5 20 5 21 bp U G >> 0.7962 -5 21 5 131 bp G A WW_cis 0.7154 -5 21 5 22 bp G G >> 0.9559 -5 21 5 132 bp G A <> 0.8480 -5 22 5 130 bp G A WW_cis 0.6564 -5 24 5 26 bp G A <> 0.9476 -5 26 5 129 bp A G >> 0.8514 -5 27 5 129 bp G G >< 0.7597 -5 28 5 29 bp G G >> 0.9723 -5 28 5 125 bp G C WW_cis 0.9265 -5 28 5 126 bp G A <> 0.9861 -5 29 5 124 bp G C WW_cis 0.9165 -5 29 5 30 bp G A >> 0.9672 -5 30 5 31 bp A G >> 0.9879 -5 30 5 123 bp A U WW_cis 0.9376 -5 31 5 32 bp G G >> 0.9774 -5 31 5 122 bp G C WW_cis 0.8971 -5 31 5 123 bp G U <> 0.6646 -5 32 5 34 bp G C >> 0.9782 -5 32 5 121 bp G U WW_cis 0.8222 -5 34 5 35 bp C A >> 0.7844 -5 34 5 120 bp C G WW_cis 0.9157 -5 35 5 36 bp A A >> 0.9735 -5 35 5 120 bp A G <> 0.9731 -5 35 5 119 bp A U WW_cis 0.9630 -5 36 5 37 bp A C >> 0.9755 -5 36 5 118 bp A U WW_cis 0.9646 -5 37 5 38 bp C A >> 0.7370 -5 37 5 117 bp C G WW_cis 0.9084 -5 38 5 116 bp A U WW_cis 0.9426 -5 38 5 39 bp A U >> 0.9628 -5 38 5 117 bp A G <> 0.9690 -5 39 5 40 bp U C >> 0.9560 -5 39 5 115 bp U G WW_cis 0.8462 -5 40 5 114 bp C G WW_cis 0.9139 -5 41 5 78 bp A A >< 0.9756 -5 42 5 45 bp A A >> 0.9053 -5 42 5 78 bp A A HW_tran 0.7206 -5 44 5 45 bp A A << 0.9649 -5 44 5 75 bp A A HH_tran 0.6916 -5 44 5 77 bp A A HW_tran 0.6517 -5 46 5 69 bp C G WW_cis 0.9082 -5 47 5 68 bp U A WW_cis 0.9536 -5 47 5 69 bp U G <> 0.7427 -5 47 5 48 bp U G >> 0.8610 -5 48 5 49 bp G U >> 0.9788 -5 48 5 67 bp G U WW_cis 0.7357 -5 48 5 68 bp G A <> 0.9676 -5 49 5 66 bp U A WW_cis 0.9346 -5 49 5 50 bp U G >> 0.7635 -5 50 5 65 bp G U WW_cis 0.8432 -5 50 5 66 bp G A <> 0.9625 -5 50 5 51 bp G G >> 0.9822 -5 51 5 64 bp G C WW_cis 0.9110 -5 51 5 52 bp G G >> 0.9698 -5 52 5 53 bp G C >> 0.9837 -5 52 5 63 bp G C WW_cis 0.9191 -5 53 5 62 bp C G WW_cis 0.9334 -5 62 5 63 bp G C >> 0.9819 -5 63 5 64 bp C C >> 0.9528 -5 64 5 65 bp C U >> 0.9626 -5 65 5 66 bp U A >> 0.8431 -5 66 5 67 bp A U >> 0.9705 -5 67 5 68 bp U A >> 0.7283 -5 68 5 69 bp A G >> 0.9845 -5 69 5 70 bp G A >> 0.9621 -5 71 5 72 bp A C >> 0.9833 -5 72 5 73 bp C U >> 0.9083 -5 73 5 74 bp U U >> 0.9246 -5 75 5 77 bp A A <> 0.9418 -5 77 5 78 bp A A >> 0.7359 -5 79 5 113 bp C G WW_cis 0.8617 -5 79 5 114 bp C G <> 0.9597 -5 80 5 82 bp G A >> 0.9182 -5 80 5 112 bp G C WW_cis 0.9225 -5 80 5 113 bp G G <> 0.9614 -5 82 5 83 bp A C >> 0.9687 -5 84 5 85 bp A U >> 0.9783 -5 84 5 110 bp A U WW_cis 0.9343 -5 85 5 109 bp U A WW_cis 0.9147 -5 86 5 87 bp G G >> 0.9765 -5 86 5 109 bp G A <> 0.9740 -5 86 5 108 bp G C WW_cis 0.9270 -5 87 5 88 bp G U >> 0.9775 -5 87 5 107 bp G C WW_cis 0.9096 -5 88 5 89 bp U U >> 0.9708 -5 88 5 106 bp U A WW_cis 0.9418 -5 89 5 90 bp U C >> 0.9707 -5 89 5 105 bp U A WW_cis 0.9219 -5 90 5 91 bp C U >> 0.9502 -5 90 5 104 bp C G WW_cis 0.9240 -5 91 5 92 bp U U >> 0.9531 -5 91 5 103 bp U A WW_cis 0.9366 -5 92 5 102 bp U C WW_cis 0.8307 -5 92 5 93 bp U G >> 0.9113 -5 92 5 103 bp U A <> 0.7692 -5 93 5 94 bp G C >> 0.9830 -5 93 5 101 bp G C WW_cis 0.8731 -5 93 5 102 bp G C <> 0.9716 -5 95 5 96 bp C U >> 0.9603 -5 98 5 99 bp U U >> 0.9685 -5 99 5 100 bp U A >> 0.9534 -5 100 5 101 bp A C >> 0.8726 -5 101 5 102 bp C C >> 0.7208 -5 102 5 103 bp C A >> 0.8540 -5 103 5 104 bp A G >> 0.9528 -5 104 5 105 bp G A >> 0.9756 -5 105 5 106 bp A A >> 0.9626 -5 106 5 107 bp A C >> 0.9823 -5 107 5 108 bp C C >> 0.9261 -5 108 5 109 bp C A >> 0.8540 -5 109 5 110 bp A U >> 0.9351 -5 110 5 111 bp U C >> 0.9583 -5 112 5 113 bp C G >> 0.8854 -5 113 5 114 bp G G >> 0.9448 -5 114 5 115 bp G G >> 0.9761 -5 115 5 116 bp G U >> 0.9876 -5 116 5 117 bp U G >> 0.9073 -5 117 5 118 bp G U >> 0.9887 -5 118 5 119 bp U U >> 0.9807 -5 119 5 120 bp U G >> 0.9596 -5 120 5 121 bp G U >> 0.9768 -5 122 5 123 bp C U >> 0.9474 -5 123 5 124 bp U C >> 0.9761 -5 124 5 125 bp C C >> 0.9611 -5 126 5 127 bp A U >> 0.9473 -5 130 5 131 bp A A >> 0.8178 -5 131 5 132 bp A A >> 0.9123 -5 134 5 135 bp A G >> 0.9799 -5 135 5 136 bp G G >> 0.9838 -5 136 5 137 bp G U >> 0.9887 -5 137 5 138 bp U A >> 0.9322 -5 138 5 139 bp A A >> 0.9665 -5 139 5 140 bp A A >> 0.9538 -5 140 5 141 bp A G >> 0.9713 -5 141 5 142 bp G C >> 0.9402 -5 142 5 143 bp C U >> 0.9480 -5 143 5 144 bp U G >> 0.8141 -5 144 5 145 bp G U >> 0.9542 -U6_Cs ----------------------------------------------------------------- -chains: 6 1 1005 -6 1 6 2 bp G U >> 0.9838 -6 1 6 25 bp G C WW_cis 0.9260 -6 2 6 24 bp U A WW_cis 0.9433 -6 2 6 3 bp U U >> 0.9536 -6 3 6 23 bp U G WW_cis 0.8741 -6 4 6 22 bp C G WW_cis 0.9119 -6 5 6 21 bp G U WW_cis 0.8536 -6 5 6 22 bp G G <> 0.9761 -6 5 6 6 bp G C >> 0.9441 -6 6 6 20 bp C G WW_cis 0.9149 -6 7 6 20 bp G G <> 0.9695 -6 7 6 8 bp G A >> 0.9746 -6 7 6 19 bp G C WW_cis 0.9142 -6 8 6 9 bp A A >> 0.9616 -6 8 6 18 bp A U WW_cis 0.9406 -6 9 6 10 bp A G >> 0.9437 -6 9 6 17 bp A U WW_cis 0.9353 -6 9 6 18 bp A U <> 0.8006 -6 10 6 16 bp G C WW_cis 0.9404 -6 10 6 17 bp G U <> 0.9609 -6 18 6 19 bp U C >> 0.9306 -6 19 6 20 bp C G >> 0.7807 -6 20 6 21 bp G U >> 0.9841 -6 22 6 23 bp G G >> 0.9903 -6 23 6 24 bp G A >> 0.9779 -6 24 6 25 bp A C >> 0.9857 -6 25 6 26 bp C A >> 0.9289 -6 26 6 27 bp A U >> 0.8653 -6 29 6 30 bp U G >> 0.9467 -6 30 6 31 bp G G >> 0.9092 -6 41 6 42 bp A A >> 0.9532 -6 42 6 43 bp A C >> 0.9774 -6 43 6 44 bp C A >> 0.7855 -6 44 6 45 bp A A >> 0.9593 -6 45 6 46 bp A U >> 0.9502 -6 46 6 47 bp U A >> 0.9632 -6 47 6 48 bp A C >> 0.9829 -6 48 6 49 bp C A >> 0.8410 -6 49 6 50 bp A G >> 0.9799 -6 52 6 80 bp G U <> 0.9591 -6 52 6 53 bp G A >> 0.9407 -6 52 6 60 bp G G WH_tran 0.8005 -6 53 6 59 bp A A WH_tran 0.7953 -6 55 6 56 bp G A >> 0.9770 -6 56 6 57 bp A U >> 0.9860 -6 57 6 58 bp U C >> 0.9848 -6 59 6 60 bp A G >> 0.9703 -6 60 6 61 bp G C >> 0.9865 -6 61 6 80 bp C U HS_cis 0.8383 -6 61 6 62 bp C A >> 0.9046 -6 62 6 63 bp A G >> 0.9446 -6 63 6 84 bp G C WW_cis 0.8846 -6 63 6 64 bp G U >> 0.9826 -6 64 6 65 bp U U >> 0.9812 -6 64 6 83 bp U A WW_cis 0.9243 -6 65 6 82 bp U A WW_cis 0.9350 -6 67 6 82 bp C A <> 0.9293 -6 67 6 81 bp C G WW_cis 0.9291 -6 67 6 68 bp C C >> 0.8865 -6 68 6 78 bp C G WW_cis 0.9112 -6 68 6 81 bp C G <> 0.9077 -6 69 6 77 bp C G WW_cis 0.9250 -6 69 6 78 bp C G <> 0.6694 -6 69 6 70 bp C U >> 0.9225 -6 70 6 76 bp U A WW_cis 0.9183 -6 70 6 77 bp U G <> 0.6981 -6 70 6 71 bp U G >> 0.9799 -6 71 6 75 bp G A SW_tran 0.8324 -6 72 6 73 bp C A >> 0.9683 -6 73 6 75 bp A A >< 0.9765 -6 75 6 76 bp A A <> 0.9515 -6 76 6 77 bp A G >> 0.9695 -6 77 6 78 bp G G >> 0.9704 -6 78 6 81 bp G G >> 0.9497 -6 81 6 82 bp G A >> 0.9625 -6 82 6 83 bp A A >> 0.9640 -6 83 6 84 bp A C >> 0.9745 -6 86 6 87 bp G U >> 0.9929 -6 87 6 88 bp U U >> 0.9880 -6 93 6 94 bp A A >> 0.9690 -6 94 6 95 bp A A >> 0.9801 -6 95 6 96 bp A G >> 0.9752 -6 96 6 97 bp G A >> 0.9752 -6 97 6 98 bp A G >> 0.9778 -6 98 6 99 bp G A >> 0.9823 -6 99 6 100 bp A U >> 0.9638 -6 100 6 101 bp U U >> 0.9632 -6 101 6 102 bp U U >> 0.9661 -6 102 6 103 bp U A >> 0.9563 -6 103 6 104 bp A U >> 0.9724 \ No newline at end of file diff --git a/rna_tools/tools/splix/db/inters_of_A25.csv b/rna_tools/tools/splix/db/inters_of_A25.csv deleted file mode 100644 index f989a6b10..000000000 --- a/rna_tools/tools/splix/db/inters_of_A25.csv +++ /dev/null @@ -1,18 +0,0 @@ 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zL1=Ad#&gGNn29;pidj2p4d@)RN?AAjxW9!+Za-Jec*JAQL`eGm;XG=0G`v5G{YfVibp|&Y zzoh|L`#{;o*utc&8$^6%t#7Q>P&Q`opC}tM0qe|3Qqd(nTOGdrkrk4mRtqbFoxb&O z!vcRVFhzC~E-iDKnl*8Bn8aAWan~UK<^x4x>+!%89PqY15HP{-JK^`<6BKUt?=QzF zsmsL{Zk9sPO-T)-i+iI~Ub{HF&}rqE^}$es5A>~IVodHwI`LTM_;{zLVe=jy!e1{G zIpi2zOo)lOx-T}mQ29=PYKTbIQk6~Kbm;ne{2Yt;lPZDvw@VoxX&+QtFhj}yyqQ$M zB^8$q;H!jp|LNi5I+G)@sK`3$J`re>$q`krH2rlPOSvn&OJi>)DH zSKoq~-avd6ZPF(mP?oyiM1H*JgL`E` z;Co;Fcf;Y%y7sF+Efh6k)poa0t2ePj-#UZV=ZiUm26`0)fB0yJgpgFy-(rxVGYb}o zT=fC%YtyQe2}g0UtT}^~PrWGW(p*^Tbya zYl9zEQ)jc&ni<*FVJD~HGJbB=Q`g?#&b&uXW=fZrSW!88G3Z?FpAQq)O1>DnPNx*g ziaz%oTD#h2HqZzyfmC8>Gozxmv4v~bHnTc~{`uohoiXkHbu(Vv?Ve^81$VH40sR|rmcau58Mt=r4 ztcutYOq=?~pQmLAs|D#ago0`r{vH*nTyXCThmFuDOLUNT3mm8w*ldI5Y4mb6W1w&j zvnt2_J};4;Bh+%Djr;dY^Mlw&Nqyo)j^F3~pZ;J;O;x65r{Cw56o&qLU1=Nn*W!sG mOc)`^|9?yV*KbMn`lhvj)G)#M>P`mucSQH74oUk|_ [0,5] - c15 = Allele('cwc15', [+1,+1]) - _302 = Allele('prp16-302', [+1,0]) - bsc = Allele('bsc', [-1, -1]) - bsg = Allele('bsg', [0,-1]) - dc15 = c15.delete() - - print(dc15 + _302) - print(c15 + bsc) - print(c15 + bsg) - - for a in gc.get_objects(): # [c15, _302]: - if isinstance(a, Allele): - print(a) diff --git a/rna_tools/tools/splix/splix_trx.py b/rna_tools/tools/splix/splix_trx.py deleted file mode 100755 index 182ff9c57..000000000 --- a/rna_tools/tools/splix/splix_trx.py +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -""" - -""" -from __future__ import print_function - -import argparse -import glob - -def get_parser(): - parser = argparse.ArgumentParser( - description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) - - #parser.add_argument('-', "--", help="", default="") - - parser.add_argument("-v", "--verbose", - action="store_true", help="be verbose") - parser.add_argument("-d", "--debug", - action="store_true", help="be verbose") - parser.add_argument("seq", help="")#, nargs='+') - parser.add_argument("--edge", help="e.g., cWW_cHS") - return parser - - -def hr(t): - l = len(t) - half = int(l/2) - print('-' * (40 - half) + ' ' + t + ' ' + '-' * (40 - half)) - -def fopen(filename, verbose=0): - import subprocess - cmd = 'mdfind -name "' + filename + '"' - if verbose: - print(cmd) - out = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True).stdout.read().decode() - first_hit = out.split('\n')[0] - return open(first_hit) - - -if __name__ == '__main__': - parser = get_parser() - args = parser.parse_args() - edge = args.edge - seq = args.seq - - import pandas as pd - df = pd.read_csv("../triples/triple-db.csv") - triple = edge + '_' + seq - - x = df[df['triple'] == triple] - r3 = fopen('Triple_' + edge + '_' + seq + '_rpr.pdb.3dcnn.csv').read() - print(triple + ':', round(int(x['instances']) / 18, 2), r3.split(',')[1].strip()) - - - - - - diff --git a/rna_tools/tools/splix/test.sh b/rna_tools/tools/splix/test.sh deleted file mode 100755 index 67c1e4b39..000000000 --- a/rna_tools/tools/splix/test.sh +++ /dev/null @@ -1,9 +0,0 @@ -set -x -splix_trx.py GCU --edge cWW_cHS #; echo 0 # bad -# H -#splix_trx.py UAU -# -splix_trx.py GCA --edge cWW_cHS #; echo 0 # bad -splix_trx.py UAU --edge cWW_cHS #; echo 1 # good -splix_trx.py UAU --edge cWW_cHW #; echo 1 # good - #GCU diff --git a/rna_tools/tools/splix/yeast-in-monte-carlo.py b/rna_tools/tools/splix/yeast-in-monte-carlo.py deleted file mode 100644 index 56f9d2da6..000000000 --- a/rna_tools/tools/splix/yeast-in-monte-carlo.py +++ /dev/null @@ -1,51 +0,0 @@ -import random -import pandas as pd - -values = [x / 10.0 for x in range(-10, 11)] -#print(values) -all = [] -def err(g, c): - return abs(g - c) # -2 - -def log(t, c15, e): - tx = '' - if t[0] < 0: - tx += str(t[3]) + ' inhibits splicing by ' + str(t[0]) + ' and '#.rjust(10) - if t[0] > 0: - tx += str(t[3]) + ' promote splicing by ' + str(t[0]) + ' and '#.rjust(12) - if t[0] == 0: - tx += str(t[3]) + ' does nothing to '#.rjust(10) - - if c15 < 0: - tx += 'cwc15 inhibits splicing by ' + str(c15) - if c15 > 0: - tx += 'cwc15 promote splicing by ' + str(c15) - if c15 == 0: - tx += 'cwc15 does nothing to ' - tx += ' with error ' + str(round(e, 2)) - print(tx) - - -for i in range(0, 100000000): - done = False - ggg = (random.choice(values), 0, -2, 'ggg') - c15 = random.choice(values) - triples = [ggg] - errg = 0 - for t in triples: - c = t[0] + c15 # -1 + 1 = 0 - g = t[1] - e1 = err(g, c) - - c2 = t[0] - c15 # -1 - +1 = -2 - g2 = t[2] - e2 = err(g2, c2) - # print(t[3], t[0], c15, e1, e2) - errg += e1 + e2 - - log(t, c15, e1 + e2) - - if errg == 0: - print('OK!') - log(t, c15, errg) - break