├── .gitignore ├── D3EMergeOutput.py ├── README.md ├── D3EMakeContol.py ├── D3EAnalysis.py ├── D3ESplitData.py ├── D3EWeb.py ├── example.txt ├── D3ECmd.py ├── D3EUtil.py └── LICENSE.md /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | .DS_store 3 | -------------------------------------------------------------------------------- /D3EMergeOutput.py: -------------------------------------------------------------------------------- 1 | ''' 2 | 3 | D3E-Merge-Output 4 | Discrete Distributional Differential Expression Command Line Tool 5 | 6 | Author: Mihails Delmans (md656@cam.ac.uk) 7 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 8 | Version: 1.0 9 | 10 | Tested with: 11 | scipy 0.15.1 12 | numpy 1.8.0rc1 13 | sympy.mpmath 0.18 14 | 15 | ''' 16 | 17 | import sys 18 | from os import listdir 19 | 20 | inDir = sys.argv[1] 21 | outFileName = sys.argv[2] 22 | label1 = sys.argv[3] 23 | label2 = sys.argv[4] 24 | 25 | outputFile = open(outFileName, 'w') 26 | hr = False 27 | 28 | for fileName in listdir(inDir): 29 | if fileName.startswith(label1+'_'+label2): 30 | inFile = open(inDir + fileName,'r') 31 | h = inFile.readline() 32 | 33 | if not hr: 34 | outputFile.write(h) 35 | hr = True 36 | 37 | inFile.readline() 38 | 39 | for line in inFile: 40 | if line.strip(): 41 | outputFile.write(line) 42 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # D³E: Discrete Distributional Differential Expression 2 | 3 | ## About 4 | D³E is a tool for identifying differentially-expressed genes, based on single-cell RNA-seq data. D³E consists of two modules: one for identifying differentially expressed (DE) genes, and one for fitting the parameters of a Poisson-Beta distribution. A web-version which can be used for small samples can be accessed at http://www.sanger.ac.uk/sanger/GeneRegulation_D3E/ 5 | 6 | ## Files 7 | - **D3EUtil.py** : a collection of methods for running the D³E analysis 8 | - **D3ECmd.py** : an actual D³E tool (requires **D3EUtil.py** for execution) 9 | - **D3EWed.py** : a light version of D³E, for running as a web-service (requires **D3EUtil.py** for execution) 10 | - **D3EMakeControl** : a script for making a control file for the analysis 11 | - **D3EAnalyse** : a script for filtering DE genes based on the result of control file analysis 12 | 13 | ## Getting Started 14 | 15 | Please visit our Wiki pages for User Guide and Example. 16 | -------------------------------------------------------------------------------- /D3EMakeContol.py: -------------------------------------------------------------------------------- 1 | ''' 2 | 3 | D3E-Cmd 4 | Discrete Distributional Differential Expression Command Line Tool 5 | 6 | Author: Mihails Delmans (md656@cam.ac.uk) 7 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 8 | Version: 1.0 9 | 10 | Tested with: 11 | scipy 0.15.1 12 | numpy 1.8.0rc1 13 | sympy.mpmath 0.18 14 | 15 | Copyright 2015 Mihails Delmans, Martin Hemberg 16 | 17 | This file is part of D3E. 18 | 19 | D3E is free software: you can redistribute it and/or modify 20 | it under the terms of the GNU General Public License as published by 21 | the Free Software Foundation, either version 3 of the License, or 22 | (at your option) any later version. 23 | 24 | D3E is distributed in the hope that it will be useful, 25 | but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | GNU General Public License for more details. 28 | 29 | You should have received a copy of the GNU General Public License 30 | along with D3E. If not, see . 31 | 32 | ''' 33 | 34 | import sys 35 | from D3EUtil import readData 36 | 37 | inFileName = sys.argv[1] 38 | outFileName = sys.argv[2] 39 | label = sys.argv[3] 40 | 41 | inFile = open(inFileName) 42 | outFileName = open(outFileName,'w') 43 | 44 | p1, p2, ids, lineStatus = readData(inFile, label, label, normalise=False, removeZeros=False, useSpikeIns = False, verbose = True) 45 | 46 | n = len(p1[0]) / 2 47 | 48 | outFileName.write('GeneID\t' + '\t'.join( [ label+'_1' ] * n + [label+'_2'] * (len(p1[0])-n) ) + '\n') 49 | 50 | for idx, p in zip(ids, p1): 51 | outFileName.write(idx + '\t' + '\t'.join( str(int(x)) for x in p ) + '\n') 52 | -------------------------------------------------------------------------------- /D3EAnalysis.py: -------------------------------------------------------------------------------- 1 | ''' 2 | 3 | D3E-Cmd 4 | Discrete Distributional Differential Expression Command Line Tool 5 | 6 | Author: Mihails Delmans (md656@cam.ac.uk) 7 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 8 | Version: 1.0 9 | 10 | Tested with: 11 | scipy 0.15.1 12 | numpy 1.8.0rc1 13 | sympy.mpmath 0.18 14 | 15 | Copyright 2015 Mihails Delmans, Martin Hemberg 16 | 17 | This file is part of D3E. 18 | 19 | D3E is free software: you can redistribute it and/or modify 20 | it under the terms of the GNU General Public License as published by 21 | the Free Software Foundation, either version 3 of the License, or 22 | (at your option) any later version. 23 | 24 | D3E is distributed in the hope that it will be useful, 25 | but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | GNU General Public License for more details. 28 | 29 | You should have received a copy of the GNU General Public License 30 | along with D3E. If not, see . 31 | 32 | ''' 33 | 34 | import sys 35 | 36 | tFileName = sys.argv[1] 37 | cFileName = sys.argv[2] 38 | oFileName = sys.argv[3] 39 | k = float(sys.argv[4]) 40 | 41 | 42 | cFile = open(cFileName) 43 | cFile.readline() 44 | cFile.readline() 45 | 46 | pMin = float('Inf') 47 | 48 | for line in cFile: 49 | p = float(line.split()[21]) 50 | if p < pMin: 51 | pMin = p 52 | 53 | tFile = open(tFileName) 54 | oFile = open(oFileName,'w') 55 | 56 | h = tFile.readline() 57 | tFile.readline() 58 | 59 | oFile.write(h + '\n') 60 | 61 | for line in tFile: 62 | tabs = line.split() 63 | p = float(tabs[21]) 64 | if p < pMin * k: 65 | oFile.write(line) 66 | -------------------------------------------------------------------------------- /D3ESplitData.py: -------------------------------------------------------------------------------- 1 | ''' 2 | D3E-Split-Data 3 | Discrete Distributional Differential Expression Command Line Tool 4 | 5 | Author: Mihails Delmans (md656@cam.ac.uk) 6 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 7 | Version: 1.0 8 | 9 | Tested with: 10 | scipy 0.13.0b1 11 | numpy 1.8.0rc1 12 | sympy.mpmath 0.18 13 | 14 | Copyright 2015 Mihails Delmans, Martin Hemberg 15 | 16 | This file is part of D3E. 17 | 18 | D3E is free software: you can redistribute it and/or modify 19 | it under the terms of the GNU General Public License as published by 20 | the Free Software Foundation, either version 3 of the License, or 21 | (at your option) any later version. 22 | 23 | D3E is distributed in the hope that it will be useful, 24 | but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | GNU General Public License for more details. 27 | 28 | You should have received a copy of the GNU General Public License 29 | along with D3E. If not, see . 30 | 31 | ''' 32 | 33 | from D3EUtil import readData 34 | import sys 35 | 36 | inFileName = sys.argv[1] 37 | label1 = sys.argv[2] 38 | label2 =sys.argv[3] 39 | outDir = sys.argv[4] 40 | n = int(sys.argv[5]) 41 | 42 | inFile = open(inFileName) 43 | 44 | data1, data2, ids, lineStatus = readData(inFile, label1, label2, normalise = True) 45 | 46 | i = 0 47 | 48 | for p1, p2, idx in zip(data1, data2, ids): 49 | if i % n == 0: 50 | ouputFile = open( outDir + label1 + '_' + label2 + '_' + str(i/n) + '.txt', 'w' ) 51 | ouputFile.write('GeneID\t' + '\t'.join( [label1] * len(data1[0]) + [label2] * len(data2[0]) ) + '\n' ) 52 | ouputFile.write('\t'.join ( [idx] + [str(x) for x in p1+p2] ) + '\n') 53 | i = i + 1 -------------------------------------------------------------------------------- /D3EWeb.py: -------------------------------------------------------------------------------- 1 | ''' 2 | D3E-Web 3 | Discrete Distributional Differential Expression Web Tool 4 | 5 | Author: Mihails Delmans (md656@cam.ac.uk) 6 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 7 | Version: 1.0 8 | 9 | Tested with: 10 | scipy 0.15.1 11 | numpy 1.8.0rc1 12 | sympy.mpmath 0.18 13 | 14 | Copyright 2015 Mihails Delmans, Martin Hemberg 15 | 16 | This file is part of D3E. 17 | 18 | D3E is free software: you can redistribute it and/or modify 19 | it under the terms of the GNU General Public License as published by 20 | the Free Software Foundation, either version 3 of the License, or 21 | (at your option) any later version. 22 | 23 | D3E is distributed in the hope that it will be useful, 24 | but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | GNU General Public License for more details. 27 | 28 | You should have received a copy of the GNU General Public License 29 | along with D3E. If not, see . 30 | 31 | ''' 32 | 33 | from __future__ import division 34 | from D3EUtil import readData, getParamsMoments, cramerVonMises, logStatus, goodnessOfFit 35 | from D3EUtil import Params, BioParams, Status 36 | 37 | from numpy import log2, mean 38 | from scipy.stats import variation 39 | 40 | import StringIO 41 | import json 42 | import sys 43 | import fileinput 44 | 45 | def getBioParams(params): 46 | alpha = params.alpha 47 | beta = params.beta 48 | gamma = params.gamma 49 | 50 | return BioParams( gamma / beta, alpha, alpha * beta / (alpha + beta) ) 51 | 52 | inputString = fileinput.input()[0].rstrip('\n') 53 | 54 | inputJSON = json.loads(inputString) 55 | inputFile = StringIO.StringIO(inputJSON['input']); 56 | label1 = inputJSON['label1'] 57 | label2 = inputJSON['label2'] 58 | normalise = int(inputJSON['normalise']) 59 | removeZeros = inputJSON['removeZeros'] 60 | useSpikeIns = inputJSON['useSpikeIns'] 61 | 62 | data1, data2, ids, lineStatus = readData(inputFile, label1, label2, normalise, removeZeros, useSpikeIns) 63 | 64 | errors = [] 65 | rows = [] 66 | cols = [] 67 | 68 | for status in lineStatus: 69 | if status.code == 1: 70 | errors.append( {'geneId': status.idx, 'message': 'Warning: ' + status.message} ) 71 | elif status.code == 2: 72 | errors.append( {'geneId': status.idx, 'message': 'Error: ' + status.message} ) 73 | 74 | 75 | rowKeys = ["geneId"] 76 | rowKeys.extend( ["col" + str(i) for i in range(1,21)] ) 77 | 78 | labels = ["Gene ID", "a1", "b1", "g1", "a2", "b2", "g2", 79 | "s1", "f1", "d1", "s2", "f2", "d2", 80 | "Rs", "Rf", "Rd", "mu1", "mu2", "cv1", "cv2", "p"] 81 | 82 | for key, label in zip(rowKeys, labels): 83 | cols.append( {"key" : key, "label" : label} ) 84 | 85 | 86 | 87 | for p1,p2,idx in zip(data1, data2, ids): 88 | 89 | difference = cramerVonMises(p1,p2) 90 | 91 | if difference == -1: 92 | errors.append({"geneId" : idx, "type" : "Warning", 93 | "message" : "Could not estimate Cramer-von Mises statistic. Further analysis aborted." }) 94 | continue 95 | 96 | params1 = getParamsMoments(p1) 97 | params2 = getParamsMoments(p2) 98 | 99 | if (params1.alpha <= 0 or params2.alpha <= 0 or params1.beta <= 0 or params2.beta <= 0 or 100 | params1.gamma <= 0 or params2.gamma <= 0): 101 | errors.append({"geneId" : idx, "type" : "Warning", 102 | "message" : "Could not estimate parameters for atleast one cell type." }) 103 | else: 104 | bioParams1 = getBioParams(params1) 105 | bioParams2 = getBioParams(params2) 106 | 107 | rowString = ('{0:s}\t{1:2.2f}\t{2:2.2f}\t{3:2.2f}\t{4:2.2f}\t{5:2.2f}\t{6:2.2f}\t' 108 | '{7:2.2f}\t{8:2.2f}\t{9:2.2f}\t{10:2.2f}\t{11:2.2f}\t{12:2.2f}\t' 109 | '{13:2.2f}\t{14:2.2f}\t{15:2.2f}\t{16:2.2f}\t{17:2.2f}\t{18:2.2f}\t{19:2.2f}\t' 110 | '{20:2.2e}\n').format(idx, 111 | params1.alpha, params1.beta, params1.gamma, 112 | params2.alpha, params2.beta, params2.gamma, 113 | bioParams1.size, bioParams1.freq, bioParams1.duty, 114 | bioParams2.size, bioParams2.freq, bioParams2.duty, 115 | log2( bioParams1.size / bioParams2.size), 116 | log2( bioParams1.freq / bioParams2.freq), 117 | log2( bioParams1.duty / bioParams2.duty), 118 | mean(p1), mean(p2), variation(p1), variation(p2), 119 | difference) 120 | rowVals = rowString.split('\t') 121 | 122 | rows.append( dict( zip( rowKeys, rowVals ) ) ) 123 | 124 | 125 | jsonOutput = { "rows" : rows, "columns" : cols, "errors" : errors } 126 | print json.dumps(jsonOutput) 127 | 128 | -------------------------------------------------------------------------------- /example.txt: -------------------------------------------------------------------------------- 1 | GeneID G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M G2M 2 | ENSMUSG00000000088 317 419 396 39 466 159 343 280 506 124 57 420 142 30 246 316 227 73 34 71 124 257 426 84 52 78 27 87 25 131 11 13 12 126 59 204 30 49 55 15 62 106 79 70 294 21 61 27 100 24 463 275 256 176 553 349 1044 295 334 488 700 652 350 188 220 350 360 1570 594 836 481 395 1479 165 158 190 251 186 149 157 229 517 376 349 143 157 252 47 168 99 166 101 93 560 300 132 346 403 125 136 3 | ENSMUSG00000000740 404 327 334 47 336 132 690 592 584 234 568 327 546 260 290 455 365 264 198 225 258 556 1097 265 205 272 120 163 183 338 75 92 143 324 262 813 266 48 273 48 436 342 351 125 330 136 94 72 442 98 920 577 508 155 1467 744 2097 1209 868 858 728 1033 445 454 418 421 790 2873 938 1408 867 180 2465 331 717 237 274 420 309 327 353 993 923 781 730 424 494 297 385 502 509 388 415 1317 836 661 498 1370 550 509 4 | ENSMUSG00000001403 113 198 208 55 704 342 852 1252 1268 580 448 858 1029 155 872 510 79 996 200 412 248 344 1113 168 285 420 349 11 980 804 1202 272 111 323 356 358 498 91 34 105 773 146 614 67 688 996 111 130 642 157 3985 1185 358 917 5374 604 4256 3613 548 1000 1989 1850 1577 2717 1353 1928 3115 4660 3517 4971 2688 1432 5116 527 3375 834 949 1443 1272 2525 1923 2376 1528 2259 1911 1603 1046 1114 1792 1668 1615 808 1212 6004 3741 889 4178 5500 1638 1587 5 | ENSMUSG00000002257 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 9 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 1 0 0 0 0 0 0 0 0 0 6 8 0 0 0 158 0 0 1 0 6 192 0 56 91 0 0 2 9 87 148 0 174 1 7 22 28 0 0 0 1 79 0 0 1 0 0 121 0 1 0 1 0 0 1 1 14 26 0 0 2 2 0 6 | ENSMUSG00000003779 678 133 1 208 692 0 1074 518 526 10 431 912 360 345 727 639 348 190 307 366 364 1047 152 715 423 491 631 163 15 320 23 133 110 182 10 748 97 0 431 0 526 471 14 2732 6 903 743 0 73 0 6 1432 409 725 1636 2835 2365 1167 740 934 1457 1418 678 607 618 21 791 25 1355 690 1149 5 1144 617 1429 1557 6 514 510 281 361 2038 655 975 611 635 763 244 162 451 1401 1027 280 690 1659 126 2763 1955 1650 1342 7 | ENSMUSG00000005397 2 2 1 98 178 46 122 45 5 768 12 1 530 132 612 9 70 386 8 1105 1 2831 461 17 32 267 231 307 12 45 308 1518 42 154 0 508 405 11 11 17 1 772 0 11 119 1112 224 147 1406 147 85 1436 768 327 960 4634 62 263 1191 797 2488 445 361 646 427 347 672 4953 534 2099 1800 669 2363 596 1062 533 653 597 1523 13 666 970 281 1093 1094 1518 870 776 1226 534 504 199 1258 640 798 809 2141 3072 209 1023 8 | ENSMUSG00000005410 722 16 1127 419 600 84 635 2228 478 660 943 2411 494 505 1497 1520 597 1504 881 579 1254 709 4582 846 1570 2047 344 9 7 443 2282 1303 29 95 1469 1087 185 1036 27 1107 532 3183 1974 879 85 907 487 1235 446 245 144 1944 2826 988 3294 0 3159 1048 2470 862 1155 1773 190 1099 694 375 1437 7611 2326 4615 2198 3442 933 1107 2180 2684 634 306 2145 455 4479 1327 1162 1085 164 2489 1665 906 759 445 2308 655 1020 5586 188 1976 2261 2437 2304 1693 9 | ENSMUSG00000006056 183 707 536 278 17 28 2 287 2788 909 254 391 602 1 877 864 180 406 715 508 456 343 1964 488 906 127 791 269 51 564 5 442 291 857 433 1041 32 65 564 11 1351 598 795 34 772 399 138 136 594 9 2831 467 1267 47 3198 74 4658 1039 612 2177 926 1672 1705 544 652 115 879 1863 1610 1418 2170 647 2037 327 2131 330 397 799 93 460 211 1050 1436 1549 2141 2355 1259 55 1351 480 1251 1757 272 1024 1531 1490 138 1574 711 665 10 | ENSMUSG00000006276 1 0 1 1 153 123 176 1 127 2 7 0 262 33 4 67 12 1 4 1 38 13 38 0 0 1 183 0 598 108 0 20 1 100 718 0 59 89 14 6 102 147 74 23 83 537 35 271 6 1 4 730 135 1 42 0 693 426 630 500 295 310 7 13 40 102 0 8 1227 614 2 104 448 136 1007 49 300 155 0 0 1516 2 822 230 907 22 263 40 10 28 433 148 289 1134 307 121 164 617 525 344 11 | ENSMUSG00000000001 43 82 5 0 2 87 49 855 45 137 733 1647 1036 1 715 643 1083 5 1250 36 541 608 114 153 38 524 177 1 502 501 0 6 836 471 435 696 0 36 169 42 0 214 1076 517 0 200 1 0 65 185 2815 562 4 529 2033 113 476 137 5 1110 848 107 15 366 269 25 175 4411 31 226 257 2 1283 417 121 15 326 124 141 0 64 238 130 268 604 624 594 1 93 7 448 32 814 547 656 17 589 573 525 568 12 | ENSMUSG00000000003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 | ENSMUSG00000000028 89 598 10 249 135 36 72 6 482 374 782 669 241 703 359 595 12 1242 21 804 97 664 962 348 134 4 761 2 170 775 1013 115 7 43 5 1000 242 866 5 1414 50 702 991 3 39 978 886 256 2 500 1 3 427 252 1300 882 1218 480 908 903 522 139 287 324 665 21 49 0 917 479 80 19 533 204 433 257 1 58 726 3 906 965 299 291 703 97 289 273 865 270 4 810 194 1118 331 330 0 873 761 220 14 | ENSMUSG00000000031 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 | ENSMUSG00000000037 1 0 0 0 0 391 3 0 118 0 32 0 0 1 1 0 0 0 0 0 81 0 0 0 0 31 7 4 1 34 1 12 0 65 1 8 5 333 0 0 0 1 192 22 0 239 23 50 2 6 13 0 55 1 243 1 0 264 2 1 606 19 0 5 5 6 0 1 1 0 386 3 0 6 0 0 1 1 8 3 6 9 1049 1 27 53 4 14 110 3 0 0 279 3 98 9 1 1 1 449 16 | ENSMUSG00000000049 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 | ENSMUSG00000000056 0 19 0 15 0 10 5 4 0 6 2 1057 0 0 4 4 0 2 5 0 0 0 65 0 1 1 15 142 32 1 0 0 1 420 29 0 3 2 1 2 0 5 1 1 0 0 35 0 15 0 0 0 5 3 63 0 0 1 0 0 0 197 45 2 9 0 521 297 78 15 226 9 42 0 0 0 0 128 0 0 0 3 1120 0 100 997 0 0 0 0 16 0 0 0 3 3 0 0 3 0 18 | ENSMUSG00000000058 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 | ENSMUSG00000000078 3 514 1 154 8 65 283 318 58 39 3 0 1 63 169 4 1 1 18 8 43 514 11 1 109 17 1 325 11 9 92 23 39 19 1 27 7 14 653 33 2 352 1 12 304 795 6 139 13 107 9 125 58 3 52 9 1879 310 93 50 352 40 175 462 4 9 697 2275 902 6 21 39 110 63 195 5 4 8 41 7 4 2 252 326 295 383 11 174 13 59 27 5 1 574 840 244 7 561 124 2 20 | ENSMUSG00000000085 2 11 0 0 0 0 0 0 138 64 6 0 0 0 5 158 0 1 0 4 163 0 0 0 52 7 8 90 9 2 0 175 2 67 174 14 0 0 0 286 1 0 66 1352 0 0 0 2 0 45 26 472 45 0 8 0 378 11 352 0 0 14 43 0 0 1 0 3 59 14 4 0 2 178 1 0 0 0 0 0 7 6 617 2 0 132 0 0 0 0 0 3 0 0 55 248 0 35 0 143 21 | -------------------------------------------------------------------------------- /D3ECmd.py: -------------------------------------------------------------------------------- 1 | ''' 2 | D3E-Cmd 3 | Discrete Distributional Differential Expression Command Line Tool 4 | 5 | Author: Mihails Delmans (md656@cam.ac.uk) 6 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 7 | Version: 1.0 8 | 9 | Tested with: 10 | scipy 0.13.0b1 11 | numpy 1.8.0rc1 12 | sympy.mpmath 0.18 13 | 14 | Copyright 2015 Mihails Delmans, Martin Hemberg 15 | 16 | This file is part of D3E. 17 | 18 | D3E is free software: you can redistribute it and/or modify 19 | it under the terms of the GNU General Public License as published by 20 | the Free Software Foundation, either version 3 of the License, or 21 | (at your option) any later version. 22 | 23 | D3E is distributed in the hope that it will be useful, 24 | but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | GNU General Public License for more details. 27 | 28 | You should have received a copy of the GNU General Public License 29 | along with D3E. If not, see . 30 | 31 | ''' 32 | from __future__ import division 33 | 34 | from D3EUtil import readData, getParamsBayesian, getParamsMoments, cramerVonMises, logStatus, goodnessOfFit, distributionTest 35 | from D3EUtil import Params, BioParams, Status, likelihoodRatio 36 | 37 | from argparse import ArgumentParser, FileType 38 | from numpy import mean, log2 39 | from scipy.stats import variation 40 | 41 | def checkCramerVonMises(pValue, comment, idx): 42 | if pValue == -1: 43 | logStatus( Status(1, idx, "Could not estimate Cramer-von Mises statistic(" + comment + ")") ) 44 | 45 | parser = ArgumentParser(description='3DExpress') 46 | parser.add_argument(action = 'store', type=FileType('r'), dest = 'inputFile', help='Input file...') 47 | parser.add_argument(action = 'store', type=FileType('w'), dest = 'outputFile', help='Output file...') 48 | parser.add_argument(action = 'store', type = str, nargs = 1, dest = 'label1', help = 'Label for the first cell type / condition') 49 | parser.add_argument(action = 'store', type = str, nargs = 1, dest = 'label2', help = 'Label for the second cell type / condition') 50 | 51 | parser.add_argument('-m', '--mode', action = 'store', type = int, dest='mode', default = 1, choices =[0,1], help = 'Mode of operation\n '\ 52 | '0: Apply Method of moments\n' 53 | '1: Apply Bayesian approach (default)\n') 54 | 55 | parser.add_argument('-t', '--test', action = 'store', type = int, dest = 'test', default = 0, choices = [0,1,2,3], help = 'Statistical test\n '\ 56 | '0: Cramer-von Mises test (default)\n' 57 | '1: Kolmogorov-Smirnov test\n' 58 | '2: Anderson-Darling test\n' 59 | '3: Likelihood Ratio test\n') 60 | parser.add_argument('-n','--normalise', action = 'store', type = int, dest='normalise', default = 1, choices = [0,1], help='Normalise the data') 61 | parser.add_argument('-z', '--removeZeros', action = 'store', type = int, dest='removeZeros', default = 0, choices = [0,1], help='Remove zeros') 62 | parser.add_argument('-s', '--useSpikeIns', action = 'store', type = int, dest='useSpikeIns', default = 0, choices = [0,1], help='Use spike-ins for normalisation. Requires at least one row with id starting with "spike" or the string set with --spikeInStart ') 63 | parser.add_argument('--spikeInStart', action = 'store', type = str, nargs = 1, dest = 'spikeInStart', default = 'spike', help = 'A string to identify spike-ins. (spike)', metavar = 'spike') 64 | parser.add_argument('-v', action = 'store_const', const = True, dest = 'verbose', default = True, help = 'verbose') 65 | parser.add_argument('-f', '--fdr', action = 'store', type = float, dest = 'fdr', default = 1, help='FDR parameter') 66 | args = parser.parse_args() 67 | 68 | data1, data2, ids, lineStatus = readData(args.inputFile, args.label1[0], args.label2[0], args.normalise, args.removeZeros, args.useSpikeIns, args.spikeInStart) 69 | 70 | if args.verbose: 71 | for status in lineStatus: 72 | logStatus(status) 73 | 74 | 75 | if args.mode == 0: 76 | args.outputFile.write('#GeneID\ta1\tb1\tg1\tGOF1\ta2\tb2\tg2\tGOF2\ts1\tf1\td1\ts2\tf2\td2\tRs\tRf\tRd\tp-value\tmu1\tcv1\tmu2\tcv2\n\n') 77 | elif args.mode == 1: 78 | args.outputFile.write('#GeneID\ta1\tb1\tg1\tGOF1\ta2\tb2\tg2\tGOF2\ts1\tf1\td1\ts2\tf2\td2\tRs\tRf\tRd\tpSize\tpFreq\tpDuty\tp-value\tmu1\tcv1\tmu2\tcv2\n\n') 79 | 80 | pVals = [] 81 | 82 | for p1,p2,idx in zip(data1, data2, ids): 83 | 84 | difference = distributionTest(p1,p2, args.test) 85 | 86 | if difference == -1: 87 | logStatus( Status(1, idx, "Could not estimate p-value. Further analysis aborted.") ) 88 | continue 89 | 90 | if args.mode == 0: 91 | params1 = getParamsMoments(p1) 92 | params2 = getParamsMoments(p2) 93 | 94 | if (params1.alpha <=0 or params1.beta <= 0 or params1.gamma <=0 or 95 | params2.alpha <=0 or params2.beta <= 0 or params2.gamma <=0): 96 | logStatus( Status(1, idx, "Could not estimate parameters.") ) 97 | 98 | params1 = Params(alpha = float('nan'), beta = float('nan'), gamma = float('nan'), c = float('nan') ) 99 | params2 = Params(alpha = float('nan'), beta = float('nan'), gamma = float('nan'), c = float('nan') ) 100 | bioParams1 = BioParams( size = float('nan'), freq = float('nan'), duty = float('nan') ) 101 | bioParams2 = BioParams( size = float('nan'), freq = float('nan'), duty = float('nan') ) 102 | else: 103 | bioParams1 = BioParams(size = params1.gamma / params1.beta, freq = 1 / params1.alpha, duty = params1.alpha / (params1.alpha + params1.beta) ) 104 | bioParams2 = BioParams(size = params2.gamma / params2.beta, freq = 1 / params2.alpha, duty = params2.alpha / (params2.alpha + params2.beta) ) 105 | 106 | elif args.mode == 1: 107 | 108 | params1, bioParams1 = getParamsBayesian(p1) 109 | params2, bioParams2 = getParamsBayesian(p2) 110 | 111 | sizeP = cramerVonMises(bioParams1.size.sample, bioParams2.size.sample) 112 | checkCramerVonMises(sizeP, 'for size', idx) 113 | 114 | freqP = cramerVonMises(bioParams1.freq.sample, bioParams2.freq.sample) 115 | checkCramerVonMises(freqP, 'for f', idx) 116 | 117 | dutyP = cramerVonMises(bioParams1.duty.sample, bioParams2.duty.sample) 118 | checkCramerVonMises(dutyP, 'for t', idx) 119 | 120 | if args.test == 3: 121 | difference = likelihoodRatio(idx, p2, params1, params2) 122 | 123 | if difference == -1: 124 | logStatus( Status(1, idx, "Could not estimate p-value. Further analysis aborted.") ) 125 | continue 126 | 127 | pVals.append(difference) 128 | 129 | gof1 = goodnessOfFit(p1, params1) 130 | checkCramerVonMises(gof1, 'Goodnes of fit for a first cell type', idx) 131 | 132 | gof2 = goodnessOfFit(p2, params2) 133 | checkCramerVonMises(gof1, 'Goodnes of fit for a second cell type', idx) 134 | 135 | if args.mode == 0: 136 | args.outputFile.write('{0:s}\t{1:4.4f}\t{2:4.4f}\t{3:4.4f}\t{4:4.4e}\t' 137 | '{5:4.4f}\t{6:4.4f}\t{7:4.4f}\t{8:4.4e}\t' 138 | '{9:4.4f}\t{10:4.4f}\t{11:4.4f}\t{12:4.4f}\t{13:4.4f}\t{14:4.4f}\t' 139 | '{15:4.4f}\t{16:4.4f}\t{17:4.4f}\t' 140 | '{18:4.4e}\t{19:4.4f}\t{20:4.4f}\t{21:4.4f}\t{22:4.4f}\n'.format(idx, 141 | params1.alpha, params1.beta, params1.gamma, gof1, 142 | params2.alpha, params2.beta, params2.gamma, gof2, 143 | bioParams1.size, bioParams1.freq, bioParams1.duty, 144 | bioParams2.size, bioParams2.freq, bioParams2.duty, 145 | log2( bioParams1.size / bioParams2.size ), 146 | log2( bioParams1.freq / bioParams2.freq ), 147 | log2( bioParams1.duty / bioParams2.duty ), 148 | difference, mean(p1), variation(p1), mean(p2), variation(p2)) ) 149 | elif args.mode == 1: 150 | args.outputFile.write('{0:s}\t{1:4.4f}\t{2:4.4f}\t{3:4.4f}\t{4:4.4e}\t' 151 | '{5:4.4f}\t{6:4.4f}\t{7:4.4f}\t{8:4.4e}\t' 152 | '{9:4.4f}\t{10:4.4f}\t{11:4.4f}\t{12:4.4f}\t{13:4.4f}\t{14:4.4f}\t' 153 | '{15:4.4f}\t{16:4.4f}\t{17:4.4f}\t' 154 | '{18:4.4e}\t{19:4.4e}\t{20:4.4e}\t{21:4.4e}\t{22:4.4f}\t{23:4.4f}\t{24:4.4f}\t{25:4.4f}\n'.format(idx, 155 | params1.alpha.mean(), params1.beta.mean(), params1.gamma.mean(), gof1, 156 | params2.alpha.mean(), params2.beta.mean(), params2.gamma.mean(), gof2, 157 | bioParams1.size.mean(), bioParams1.freq.mean(), bioParams1.duty.mean(), 158 | bioParams2.size.mean(), bioParams2.freq.mean(), bioParams2.duty.mean(), 159 | log2( bioParams2.size.mean() / bioParams1.size.mean()), 160 | log2( bioParams2.freq.mean() / bioParams1.freq.mean()), 161 | log2( bioParams2.duty.mean() / bioParams1.duty.mean()), 162 | sizeP,freqP, dutyP, difference, mean(p1), variation(p1), mean(p2), variation(p2) ) ) 163 | 164 | logStatus( Status(0, idx, "Analysis complete.") ) 165 | 166 | pVals.sort(reverse = True) 167 | n = len(pVals) 168 | 169 | for i in range(1,n+1): 170 | if pVals[i-1] <= args.fdr * i / len(pVals): 171 | logStatus(Status(0, "D3E", "Significance threshold with given fdr(" + str(args.fdr) + ") is: " + str(pVals[i-1]) )) 172 | break 173 | 174 | args.outputFile.close() 175 | -------------------------------------------------------------------------------- /D3EUtil.py: -------------------------------------------------------------------------------- 1 | ''' 2 | 3 | D3E-Cmd 4 | Discrete Distributional Differential Expression Command Line Tool 5 | 6 | Author: Mihails Delmans (md656@cam.ac.uk) 7 | Advisor: Martin Hemberg (mh26@sanger.ac.uk) 8 | Version: 1.0 9 | 10 | Tested with: 11 | scipy 0.15.1 12 | numpy 1.8.0rc1 13 | sympy.mpmath 0.18 14 | 15 | Copyright 2015 Mihails Delmans, Martin Hemberg 16 | 17 | This file is part of D3E. 18 | 19 | D3E is free software: you can redistribute it and/or modify 20 | it under the terms of the GNU General Public License as published by 21 | the Free Software Foundation, either version 3 of the License, or 22 | (at your option) any later version. 23 | 24 | D3E is distributed in the hope that it will be useful, 25 | but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | GNU General Public License for more details. 28 | 29 | You should have received a copy of the GNU General Public License 30 | along with D3E. If not, see . 31 | 32 | ''' 33 | 34 | from __future__ import division 35 | from scipy.special import kv, gammaln, gamma, hyp1f1, factorial 36 | from scipy.stats import gmean, ks_2samp, anderson_ksamp, chi2 37 | from scipy.stats import poisson as poissonF 38 | from decimal import Decimal, getcontext 39 | from collections import namedtuple 40 | from numpy import log, array, zeros, median, rint, power, hstack, hsplit, seterr, mean, isnan, floor, divide, exp, round, where 41 | from numpy.random import beta, poisson, random 42 | import mpmath as mp 43 | 44 | seterr(all='ignore') 45 | 46 | mp.mp.dps = 30 47 | mp.mp.pretty = True 48 | 49 | Params = namedtuple("Params", ["alpha", "beta", "gamma", "c"]) 50 | BioParams = namedtuple("BioParams", ["size", "freq", "duty"]) 51 | Status = namedtuple("LineStatus", ["code", "idx", "message"]) 52 | 53 | 54 | class RVar: 55 | 56 | def __init__(self, value=0): 57 | self.value = value 58 | self.leftLimit = 0 59 | self.rightLimit = float('Inf') 60 | self.sample = [] 61 | 62 | def mean(self): 63 | return mean(self.sample) 64 | 65 | def setSampleFunction(self, function): 66 | self.sampleFunction = function 67 | 68 | def draw(self, maxSteps=1000, saveToSample = False): 69 | 70 | x0 = self.value 71 | w = abs(self.value / 2) 72 | 73 | f = self.sampleFunction; 74 | 75 | logPx = f(x0) 76 | logSlice = log(random()) + logPx 77 | 78 | xLeft = x0 - random() * w 79 | xRight = xLeft + w 80 | 81 | if xLeft < self.leftLimit: 82 | xLeft = self.leftLimit 83 | if xRight > self.rightLimit: 84 | xRight = self.rightLimit 85 | 86 | v = random() 87 | 88 | j = floor(maxSteps*v) 89 | k = maxSteps-1 - j 90 | 91 | while j > 0 and logSlice < f(xLeft) and xLeft - w > self.leftLimit: 92 | j = j-1 93 | xLeft = xLeft - w 94 | 95 | 96 | while k > 0 and logSlice < f(xRight) and xRight + w < self.rightLimit: 97 | k = k - 1 98 | xRight = xRight + w 99 | 100 | n = 10000 101 | 102 | while 1: 103 | n = n - 1 104 | if n < 0 : 105 | print "Warning: Can't find a new value." 106 | return x0 107 | 108 | 109 | x1 = (xRight - xLeft) * random() + xLeft 110 | 111 | if logSlice <= f(x1): 112 | break 113 | if x1 < x0: 114 | xLeft = x1 115 | else: 116 | xRight = x1 117 | self.value = x1 118 | 119 | if saveToSample: 120 | self.sample.append(x1) 121 | 122 | return x1 123 | 124 | 125 | def logStatus(status): 126 | statusType = ['Log','Warning','Error'] 127 | print status.idx + ' - ' + statusType[status.code] + ': ' + status.message 128 | 129 | # Read a header of an input file, get indeces of colums that match specified labels 130 | def _readHeader(header, label1, label2): 131 | 132 | if header.lower().startswith('geneid'): 133 | tabs = header.split('\t') 134 | 135 | colIdx1 = [i for i,x in enumerate(tabs) if x == label1 ] 136 | colIdx2 = [i for i,x in enumerate(tabs) if x == label2 ] 137 | else: 138 | return [],[], 1 139 | 140 | return colIdx1, colIdx2, 0 141 | 142 | 143 | def _normalisationWeights(data): 144 | nGenes = data.shape[0] 145 | nCells = data.shape[1] 146 | geneGM = gmean(data+1, 1) 147 | weights = array( [median( (data[:,i]+1) / geneGM) for i in range(nCells)] ) 148 | return weights 149 | 150 | # Read input data file, extract read counts, normalise, report errors 151 | def readData(inputFile, label1, label2, normalise=True, removeZeros=False, useSpikeIns = False, verbose = False, spikeInStart = 'spike'): 152 | 153 | data1 = [] 154 | data2 = [] 155 | spikeIns = [] 156 | lineStatus = [] 157 | ids = [] 158 | empty = [] 159 | 160 | header = inputFile.readline() 161 | 162 | colIdx1, colIdx2, status = _readHeader(header, label1, label2) 163 | 164 | if status == 1: 165 | lineStatus.append( Status(2, 'Header', 'Invalid header format') ) 166 | return [],[],[],lineStatus 167 | else: 168 | if not colIdx1: 169 | lineStatus.append( Status(2, 'Header', "No colums with label '" + label1 + "' found") ) 170 | return [],[],[],lineStatus 171 | elif not colIdx2: 172 | lineStatus.append( Status(2, 'Header', "No colums with label '" + label2 + "' found") ) 173 | return [],[],[],lineStatus 174 | else: 175 | lineStatus.append( Status(0, 'Header', "Read OK") ) 176 | 177 | for line in inputFile: 178 | if line.strip(): 179 | cols = line.split() 180 | 181 | idx = cols[0] 182 | 183 | p1 = [ float(cols[x]) for x in colIdx1 ] 184 | p2 = [ float(cols[x]) for x in colIdx2 ] 185 | 186 | if max(p1) == 0 and max(p2) == 0: 187 | lineStatus.append( Status(1, idx, "Null expression detected") ) 188 | continue 189 | else: 190 | lineStatus.append( Status(0, idx, "Line read OK") ) 191 | 192 | 193 | if idx.lower().startswith(spikeInStart): 194 | spikeIns.append( p1 + p2 ) 195 | lineStatus.append( Status(0, idx, "Spike-in detected") ) 196 | continue 197 | 198 | data1.append(p1) 199 | data2.append(p2) 200 | ids.append(idx) 201 | 202 | if normalise: 203 | 204 | if useSpikeIns: 205 | if len(spikeIns) == 0: 206 | lineStatus.append(Status(2, 'Spike-ins','No spike-ins data detected') ) 207 | return [],[],[],lineStatus 208 | 209 | weights = _normalisationWeights(array(spikeIns)) 210 | 211 | else: 212 | weights = _normalisationWeights( hstack( ( array(data1), array(data2) ) ) ) 213 | 214 | splitColumn = array(data1).shape[1] 215 | 216 | data1 = [ (array(readLine) / weights[:splitColumn]).tolist() for readLine in data1 ] 217 | data2 = [ (array(readLine) / weights[splitColumn:]).tolist() for readLine in data2 ] 218 | 219 | if removeZeros: 220 | 221 | dataFiltered1 = [] 222 | dataFiltered2 = [] 223 | idsFiltered = [] 224 | 225 | for p1, p2, idx in zip(data1,data2,ids): 226 | p1 = filter(lambda x: x!=0, p1) 227 | p2 = filter(lambda x: x!=0, p2) 228 | 229 | if len(p1) != 0 and len(p2) != 0: 230 | dataFiltered1.append(p1) 231 | dataFiltered2.append(p2) 232 | idsFiltered.append(idx) 233 | else: 234 | lineStatus.append( Status(1, idx, "Empty expression after zero removal") ) 235 | 236 | data1 = dataFiltered1 237 | data2 = dataFiltered2 238 | ids = idsFiltered 239 | 240 | inputFile.close() 241 | 242 | return data1, data2, ids, lineStatus 243 | 244 | 245 | # Sorts set x and returns a rank of elements in a sorted set 246 | def _sortRank(x): 247 | 248 | xs = sorted(x) 249 | r = [] 250 | 251 | i = 1 252 | while i <= len(xs): 253 | rStart = i 254 | rEnd = i 255 | 256 | if i < len(xs): 257 | while xs[i-1] == xs[i]: 258 | i += 1 259 | rEnd = i 260 | if i >= len(xs): 261 | break 262 | 263 | i += 1 264 | n = (rEnd-rStart + 1) 265 | r.extend([ (rStart + rEnd) / 2 for j in range(n)]) 266 | 267 | return xs, r 268 | 269 | # Perform a Cramer - von Mises test of two samples x and y. H0: samples x and y are drawn from the same distribution. Returns a p-value. 270 | # Anderson, Theodore W., On the Distribution of the Two-Sample Cramer-von Mises Criterion, 1962, The Annals of Mathematical Statistics 33, 1148-1159 271 | # Anderson, Theodore W., Donald A. Darling, 1952, Asymptotic Theory of Certain Goodness of Fit Criteria Based on Stochastic Processes, The Annals of Mathematical Statistics 23, 193-212. 272 | def cramerVonMises(x, y): 273 | 274 | try: 275 | x = sorted(x); 276 | y = sorted(y); 277 | 278 | pool = x + y; 279 | 280 | ps, pr = _sortRank(pool) 281 | 282 | rx = array ( [ pr[ind] for ind in [ ps.index(element) for element in x ] ] ) 283 | ry = array ( [ pr[ind] for ind in [ ps.index(element) for element in y ] ] ) 284 | 285 | n = len(x) 286 | m = len(y) 287 | 288 | i = array(range(1, n+1)) 289 | j = array(range(1, m+1)) 290 | 291 | u = n * sum ( power( (rx - i), 2 ) ) + m * sum ( power((ry - j), 2) ) 292 | 293 | t = u / (n*m*(n+m)) - (4*n*m-1) / (6 * (n+m)) 294 | Tmu = 1/6 + 1 / (6*(n+m)) 295 | Tvar = 1/45 * ( (m+n+1) / power((m+n),2) ) * (4*m*n*(m+n) - 3*(power(m,2) + power(n,2)) - 2*m*n) / (4*m*n) 296 | t = (t - Tmu) / power(45*Tvar, 0.5) + 1/6 297 | 298 | if t < 0: 299 | return -1 300 | elif t <= 12: 301 | a = 1-mp.nsum(lambda x : ( mp.gamma(x+0.5) / ( mp.gamma(0.5) * mp.fac(x) ) ) * 302 | mp.power( 4*x + 1, 0.5 ) * mp.exp ( - mp.power(4*x + 1, 2) / (16*t) ) * 303 | mp.besselk(0.25 , mp.power(4*x + 1, 2) / (16*t) ), [0,100] ) / (mp.pi*mp.sqrt(t)) 304 | return float(mp.nstr(a,3)) 305 | else: 306 | return 0 307 | except Exception as e: 308 | print e 309 | return -1 310 | 311 | # Perform a Kolmogorov-Smirnov test of two samples x and y. H0: samples x and y are drawn from the same distribution. Returns a p-value. 312 | def KSTest(x, y): 313 | try: 314 | return ks_2samp(x,y)[1] 315 | 316 | except Exception as e: 317 | print e 318 | return -1 319 | 320 | # Perform a Anderson-Darling test of two samples x and y. H0: samples x and y are drawn from the same distribution. Returns am interpolated p-value. 321 | def ADTest(x,y): 322 | try: 323 | return anderson_ksamp([x,y])[2] 324 | except Exception as e: 325 | print e 326 | return -1 327 | 328 | def distributionTest(x,y,method): 329 | if method == 1: 330 | return KSTest(x,y) 331 | elif method == 2: 332 | return ADTest(x,y) 333 | elif method == 3: 334 | return 0 335 | else: 336 | return cramerVonMises(x,y) 337 | 338 | # Generation of a sample from Poisson-beta distribution with given parameters parms and size n 339 | def randPoissonBeta(params,n): 340 | 341 | x = beta( params.alpha, params.beta, n ) 342 | p = poisson( x * params.gamma ) 343 | 344 | return p 345 | 346 | # Estimation of the parameters of a sample drawn from a Poisson-beta distribution using momet matching technique from 347 | # Peccoud, Jean, Bernard Ycart, 1995, Markovian modelling of gene product synthesis, Theoretical Population Biology 48, 222-234. 348 | def getParamsMoments(p): 349 | 350 | try: 351 | rm1 = sum(p) / len(p) 352 | rm2 = sum( [pow(x,2) for x in p] ) / len(p) 353 | rm3 = sum( [pow(x,3) for x in p] ) / len(p) 354 | 355 | fm1 = rm1 356 | fm2 = rm2 - rm1 357 | fm3 = rm3 - 3*rm2 + 2*rm1 358 | 359 | r1 = fm1 360 | r2 = fm2 / fm1 361 | r3 = fm3 / fm2 362 | 363 | alpha = 2*r1 * (r3 - r2) / (r1*r2 - 2*r1*r3 + r2*r3) 364 | beta = 2 * (r2 - r1) * (r1 - r3) * (r3 - r2) / ((r1*r2 - 2*r1*r3 + r2*r3) *(r1 - 2*r2 + r3)) 365 | gamma = (-r1*r2 + 2*r1*r3 - r2*r3) / (r1 - 2*r2 +r3) 366 | except: 367 | return Params(-1,-1,-1,-1) 368 | 369 | return Params(alpha, beta, gamma, 0) 370 | 371 | # Esimation of the parameters of a sample drawn from a Poisson-beta distribution using bayesian inference method 372 | # Kim, Jong Kyoung, John C. Marioni, 2013, Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data, Genome Biology 14, R7. 373 | def getParamsBayesian(p, iterN=1000): 374 | 375 | HyperParams = namedtuple("HyperParams", ["k_alpha", "theta_alpha", "k_beta", "theta_beta", "k_gamma", "theta_gamma"]) 376 | 377 | parFit = getParamsMoments(p) 378 | 379 | hyperParams = HyperParams(k_alpha = 1, theta_alpha = 100, k_beta = 1, theta_beta = 100, k_gamma = 1, theta_gamma = max(p) ) 380 | 381 | if parFit.alpha > 0 and parFit.beta > 0 and parFit.gamma > 0: 382 | 383 | params = Params(alpha = RVar(parFit.alpha), beta = RVar(parFit.beta), gamma = RVar(parFit.gamma), c = [ RVar(0.5) for i in range(len(p)) ] ) 384 | else: 385 | params = Params(alpha = RVar(0.5), beta = RVar(0.5), gamma = RVar(mean(p)+1e6), c = [ RVar(0.5) for i in range(len(p)) ] ) 386 | 387 | bioParams = BioParams(size = RVar(), freq = RVar(), duty = RVar() ) 388 | 389 | save = False 390 | 391 | for i in range(iterN): 392 | 393 | if i > iterN / 2: 394 | save = True 395 | 396 | alpha = params.alpha.value 397 | beta = params.beta.value 398 | gamma = params.gamma.value 399 | 400 | bioParams.size.sample.append( gamma / beta ) 401 | bioParams.freq.sample.append( alpha*beta / (alpha + beta) ) 402 | bioParams.duty.sample.append( alpha / (alpha + beta) ) 403 | 404 | for c,pi in zip(params.c,p): 405 | c.setSampleFunction(lambda x: (params.alpha.value - 1 ) * log(x) + (params.beta.value - 1) * log(1-x) + pi * log(x) - params.gamma.value * x) 406 | c.draw(saveToSample = save) 407 | 408 | params.gamma.setSampleFunction( lambda x: (hyperParams.k_gamma-1)*log(x) - x / hyperParams.theta_gamma + log(x) * sum(p) - x * sum( [c.value for c in params.c] ) ) 409 | params.gamma.draw(saveToSample = save) 410 | 411 | params.alpha.setSampleFunction( lambda x: (hyperParams.k_alpha-1)*log(x) - x / hyperParams.theta_alpha + len(p)*(gammaln(x + params.beta.value) - gammaln(x)) + (x-1) * sum([ log(c.value) for c in params.c ]) ) 412 | params.alpha.draw(saveToSample = save) 413 | 414 | params.beta.setSampleFunction( lambda x: (hyperParams.k_beta-1)*log(x) - x / hyperParams.theta_beta + len(p)*(gammaln(x + params.alpha.value) - gammaln(x)) + (x-1) * sum([ log(1-c.value) for c in params.c ]) ) 415 | params.beta.draw(saveToSample = save) 416 | 417 | return params, bioParams 418 | 419 | def goodnessOfFit(p, params): 420 | 421 | try: 422 | alpha = params.alpha.mean() 423 | beta = params.beta.mean() 424 | gamma = params.gamma.mean() 425 | except: 426 | alpha = params.alpha 427 | beta = params.beta 428 | gamma = params.gamma 429 | 430 | pr = randPoissonBeta( Params(alpha,beta,gamma,0), len(p)) 431 | 432 | return cramerVonMises(pr,p) 433 | 434 | # Find log of likelihood for sample 'p' with parameters 'params', doing poisson-beta sampling 'n' times 435 | def logLikelihood(p, params, n, idx): 436 | 437 | try: 438 | alpha = params.alpha.mean() 439 | beta_ = params.beta.mean() 440 | gamma = int(round(params.gamma.mean()))+1 441 | except: 442 | alpha = params.alpha 443 | beta_ = params.beta 444 | gamma = int(round(params.gamma))+1 445 | 446 | 447 | if n * gamma > 1e9: 448 | n = int( round(1e9 / gamma) ) 449 | logStatus( Status(1, idx, "Reduced Poisson-Beta sample to " + str(n) + ".") ) 450 | 451 | pVal = [] 452 | 453 | for item in p: 454 | x = beta(alpha, beta_, n) 455 | pTemp = 0 456 | 457 | for i in range(n): 458 | pTemp += poissonF.pmf(item, gamma*x[i]) 459 | pVal.append(pTemp / n) 460 | 461 | pVal = array(pVal) 462 | pVal[where(pVal==0)] = 1/n 463 | 464 | return sum(log(pVal)) 465 | 466 | # Perform likelihood ratio test fitted parameters 467 | def likelihoodRatio(idx, p, params1, params2, n=100): 468 | 469 | try: 470 | alpha1 = params1.alpha.mean() 471 | beta1 = params1.beta.mean() 472 | gamma1 = round(params1.gamma.mean()) + 1 473 | except: 474 | alpha1 = params1.alpha 475 | beta1 = params1.beta 476 | gamma1 = round(params1.gamma) + 1 477 | 478 | try: 479 | alpha2 = params2.alpha.mean() 480 | beta2 = params2.beta.mean() 481 | gamma2 = round(params2.gamma.mean()) + 1 482 | except: 483 | alpha2 = params2.alpha 484 | beta2 = params2.beta 485 | gamma2 = round(params2.gamma) + 1 486 | 487 | sum1 = logLikelihood([int(x) for x in round(p)], params1, n, idx) 488 | sum2 = logLikelihood([int(x) for x in round(p)], params2, n, idx) 489 | 490 | ratio = sum1 - sum2 491 | 492 | if ratio >= 0: 493 | logStatus( Status(1, idx, "Could not perform likelihood ratio test.") ) 494 | return float('nan') 495 | 496 | pVal = chi2.pdf(-2*ratio,3) 497 | 498 | return pVal 499 | 500 | 501 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. We, the Free Software Foundation, use the 18 | GNU General Public License for most of our software; it applies also to 19 | any other work released this way by its authors. You can apply it to 20 | your programs, too. 21 | 22 | When we speak of free software, we are referring to freedom, not 23 | price. Our General Public Licenses are designed to make sure that you 24 | have the freedom to distribute copies of free software (and charge for 25 | them if you wish), that you receive source code or can get it if you 26 | want it, that you can change the software or use pieces of it in new 27 | free programs, and that you know you can do these things. 28 | 29 | To protect your rights, we need to prevent others from denying you 30 | these rights or asking you to surrender the rights. Therefore, you have 31 | certain responsibilities if you distribute copies of the software, or if 32 | you modify it: responsibilities to respect the freedom of others. 33 | 34 | For example, if you distribute copies of such a program, whether 35 | gratis or for a fee, you must pass on to the recipients the same 36 | freedoms that you received. You must make sure that they, too, receive 37 | or can get the source code. And you must show them these terms so they 38 | know their rights. 39 | 40 | Developers that use the GNU GPL protect your rights with two steps: 41 | (1) assert copyright on the software, and (2) offer you this License 42 | giving you legal permission to copy, distribute and/or modify it. 43 | 44 | For the developers' and authors' protection, the GPL clearly explains 45 | that there is no warranty for this free software. For both users' and 46 | authors' sake, the GPL requires that modified versions be marked as 47 | changed, so that their problems will not be attributed erroneously to 48 | authors of previous versions. 49 | 50 | Some devices are designed to deny users access to install or run 51 | modified versions of the software inside them, although the manufacturer 52 | can do so. This is fundamentally incompatible with the aim of 53 | protecting users' freedom to change the software. The systematic 54 | pattern of such abuse occurs in the area of products for individuals to 55 | use, which is precisely where it is most unacceptable. Therefore, we 56 | have designed this version of the GPL to prohibit the practice for those 57 | products. If such problems arise substantially in other domains, we 58 | stand ready to extend this provision to those domains in future versions 59 | of the GPL, as needed to protect the freedom of users. 60 | 61 | Finally, every program is threatened constantly by software patents. 62 | States should not allow patents to restrict development and use of 63 | software on general-purpose computers, but in those that do, we wish to 64 | avoid the special danger that patents applied to a free program could 65 | make it effectively proprietary. To prevent this, the GPL assures that 66 | patents cannot be used to render the program non-free. 67 | 68 | The precise terms and conditions for copying, distribution and 69 | modification follow. 70 | 71 | TERMS AND CONDITIONS 72 | 73 | 0. Definitions. 74 | 75 | "This License" refers to version 3 of the GNU General Public License. 76 | 77 | "Copyright" also means copyright-like laws that apply to other kinds of 78 | works, such as semiconductor masks. 79 | 80 | "The Program" refers to any copyrightable work licensed under this 81 | License. Each licensee is addressed as "you". "Licensees" and 82 | "recipients" may be individuals or organizations. 83 | 84 | To "modify" a work means to copy from or adapt all or part of the work 85 | in a fashion requiring copyright permission, other than the making of an 86 | exact copy. The resulting work is called a "modified version" of the 87 | earlier work or a work "based on" the earlier work. 88 | 89 | A "covered work" means either the unmodified Program or a work based 90 | on the Program. 91 | 92 | To "propagate" a work means to do anything with it that, without 93 | permission, would make you directly or secondarily liable for 94 | infringement under applicable copyright law, except executing it on a 95 | computer or modifying a private copy. Propagation includes copying, 96 | distribution (with or without modification), making available to the 97 | public, and in some countries other activities as well. 98 | 99 | To "convey" a work means any kind of propagation that enables other 100 | parties to make or receive copies. Mere interaction with a user through 101 | a computer network, with no transfer of a copy, is not conveying. 102 | 103 | An interactive user interface displays "Appropriate Legal Notices" 104 | to the extent that it includes a convenient and prominently visible 105 | feature that (1) displays an appropriate copyright notice, and (2) 106 | tells the user that there is no warranty for the work (except to the 107 | extent that warranties are provided), that licensees may convey the 108 | work under this License, and how to view a copy of this License. If 109 | the interface presents a list of user commands or options, such as a 110 | menu, a prominent item in the list meets this criterion. 111 | 112 | 1. Source Code. 113 | 114 | The "source code" for a work means the preferred form of the work 115 | for making modifications to it. "Object code" means any non-source 116 | form of a work. 117 | 118 | A "Standard Interface" means an interface that either is an official 119 | standard defined by a recognized standards body, or, in the case of 120 | interfaces specified for a particular programming language, one that 121 | is widely used among developers working in that language. 122 | 123 | The "System Libraries" of an executable work include anything, other 124 | than the work as a whole, that (a) is included in the normal form of 125 | packaging a Major Component, but which is not part of that Major 126 | Component, and (b) serves only to enable use of the work with that 127 | Major Component, or to implement a Standard Interface for which an 128 | implementation is available to the public in source code form. A 129 | "Major Component", in this context, means a major essential component 130 | (kernel, window system, and so on) of the specific operating system 131 | (if any) on which the executable work runs, or a compiler used to 132 | produce the work, or an object code interpreter used to run it. 133 | 134 | The "Corresponding Source" for a work in object code form means all 135 | the source code needed to generate, install, and (for an executable 136 | work) run the object code and to modify the work, including scripts to 137 | control those activities. However, it does not include the work's 138 | System Libraries, or general-purpose tools or generally available free 139 | programs which are used unmodified in performing those activities but 140 | which are not part of the work. For example, Corresponding Source 141 | includes interface definition files associated with source files for 142 | the work, and the source code for shared libraries and dynamically 143 | linked subprograms that the work is specifically designed to require, 144 | such as by intimate data communication or control flow between those 145 | subprograms and other parts of the work. 146 | 147 | The Corresponding Source need not include anything that users 148 | can regenerate automatically from other parts of the Corresponding 149 | Source. 150 | 151 | The Corresponding Source for a work in source code form is that 152 | same work. 153 | 154 | 2. Basic Permissions. 155 | 156 | All rights granted under this License are granted for the term of 157 | copyright on the Program, and are irrevocable provided the stated 158 | conditions are met. This License explicitly affirms your unlimited 159 | permission to run the unmodified Program. The output from running a 160 | covered work is covered by this License only if the output, given its 161 | content, constitutes a covered work. This License acknowledges your 162 | rights of fair use or other equivalent, as provided by copyright law. 163 | 164 | You may make, run and propagate covered works that you do not 165 | convey, without conditions so long as your license otherwise remains 166 | in force. You may convey covered works to others for the sole purpose 167 | of having them make modifications exclusively for you, or provide you 168 | with facilities for running those works, provided that you comply with 169 | the terms of this License in conveying all material for which you do 170 | not control copyright. Those thus making or running the covered works 171 | for you must do so exclusively on your behalf, under your direction 172 | and control, on terms that prohibit them from making any copies of 173 | your copyrighted material outside their relationship with you. 174 | 175 | Conveying under any other circumstances is permitted solely under 176 | the conditions stated below. Sublicensing is not allowed; section 10 177 | makes it unnecessary. 178 | 179 | 3. Protecting Users' Legal Rights From Anti-Circumvention Law. 180 | 181 | No covered work shall be deemed part of an effective technological 182 | measure under any applicable law fulfilling obligations under article 183 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or 184 | similar laws prohibiting or restricting circumvention of such 185 | measures. 186 | 187 | When you convey a covered work, you waive any legal power to forbid 188 | circumvention of technological measures to the extent such circumvention 189 | is effected by exercising rights under this License with respect to 190 | the covered work, and you disclaim any intention to limit operation or 191 | modification of the work as a means of enforcing, against the work's 192 | users, your or third parties' legal rights to forbid circumvention of 193 | technological measures. 194 | 195 | 4. Conveying Verbatim Copies. 196 | 197 | You may convey verbatim copies of the Program's source code as you 198 | receive it, in any medium, provided that you conspicuously and 199 | appropriately publish on each copy an appropriate copyright notice; 200 | keep intact all notices stating that this License and any 201 | non-permissive terms added in accord with section 7 apply to the code; 202 | keep intact all notices of the absence of any warranty; and give all 203 | recipients a copy of this License along with the Program. 204 | 205 | You may charge any price or no price for each copy that you convey, 206 | and you may offer support or warranty protection for a fee. 207 | 208 | 5. Conveying Modified Source Versions. 209 | 210 | You may convey a work based on the Program, or the modifications to 211 | produce it from the Program, in the form of source code under the 212 | terms of section 4, provided that you also meet all of these conditions: 213 | 214 | a) The work must carry prominent notices stating that you modified 215 | it, and giving a relevant date. 216 | 217 | b) The work must carry prominent notices stating that it is 218 | released under this License and any conditions added under section 219 | 7. This requirement modifies the requirement in section 4 to 220 | "keep intact all notices". 221 | 222 | c) You must license the entire work, as a whole, under this 223 | License to anyone who comes into possession of a copy. This 224 | License will therefore apply, along with any applicable section 7 225 | additional terms, to the whole of the work, and all its parts, 226 | regardless of how they are packaged. This License gives no 227 | permission to license the work in any other way, but it does not 228 | invalidate such permission if you have separately received it. 229 | 230 | d) If the work has interactive user interfaces, each must display 231 | Appropriate Legal Notices; however, if the Program has interactive 232 | interfaces that do not display Appropriate Legal Notices, your 233 | work need not make them do so. 234 | 235 | A compilation of a covered work with other separate and independent 236 | works, which are not by their nature extensions of the covered work, 237 | and which are not combined with it such as to form a larger program, 238 | in or on a volume of a storage or distribution medium, is called an 239 | "aggregate" if the compilation and its resulting copyright are not 240 | used to limit the access or legal rights of the compilation's users 241 | beyond what the individual works permit. Inclusion of a covered work 242 | in an aggregate does not cause this License to apply to the other 243 | parts of the aggregate. 244 | 245 | 6. Conveying Non-Source Forms. 246 | 247 | You may convey a covered work in object code form under the terms 248 | of sections 4 and 5, provided that you also convey the 249 | machine-readable Corresponding Source under the terms of this License, 250 | in one of these ways: 251 | 252 | a) Convey the object code in, or embodied in, a physical product 253 | (including a physical distribution medium), accompanied by the 254 | Corresponding Source fixed on a durable physical medium 255 | customarily used for software interchange. 256 | 257 | b) Convey the object code in, or embodied in, a physical product 258 | (including a physical distribution medium), accompanied by a 259 | written offer, valid for at least three years and valid for as 260 | long as you offer spare parts or customer support for that product 261 | model, to give anyone who possesses the object code either (1) a 262 | copy of the Corresponding Source for all the software in the 263 | product that is covered by this License, on a durable physical 264 | medium customarily used for software interchange, for a price no 265 | more than your reasonable cost of physically performing this 266 | conveying of source, or (2) access to copy the 267 | Corresponding Source from a network server at no charge. 268 | 269 | c) Convey individual copies of the object code with a copy of the 270 | written offer to provide the Corresponding Source. This 271 | alternative is allowed only occasionally and noncommercially, and 272 | only if you received the object code with such an offer, in accord 273 | with subsection 6b. 274 | 275 | d) Convey the object code by offering access from a designated 276 | place (gratis or for a charge), and offer equivalent access to the 277 | Corresponding Source in the same way through the same place at no 278 | further charge. You need not require recipients to copy the 279 | Corresponding Source along with the object code. If the place to 280 | copy the object code is a network server, the Corresponding Source 281 | may be on a different server (operated by you or a third party) 282 | that supports equivalent copying facilities, provided you maintain 283 | clear directions next to the object code saying where to find the 284 | Corresponding Source. Regardless of what server hosts the 285 | Corresponding Source, you remain obligated to ensure that it is 286 | available for as long as needed to satisfy these requirements. 287 | 288 | e) Convey the object code using peer-to-peer transmission, provided 289 | you inform other peers where the object code and Corresponding 290 | Source of the work are being offered to the general public at no 291 | charge under subsection 6d. 292 | 293 | A separable portion of the object code, whose source code is excluded 294 | from the Corresponding Source as a System Library, need not be 295 | included in conveying the object code work. 296 | 297 | A "User Product" is either (1) a "consumer product", which means any 298 | tangible personal property which is normally used for personal, family, 299 | or household purposes, or (2) anything designed or sold for incorporation 300 | into a dwelling. In determining whether a product is a consumer product, 301 | doubtful cases shall be resolved in favor of coverage. For a particular 302 | product received by a particular user, "normally used" refers to a 303 | typical or common use of that class of product, regardless of the status 304 | of the particular user or of the way in which the particular user 305 | actually uses, or expects or is expected to use, the product. A product 306 | is a consumer product regardless of whether the product has substantial 307 | commercial, industrial or non-consumer uses, unless such uses represent 308 | the only significant mode of use of the product. 309 | 310 | "Installation Information" for a User Product means any methods, 311 | procedures, authorization keys, or other information required to install 312 | and execute modified versions of a covered work in that User Product from 313 | a modified version of its Corresponding Source. The information must 314 | suffice to ensure that the continued functioning of the modified object 315 | code is in no case prevented or interfered with solely because 316 | modification has been made. 317 | 318 | If you convey an object code work under this section in, or with, or 319 | specifically for use in, a User Product, and the conveying occurs as 320 | part of a transaction in which the right of possession and use of the 321 | User Product is transferred to the recipient in perpetuity or for a 322 | fixed term (regardless of how the transaction is characterized), the 323 | Corresponding Source conveyed under this section must be accompanied 324 | by the Installation Information. But this requirement does not apply 325 | if neither you nor any third party retains the ability to install 326 | modified object code on the User Product (for example, the work has 327 | been installed in ROM). 328 | 329 | The requirement to provide Installation Information does not include a 330 | requirement to continue to provide support service, warranty, or updates 331 | for a work that has been modified or installed by the recipient, or for 332 | the User Product in which it has been modified or installed. Access to a 333 | network may be denied when the modification itself materially and 334 | adversely affects the operation of the network or violates the rules and 335 | protocols for communication across the network. 336 | 337 | Corresponding Source conveyed, and Installation Information provided, 338 | in accord with this section must be in a format that is publicly 339 | documented (and with an implementation available to the public in 340 | source code form), and must require no special password or key for 341 | unpacking, reading or copying. 342 | 343 | 7. Additional Terms. 344 | 345 | "Additional permissions" are terms that supplement the terms of this 346 | License by making exceptions from one or more of its conditions. 347 | Additional permissions that are applicable to the entire Program shall 348 | be treated as though they were included in this License, to the extent 349 | that they are valid under applicable law. If additional permissions 350 | apply only to part of the Program, that part may be used separately 351 | under those permissions, but the entire Program remains governed by 352 | this License without regard to the additional permissions. 353 | 354 | When you convey a copy of a covered work, you may at your option 355 | remove any additional permissions from that copy, or from any part of 356 | it. (Additional permissions may be written to require their own 357 | removal in certain cases when you modify the work.) You may place 358 | additional permissions on material, added by you to a covered work, 359 | for which you have or can give appropriate copyright permission. 360 | 361 | Notwithstanding any other provision of this License, for material you 362 | add to a covered work, you may (if authorized by the copyright holders of 363 | that material) supplement the terms of this License with terms: 364 | 365 | a) Disclaiming warranty or limiting liability differently from the 366 | terms of sections 15 and 16 of this License; or 367 | 368 | b) Requiring preservation of specified reasonable legal notices or 369 | author attributions in that material or in the Appropriate Legal 370 | Notices displayed by works containing it; or 371 | 372 | c) Prohibiting misrepresentation of the origin of that material, or 373 | requiring that modified versions of such material be marked in 374 | reasonable ways as different from the original version; or 375 | 376 | d) Limiting the use for publicity purposes of names of licensors or 377 | authors of the material; or 378 | 379 | e) Declining to grant rights under trademark law for use of some 380 | trade names, trademarks, or service marks; or 381 | 382 | f) Requiring indemnification of licensors and authors of that 383 | material by anyone who conveys the material (or modified versions of 384 | it) with contractual assumptions of liability to the recipient, for 385 | any liability that these contractual assumptions directly impose on 386 | those licensors and authors. 387 | 388 | All other non-permissive additional terms are considered "further 389 | restrictions" within the meaning of section 10. If the Program as you 390 | received it, or any part of it, contains a notice stating that it is 391 | governed by this License along with a term that is a further 392 | restriction, you may remove that term. If a license document contains 393 | a further restriction but permits relicensing or conveying under this 394 | License, you may add to a covered work material governed by the terms 395 | of that license document, provided that the further restriction does 396 | not survive such relicensing or conveying. 397 | 398 | If you add terms to a covered work in accord with this section, you 399 | must place, in the relevant source files, a statement of the 400 | additional terms that apply to those files, or a notice indicating 401 | where to find the applicable terms. 402 | 403 | Additional terms, permissive or non-permissive, may be stated in the 404 | form of a separately written license, or stated as exceptions; 405 | the above requirements apply either way. 406 | 407 | 8. Termination. 408 | 409 | You may not propagate or modify a covered work except as expressly 410 | provided under this License. Any attempt otherwise to propagate or 411 | modify it is void, and will automatically terminate your rights under 412 | this License (including any patent licenses granted under the third 413 | paragraph of section 11). 414 | 415 | However, if you cease all violation of this License, then your 416 | license from a particular copyright holder is reinstated (a) 417 | provisionally, unless and until the copyright holder explicitly and 418 | finally terminates your license, and (b) permanently, if the copyright 419 | holder fails to notify you of the violation by some reasonable means 420 | prior to 60 days after the cessation. 421 | 422 | Moreover, your license from a particular copyright holder is 423 | reinstated permanently if the copyright holder notifies you of the 424 | violation by some reasonable means, this is the first time you have 425 | received notice of violation of this License (for any work) from that 426 | copyright holder, and you cure the violation prior to 30 days after 427 | your receipt of the notice. 428 | 429 | Termination of your rights under this section does not terminate the 430 | licenses of parties who have received copies or rights from you under 431 | this License. If your rights have been terminated and not permanently 432 | reinstated, you do not qualify to receive new licenses for the same 433 | material under section 10. 434 | 435 | 9. Acceptance Not Required for Having Copies. 436 | 437 | You are not required to accept this License in order to receive or 438 | run a copy of the Program. Ancillary propagation of a covered work 439 | occurring solely as a consequence of using peer-to-peer transmission 440 | to receive a copy likewise does not require acceptance. However, 441 | nothing other than this License grants you permission to propagate or 442 | modify any covered work. These actions infringe copyright if you do 443 | not accept this License. Therefore, by modifying or propagating a 444 | covered work, you indicate your acceptance of this License to do so. 445 | 446 | 10. Automatic Licensing of Downstream Recipients. 447 | 448 | Each time you convey a covered work, the recipient automatically 449 | receives a license from the original licensors, to run, modify and 450 | propagate that work, subject to this License. You are not responsible 451 | for enforcing compliance by third parties with this License. 452 | 453 | An "entity transaction" is a transaction transferring control of an 454 | organization, or substantially all assets of one, or subdividing an 455 | organization, or merging organizations. If propagation of a covered 456 | work results from an entity transaction, each party to that 457 | transaction who receives a copy of the work also receives whatever 458 | licenses to the work the party's predecessor in interest had or could 459 | give under the previous paragraph, plus a right to possession of the 460 | Corresponding Source of the work from the predecessor in interest, if 461 | the predecessor has it or can get it with reasonable efforts. 462 | 463 | You may not impose any further restrictions on the exercise of the 464 | rights granted or affirmed under this License. For example, you may 465 | not impose a license fee, royalty, or other charge for exercise of 466 | rights granted under this License, and you may not initiate litigation 467 | (including a cross-claim or counterclaim in a lawsuit) alleging that 468 | any patent claim is infringed by making, using, selling, offering for 469 | sale, or importing the Program or any portion of it. 470 | 471 | 11. Patents. 472 | 473 | A "contributor" is a copyright holder who authorizes use under this 474 | License of the Program or a work on which the Program is based. The 475 | work thus licensed is called the contributor's "contributor version". 476 | 477 | A contributor's "essential patent claims" are all patent claims 478 | owned or controlled by the contributor, whether already acquired or 479 | hereafter acquired, that would be infringed by some manner, permitted 480 | by this License, of making, using, or selling its contributor version, 481 | but do not include claims that would be infringed only as a 482 | consequence of further modification of the contributor version. For 483 | purposes of this definition, "control" includes the right to grant 484 | patent sublicenses in a manner consistent with the requirements of 485 | this License. 486 | 487 | Each contributor grants you a non-exclusive, worldwide, royalty-free 488 | patent license under the contributor's essential patent claims, to 489 | make, use, sell, offer for sale, import and otherwise run, modify and 490 | propagate the contents of its contributor version. 491 | 492 | In the following three paragraphs, a "patent license" is any express 493 | agreement or commitment, however denominated, not to enforce a patent 494 | (such as an express permission to practice a patent or covenant not to 495 | sue for patent infringement). To "grant" such a patent license to a 496 | party means to make such an agreement or commitment not to enforce a 497 | patent against the party. 498 | 499 | If you convey a covered work, knowingly relying on a patent license, 500 | and the Corresponding Source of the work is not available for anyone 501 | to copy, free of charge and under the terms of this License, through a 502 | publicly available network server or other readily accessible means, 503 | then you must either (1) cause the Corresponding Source to be so 504 | available, or (2) arrange to deprive yourself of the benefit of the 505 | patent license for this particular work, or (3) arrange, in a manner 506 | consistent with the requirements of this License, to extend the patent 507 | license to downstream recipients. "Knowingly relying" means you have 508 | actual knowledge that, but for the patent license, your conveying the 509 | covered work in a country, or your recipient's use of the covered work 510 | in a country, would infringe one or more identifiable patents in that 511 | country that you have reason to believe are valid. 512 | 513 | If, pursuant to or in connection with a single transaction or 514 | arrangement, you convey, or propagate by procuring conveyance of, a 515 | covered work, and grant a patent license to some of the parties 516 | receiving the covered work authorizing them to use, propagate, modify 517 | or convey a specific copy of the covered work, then the patent license 518 | you grant is automatically extended to all recipients of the covered 519 | work and works based on it. 520 | 521 | A patent license is "discriminatory" if it does not include within 522 | the scope of its coverage, prohibits the exercise of, or is 523 | conditioned on the non-exercise of one or more of the rights that are 524 | specifically granted under this License. You may not convey a covered 525 | work if you are a party to an arrangement with a third party that is 526 | in the business of distributing software, under which you make payment 527 | to the third party based on the extent of your activity of conveying 528 | the work, and under which the third party grants, to any of the 529 | parties who would receive the covered work from you, a discriminatory 530 | patent license (a) in connection with copies of the covered work 531 | conveyed by you (or copies made from those copies), or (b) primarily 532 | for and in connection with specific products or compilations that 533 | contain the covered work, unless you entered into that arrangement, 534 | or that patent license was granted, prior to 28 March 2007. 535 | 536 | Nothing in this License shall be construed as excluding or limiting 537 | any implied license or other defenses to infringement that may 538 | otherwise be available to you under applicable patent law. 539 | 540 | 12. No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS --------------------------------------------------------------------------------