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did some runs

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Antonio De Lucreziis 1 month ago
parent 98e324786c
commit 9f95680620
5 changed files with 3973 additions and 84 deletions
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917
003.log
Unescape Escape View File

@ -0,0 +1,917 @@
Estimating line count...
Parsing GFA file...
Skipped 2418 lines of type: P
Number of entries: 8347110
Removing 78 invalid nodes...
Computing graph stats...
Computing nodes degrees...
Computing histogram...
Stats:
- Nodes: 3460777
- Edges: 4886726
Graph degrees histogram (degree/count):
- 0: 3
- 1: 2121
- 2: 2017208
- 3: 280128
- 4: 1047576
- 5: 69562
- 6: 20938
- 7: 8895
- 8: 4708
- 9: 2768
- 10: 1740
- 11: 1140
- 12: 873
- 13: 644
- 14: 436
- 15: 339
- 16: 267
- 17: 210
- 18: 183
- 19: 127
- 20: 100
- 21: 97
- 22: 77
- 23: 55
- 24: 48
- 25: 48
- 26: 28
- 27: 33
- 28: 32
- 29: 39
- 30: 29
- 31: 19
- 32: 18
- 33: 17
- 34: 8
- 35: 15
- 36: 7
- 37: 12
- 38: 14
- 39: 10
- 40: 8
- 41: 6
- 42: 8
- 43: 8
- 44: 6
- 45: 10
- 46: 5
- 47: 5
- 48: 6
- 49: 5
- 50: 9
- 51: 2
- 52: 6
- 53: 3
- 54: 4
- 55: 2
- 56: 1
- 57: 8
- 58: 1
- 59: 3
- 60: 3
- 61: 1
- 62: 1
- 63: 5
- 64: 1
- 65: 3
- 66: 1
- 67: 6
- 68: 2
- 69: 1
- 71: 3
- 72: 3
- 73: 2
- 74: 2
- 75: 1
- 78: 1
- 79: 1
- 80: 2
- 81: 1
- 83: 1
- 84: 2
- 85: 2
- 87: 2
- 90: 1
- 91: 1
- 93: 1
- 96: 2
- 97: 3
- 99: 1
- 100: 1
- 101: 2
- 105: 2
- 108: 1
- 110: 1
- 112: 1
- 115: 2
- 116: 1
- 118: 1
- 119: 2
- 126: 1
- 127: 1
- 130: 1
- 131: 1
- 132: 1
- 135: 1
- 136: 1
- 142: 1
- 143: 1
- 150: 1
- 151: 2
- 164: 1
- 165: 1
- 168: 2
- 176: 1
- 183: 1
- 186: 1
- 197: 1
- 206: 1
- 208: 1
- 211: 1
- 229: 1
- 235: 1
- 269: 1
- 310: 1
- 439: 1
- 454: 1
In-degrees histogram (degree/count):
- 0: 1312
- 1: 2153708
- 2: 1239763
- 3: 49275
- 4: 9903
- 5: 2894
- 6: 1249
- 7: 663
- 8: 366
- 9: 240
- 10: 199
- 11: 146
- 12: 118
- 13: 92
- 14: 90
- 15: 62
- 16: 59
- 17: 59
- 18: 41
- 19: 39
- 20: 41
- 21: 33
- 22: 29
- 23: 30
- 24: 26
- 25: 24
- 26: 15
- 27: 15
- 28: 14
- 29: 19
- 30: 15
- 31: 12
- 32: 10
- 33: 10
- 34: 7
- 35: 6
- 36: 14
- 37: 9
- 38: 3
- 39: 7
- 40: 7
- 41: 5
- 42: 2
- 43: 9
- 44: 8
- 45: 5
- 46: 4
- 47: 8
- 48: 3
- 50: 2
- 51: 2
- 52: 3
- 53: 4
- 54: 2
- 55: 3
- 56: 3
- 57: 1
- 58: 2
- 59: 1
- 60: 1
- 62: 1
- 63: 3
- 64: 2
- 65: 4
- 66: 4
- 67: 1
- 68: 1
- 69: 1
- 70: 2
- 71: 1
- 72: 1
- 74: 3
- 78: 3
- 79: 1
- 80: 1
- 81: 2
- 83: 2
- 84: 1
- 85: 2
- 88: 1
- 90: 2
- 92: 2
- 94: 1
- 96: 1
- 97: 1
- 100: 3
- 101: 1
- 102: 1
- 104: 1
- 108: 2
- 110: 1
- 111: 1
- 115: 2
- 117: 1
- 118: 1
- 124: 1
- 125: 1
- 129: 1
- 131: 4
- 140: 1
- 147: 1
- 149: 1
- 162: 2
- 163: 1
- 166: 2
- 179: 2
- 184: 1
- 204: 2
- 209: 1
- 226: 1
- 232: 1
- 256: 1
- 302: 1
- 434: 1
- 450: 1
Out-degrees histogram (degree/count):
- 0: 887
- 1: 2203729
- 2: 1169135
- 3: 54639
- 4: 15245
- 5: 6598
- 6: 3677
- 7: 2248
- 8: 1376
- 9: 897
- 10: 672
- 11: 482
- 12: 320
- 13: 226
- 14: 155
- 15: 119
- 16: 94
- 17: 62
- 18: 48
- 19: 44
- 20: 34
- 21: 23
- 22: 17
- 23: 15
- 24: 1
- 25: 3
- 26: 5
- 27: 9
- 28: 3
- 29: 1
- 30: 5
- 32: 1
- 34: 1
- 35: 1
- 41: 1
- 43: 1
- 44: 2
- 58: 1
Computing edge types...
Computing edge types histogram...
Node count: 3460774
Edge count: 4853330, Total edge count: 4853330
Edge types histogram (type/count):
- TreeEdge: 3459200
- ForwardEdge: 352721
- CrossEdge: 1041409
Computing connected components...
Computing sizes histogram...
Connected components histogram (size/count):
- 2: 530
- 3: 1
- 4: 2
- 8: 1
- 92: 1
- 135: 1
- 293: 1
- 305: 1
- 2286: 1
- 5040: 1
- 5639: 1
- 9714: 1
- 12885: 1
- 30694: 1
- 40082: 1
- 50661: 1
- 58952: 1
- 101785: 1
- 149492: 1
- 160217: 1
- 518117: 1
- 951450: 1
- 1361856: 1
Picking largest connected component...
Computing graph stats...
Computing nodes degrees...
Computing histogram...
Stats:
- Nodes: 1361856
- Edges: 1914711
Graph degrees histogram (degree/count):
- 1: 2545
- 2: 790746
- 3: 124057
- 4: 397682
- 5: 29479
- 6: 8481
- 7: 3512
- 8: 1819
- 9: 1032
- 10: 666
- 11: 448
- 12: 346
- 13: 207
- 14: 167
- 15: 139
- 16: 92
- 17: 81
- 18: 58
- 19: 44
- 20: 35
- 21: 29
- 22: 28
- 23: 24
- 24: 24
- 25: 11
- 26: 4
- 27: 13
- 28: 9
- 29: 13
- 30: 5
- 31: 4
- 32: 2
- 33: 3
- 34: 5
- 35: 2
- 36: 4
- 37: 1
- 38: 1
- 39: 1
- 40: 1
- 41: 1
- 42: 1
- 43: 5
- 44: 4
- 45: 2
- 47: 1
- 50: 1
- 52: 1
- 54: 2
- 57: 1
- 64: 1
- 67: 1
- 72: 1
- 73: 1
- 78: 1
- 83: 1
- 96: 1
- 99: 1
- 100: 1
- 109: 1
- 115: 1
- 119: 1
- 129: 1
- 149: 1
- 163: 1
- 182: 1
- 235: 1
In-degrees histogram (degree/count):
- 0: 223
- 1: 859347
- 2: 472782
- 3: 21590
- 4: 4517
- 5: 1479
- 6: 669
- 7: 371
- 8: 218
- 9: 126
- 10: 97
- 11: 81
- 12: 52
- 13: 46
- 14: 36
- 15: 24
- 16: 31
- 17: 22
- 18: 10
- 19: 13
- 20: 12
- 21: 16
- 22: 8
- 23: 8
- 24: 7
- 25: 8
- 26: 4
- 27: 3
- 28: 4
- 29: 5
- 30: 2
- 31: 2
- 32: 3
- 33: 1
- 34: 1
- 35: 1
- 36: 3
- 37: 1
- 38: 1
- 39: 1
- 40: 1
- 41: 2
- 43: 5
- 44: 1
- 45: 1
- 48: 1
- 51: 1
- 53: 1
- 56: 1
- 63: 1
- 66: 1
- 70: 1
- 71: 1
- 74: 1
- 83: 1
- 96: 1
- 97: 1
- 100: 1
- 108: 1
- 115: 1
- 118: 1
- 129: 1
- 149: 1
- 162: 1
- 179: 1
- 232: 1
Out-degrees histogram (degree/count):
- 0: 5593
- 1: 864226
- 2: 455228
- 3: 24556
- 4: 6340
- 5: 2439
- 6: 1296
- 7: 684
- 8: 444
- 9: 289
- 10: 212
- 11: 136
- 12: 101
- 13: 74
- 14: 48
- 15: 41
- 16: 29
- 17: 22
- 18: 24
- 19: 20
- 20: 12
- 21: 7
- 22: 8
- 23: 3
- 25: 3
- 26: 4
- 27: 6
- 29: 3
- 30: 3
- 33: 1
- 41: 1
- 42: 1
- 44: 1
- 52: 1
Computing edge types...
Computing edge types histogram...
Node count: 1361856
Edge count: 1914711, Total edge count: 1914711
Edge types histogram (type/count):
- TreeEdge: 1361619
- ForwardEdge: 110203
- CrossEdge: 442889
Searching for a start node...
Start node: ("1125070", Reverse)
NodeDegree { degree: 2, in_degree: 0, out_degree: 2 }
Orientation histogram:
- Forward: 1361803
- Reverse: 53
Visiting the graph, searching 1 paths...
Path #1 of length 4146
Sequence #1 of length 390758
Searching ACGT in the sequence (naive)...
Occurrences: [224, 516, 1163, 2921, 3458, 3487, 4201, 4506, 4778, 5847, 5949, 6053, 6266, 6532, 6568, 7026, 7564, 7816, 7935, 7950, 8998, 10867, 12258, 12779, 12970, 14877, 15383, 16423, 20017, 20535, 20802, 22518, 23177, 23947, 24491, 24597, 25118, 26238, 26363, 26926, 26944, 28530, 28798, 30151, 30571, 31459, 32440, 33105, 35476, 35585, 40104, 41617, 42223, 42423, 44627, 44660, 45366, 45588, 47850, 52405, 54283, 56647, 57635, 57942, 58069, 59830, 60076, 63424, 64128, 65087, 65197, 65791, 66269, 66791, 68001, 68581, 68931, 70623, 70907, 71916, 73213, 73445, 75357, 76757, 78201, 79140, 79723, 81794, 82887, 83147, 85157, 87135, 90712, 91304, 91700, 92410, 93060, 93948, 94493, 95003, 96089, 96977, 97917, 99575, 99922, 101150, 101372, 102309, 103486, 104836, 106491, 107057, 107146, 107710, 108252, 108838, 110492, 112248, 112820, 113409, 113490, 115079, 118146, 118560, 119821, 119850, 119920, 120811, 121113, 122957, 126968, 127784, 127793, 129165, 130005, 130068, 130113, 132514, 133552, 133736, 134342, 134751, 135407, 135416, 135697, 137146, 137451, 138032, 138076, 138799, 139051, 139738, 140166, 140255, 140395, 140747, 144270, 145441, 145840, 148891, 148923, 152343, 152993, 153132, 153269, 153963, 154186, 155125, 155666, 155792, 155842, 156284, 156424, 156512, 156889, 157318, 158919, 161299, 161567, 162923, 163849, 164935, 165293, 166627, 169525, 169554, 169663, 170351, 171021, 171031, 171069, 171093, 171129, 171152, 172352, 172744, 172875, 172984, 173013, 173899, 173925, 174007, 174910, 176510, 176939, 177316, 177404, 177544, 177670, 179988, 180211, 181426, 181846, 183021, 186545, 186887, 187027, 187116, 187544, 188233, 188484, 189207, 189251, 189832, 190137, 191586, 191867, 191876, 192532, 192941, 193548, 193732, 196126, 196692, 196742, 196868, 197408, 198344, 198744, 199727, 200792, 201544, 204982, 205431, 206080, 207721, 209377, 212438, 213562, 213584, 214268, 215359, 216165, 216652, 216927, 217153, 218780, 222928, 225043, 225132, 227447, 227644, 227887, 228221, 228511, 229614, 231065, 232180, 234306, 235317, 235648, 240151, 240539, 240913, 242500, 242762, 243210, 244676, 244685, 245082, 246301, 248115, 248412, 248824, 252013, 253657, 254576, 255340, 257458, 258253, 258397, 258509, 263678, 264491, 264754, 264835, 266523, 272073, 274004, 274289, 274843, 275171, 280510, 281552, 281744, 282697, 283688, 284051, 284086, 285696, 285827, 289829, 290921, 292114, 293394, 294480, 295216, 295463, 295541, 296529, 296619, 296666, 296688, 296743, 297452, 298265, 300030, 300165, 300447, 301087, 302337, 303430, 303775, 304979, 305572, 305584, 306559, 306617, 307163, 309846, 311090, 312659, 313326, 313334, 313418, 313746, 315506, 316731, 316959, 317278, 318473, 320032, 321284, 323330, 324048, 324199, 324425, 324583, 324911, 325022, 325096, 325282, 325570, 326300, 327236, 328264, 329039, 329654, 329857, 330470, 330776, 331165, 331417, 331438, 331529, 333140, 334242, 335027, 335104, 337813, 337868, 337890, 337937, 338027, 339093, 339340, 340076, 341162, 342446, 343639, 347506, 348399, 349686, 351314, 351461, 353952, 359726, 362750, 365116, 365154, 366194, 367763, 368244, 368566, 368575, 369179, 369981, 370825, 377002, 378226, 380058, 380657, 381712, 382463, 382844, 384607, 385676, 385877, 385915, 386191, 386429, 386577, 387277]
Searching ACGT in the sequence (rolling hash)...
Hash match at position 2205
=> False positive
Hash match at position 6373
=> False positive
Hash match at position 12954
=> False positive
Hash match at position 14196
=> False positive
Hash match at position 16087
=> False positive
Hash match at position 16479
=> False positive
Hash match at position 28799
=> False positive
Hash match at position 40931
=> False positive
Hash match at position 45378
=> False positive
Hash match at position 54233
=> False positive
Hash match at position 56472
=> False positive
Hash match at position 62590
=> False positive
Hash match at position 66523
=> False positive
Hash match at position 70805
=> False positive
Hash match at position 72998
=> False positive
Hash match at position 95694
=> False positive
Hash match at position 111110
=> False positive
Hash match at position 113640
=> False positive
Hash match at position 117003
=> False positive
Hash match at position 126606
=> False positive
Hash match at position 134592
=> False positive
Hash match at position 142190
=> False positive
Hash match at position 143582
=> False positive
Hash match at position 144833
=> False positive
Hash match at position 152670
=> False positive
Hash match at position 157126
=> False positive
Hash match at position 183862
=> False positive
Hash match at position 189224
=> False positive
Hash match at position 195311
=> False positive
Hash match at position 195350
=> False positive
Hash match at position 195972
=> False positive
Hash match at position 197090
=> False positive
Hash match at position 213266
=> False positive
Hash match at position 213618
=> False positive
Hash match at position 218768
=> False positive
Hash match at position 225624
=> False positive
Hash match at position 231613
=> False positive
Hash match at position 232308
=> False positive
Hash match at position 245358
=> False positive
Hash match at position 266712
=> False positive
Hash match at position 267010
=> False positive
Hash match at position 272362
=> False positive
Hash match at position 284700
=> False positive
Hash match at position 299659
=> False positive
Hash match at position 308836
=> False positive
Hash match at position 313218
=> False positive
Hash match at position 315397
=> False positive
Hash match at position 324268
=> False positive
Hash match at position 324848
=> False positive
Hash match at position 329852
=> False positive
Hash match at position 330578
=> False positive
Hash match at position 330906
=> False positive
Hash match at position 344318
=> False positive
Hash match at position 346430
=> False positive
Hash match at position 348288
=> False positive
Hash match at position 350788
=> False positive
Hash match at position 354756
=> False positive
Hash match at position 366826
=> False positive
Hash match at position 380496
=> False positive
Hash match at position 387102
=> False positive
Hash match at position 388787
=> False positive
Occurrences: []
Computing k-mer histogram...
K-mer histogram (kmers/count):
- AAAA: 1175611
- AAAC: 592605
- AAAG: 1009217
- AAAT: 781229
- AACA: 428345
- AACC: 198507
- AACG: 143889
- AACT: 577756
- AAGA: 725774
- AAGC: 291817
- AAGG: 439126
- AAGT: 426031
- AATA: 584842
- AATC: 386240
- AATG: 628293
- AATT: 413295
- ACAA: 553292
- ACAC: 228634
- ACAG: 374733
- ACAT: 379962
- ACCA: 272469
- ACCC: 152578
- ACCG: 48967
- ACCT: 233158
- ACGA: 117310
- ACGC: 19760
- ACGG: 19777
- ACGT: 103956
- ACTA: 225547
- ACTC: 336757
- ACTG: 323813
- ACTT: 395383
- AGAA: 764137
- AGAC: 208058
- AGAG: 488851
- AGAT: 486804
- AGCA: 282363
- AGCC: 199259
- AGCG: 58006
- AGCT: 285797
- AGGA: 381807
- AGGC: 322385
- AGGG: 218979
- AGGT: 312993
- AGTA: 202194
- AGTC: 191875
- AGTG: 403423
- AGTT: 658789
- ATAA: 384886
- ATAC: 254291
- ATAG: 255899
- ATAT: 638550
- ATCA: 544681
- ATCC: 374829
- ATCG: 51114
- ATCT: 376117
- ATGA: 352159
- ATGC: 407298
- ATGG: 248757
- ATGT: 422236
- ATTA: 328822
- ATTC: 480158
- ATTG: 277827
- ATTT: 616451
- CAAA: 1160025
- CAAC: 339887
- CAAG: 226176
- CAAT: 347394
- CACA: 498118
- CACC: 214464
- CACG: 45495
- CACT: 336532
- CAGA: 547232
- CAGC: 226023
- CAGG: 289052
- CAGT: 352994
- CATA: 278596
- CATC: 444599
- CATG: 270898
- CATT: 354977
- CCAA: 506643
- CCAC: 410796
- CCAG: 258463
- CCAT: 357414
- CCCA: 265718
- CCCC: 162653
- CCCG: 129507
- CCCT: 229539
- CCGA: 35537
- CCGC: 33789
- CCGG: 21445
- CCGT: 188174
- CCTA: 151771
- CCTC: 314128
- CCTG: 289664
- CCTT: 355294
- CGAA: 195019
- CGAC: 19670
- CGAG: 57008
- CGAT: 20153
- CGCA: 39599
- CGCC: 26346
- CGCG: 5115
- CGCT: 61558
- CGGA: 32300
- CGGC: 24269
- CGGG: 26133
- CGGT: 37131
- CGTA: 47617
- CGTC: 78825
- CGTG: 67427
- CGTT: 196299
- CTAA: 203954
- CTAC: 297972
- CTAG: 168160
- CTAT: 310682
- CTCA: 388310
- CTCC: 395302
- CTCG: 73353
- CTCT: 522428
- CTGA: 445358
- CTGC: 386881
- CTGG: 268904
- CTGT: 413674
- CTTA: 200567
- CTTC: 459048
- CTTG: 341872
- CTTT: 561621
- GAAA: 725011
- GAAC: 258832
- GAAG: 470722
- GAAT: 590617
- GACA: 205961
- GACC: 98841
- GACG: 31274
- GACT: 155226
- GAGA: 436593
- GAGC: 145298
- GAGG: 292767
- GAGT: 402316
- GATA: 232148
- GATC: 159086
- GATG: 199667
- GATT: 423158
- GCAA: 294115
- GCAC: 127547
- GCAG: 403864
- GCAT: 198530
- GCCA: 223527
- GCCC: 128294
- GCCG: 20061
- GCCT: 260304
- GCGA: 36380
- GCGC: 41978
- GCGG: 58791
- GCGT: 22413
- GCTA: 181358
- GCTC: 314922
- GCTG: 233316
- GCTT: 351866
- GGAA: 406305
- GGAC: 93015
- GGAG: 249228
- GGAT: 203915
- GGCA: 196570
- GGCC: 199076
- GGCG: 26020
- GGCT: 201531
- GGGA: 256032
- GGGC: 98165
- GGGG: 117316
- GGGT: 172815
- GGTA: 125848
- GGTC: 200007
- GGTG: 199107
- GGTT: 256618
- GTAA: 168075
- GTAC: 96394
- GTAG: 176689
- GTAT: 212807
- GTCA: 195726
- GTCC: 253476
- GTCG: 40374
- GTCT: 221768
- GTGA: 429479
- GTGC: 130381
- GTGG: 228989
- GTGT: 387431
- GTTA: 221644
- GTTC: 365100
- GTTG: 274241
- GTTT: 831132
- TAAA: 491909
- TAAC: 158133
- TAAG: 179785
- TAAT: 296553
- TACA: 406100
- TACC: 195575
- TACG: 40160
- TACT: 214082
- TAGA: 241403
- TAGC: 163290
- TAGG: 215852
- TAGT: 275266
- TATA: 438366
- TATC: 359197
- TATG: 332743
- TATT: 513098
- TCAA: 720108
- TCAC: 328384
- TCAG: 377692
- TCAT: 414551
- TCCA: 770252
- TCCC: 344157
- TCCG: 79751
- TCCT: 388066
- TCGA: 102765
- TCGC: 37104
- TCGG: 20005
- TCGT: 75840
- TCTA: 422777
- TCTC: 414391
- TCTG: 669170
- TCTT: 460545
- TGAA: 678939
- TGAC: 170455
- TGAG: 481199
- TGAT: 304456
- TGCA: 504436
- TGCC: 208124
- TGCG: 70442
- TGCT: 532425
- TGGA: 282231
- TGGC: 177301
- TGGG: 280422
- TGGT: 257907
- TGTA: 277680
- TGTC: 240123
- TGTG: 503080
- TGTT: 575702
- TTAA: 369807
- TTAC: 207236
- TTAG: 294207
- TTAT: 479726
- TTCA: 714087
- TTCC: 560032
- TTCG: 70939
- TTCT: 849599
- TTGA: 406602
- TTGC: 391294
- TTGG: 250912
- TTGT: 371033
- TTTA: 600182
- TTTC: 890566
- TTTG: 525339
- TTTT: 1047325
Found 256 of 256 possible kmers (about 100.00% coverage)
Cleaning up...
cargo run --release -- show -i dataset/chrX.hprc-v1.0-pggb.local.gfa -c 1 -p 230.46s user 32.90s system 98% cpu 4:26.69 total

2907
004.log
View File

File diff suppressed because it is too large Load Diff

20
src/gfa/parser.rs
Unescape Escape View File

@ -141,16 +141,9 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
let mut entries = Vec::new();
let mut skipped = Vec::new();
for line in BufReader::new(reader)
.lines()
.progress_count(line_count)
.with_style(
indicatif::ProgressStyle::default_bar()
.template("{prefix} {spinner} [{elapsed_precise}] [{wide_bar}] {pos}/{len}")
.unwrap(),
)
.with_prefix("parsing source file")
{
println!("Parsing GFA file...");
for line in BufReader::new(reader).lines().progress_count(line_count) {
let line = line?;
let line = line.trim();
@ -174,6 +167,7 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
entries.push(entry);
}
// Print skipped lines by compacting same ones together
for (s, count) in skipped.iter().fold(Vec::new(), |mut acc, s| {
if let Some((last, count)) = acc.last_mut() {
if *last == s {
@ -187,11 +181,7 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
acc
}) {
if count > 1 {
eprintln!("skipped {} lines of type: {}", count, s);
} else {
eprintln!("skipped line type: {}", s);
}
eprintln!("Skipped {} lines of type: {}", count, s);
}
Ok(entries)

194
src/main.rs
Unescape Escape View File

@ -49,7 +49,7 @@ struct CommandShow {
#[argh(option, short = 'k', default = "4")]
/// k-mer length
k: usize,
kmer_size: usize,
}
fn main() -> std::io::Result<()> {
@ -63,25 +63,32 @@ fn main() -> std::io::Result<()> {
process::exit(1);
}
println!("Estimating line count...");
let file_lines_count = BufReader::new(std::fs::File::open(&opts.input)?)
.lines()
.progress_with(
indicatif::ProgressBar::new_spinner().with_message("estimating line count"),
)
.progress_with(indicatif::ProgressBar::new_spinner())
.count() as u64;
let file = std::fs::File::open(opts.input)?;
let entries = gfa::parser::parse_source(file, file_lines_count)?;
let entries =
gfa::parser::parse_source(std::fs::File::open(opts.input)?, file_lines_count)?;
println!("Number of entries: {}", entries.len());
let mut sequence_map = HashMap::new();
let mut graph: AdjacencyGraph<(String, Orientation)> = AdjacencyGraph::new();
let mut invalid_nodes = vec![];
for entry in entries {
match entry {
Entry::Segment { id, sequence } => {
// validate sequence is a valid DNA sequence
if sequence.chars().any(|c| !"ACGT".contains(c)) {
invalid_nodes.push(id.clone());
continue;
}
sequence_map.insert(id.clone(), sequence);
}
Entry::Link {
@ -96,21 +103,18 @@ fn main() -> std::io::Result<()> {
}
}
println!("Removing {} invalid nodes...", invalid_nodes.len());
// remove invalid nodes
for id in invalid_nodes.iter().progress() {
graph.remove_node(&(id.clone(), Orientation::Forward));
graph.remove_node(&(id.clone(), Orientation::Reverse));
}
println!();
compute_graph_degrees(&graph);
let dag = graph.dag();
// let edge_types = compute_edge_types(&graph);
// for ((from, to), edge_type) in edge_types.iter() {
// match edge_type {
// graph::edge_types::EdgeType::BackEdge => {
// graph.remove_edge(from, to);
// }
// _ => {}
// }
// }
compute_edge_types(&dag.0);
let ccs = compute_ccs(&dag.0);
@ -151,25 +155,77 @@ fn main() -> std::io::Result<()> {
for (i, sequence) in sequences.iter().enumerate() {
println!("Sequence #{} of length {}", i + 1, sequence.len());
println!("Searching {} in the sequence (naive)...", opts.pattern);
let occurrences = compute_sequence_occurrences_naive(sequence, &opts.pattern);
println!("Occurrences: {:?}\n", occurrences);
println!("Searching {} (naive)...", opts.pattern);
println!(
"Occurrences: {:?}\n",
compute_sequence_occurrences_naive(sequence, &opts.pattern)
);
println!("Searching {} (rolling hash)...", opts.pattern);
println!(
"Searching {} in the sequence (rolling hash)...",
opts.pattern
"Occurrences: {:?}\n",
compute_sequence_occurrences_rolling_hash(sequence, &opts.pattern)
);
let occurrences =
compute_sequence_occurrences_rolling_hash(sequence, &opts.pattern);
println!("Occurrences: {:?}\n", occurrences);
}
compute_kmer_histogram_lb(&sequence_map, &largest_cc_graph, opts.kmer_size);
println!("Cleaning up...");
process::exit(0);
}
}
}
fn compute_kmer_histogram_lb(
sequence_map: &HashMap<String, String>,
graph: &DirectedAcyclicGraph<(String, Orientation)>,
k: usize,
) {
println!("Computing k-mer histogram...");
let mut kmer_counts = HashMap::new();
for node in graph.nodes().iter().progress() {
let sequence = get_node_sequence(sequence_map, &node);
let kmer_counts_node = sequence_kmer_histogram(&sequence, k);
for (kmer, count) in kmer_counts_node {
*kmer_counts.entry(kmer).or_insert(0) += count;
}
}
let mut kmer_counts = kmer_counts.into_iter().collect::<Vec<_>>();
kmer_counts.sort_by(|a, b| b.1.cmp(&a.1).reverse());
println!("K-mer histogram (kmers/count):");
for (kmer, count) in &kmer_counts {
println!("- {}: {}", kmer, count);
}
println!(
"Found {} of {} possible kmers (about {:.2}% coverage)",
kmer_counts.len(),
4usize.pow(k as u32),
(kmer_counts.len() as f64 / 4usize.pow(k as u32) as f64) * 100.0
);
}
fn sequence_kmer_histogram(sequence: &str, k: usize) -> BTreeMap<String, usize> {
let mut counts: BTreeMap<String, usize> = BTreeMap::new();
if sequence.len() < k {
return counts;
}
for i in 0..sequence.len() - k {
let kmer = &sequence[i..i + k];
*counts.entry(kmer.to_string()).or_insert(0) += 1;
}
counts
}
fn letter_to_number(letter: char) -> u64 {
match letter {
'A' => 1,
@ -180,6 +236,29 @@ fn letter_to_number(letter: char) -> u64 {
}
}
fn letter_complement(letter: char) -> char {
match letter {
'A' => 'T',
'T' => 'A',
'C' => 'G',
'G' => 'C',
_ => panic!("Invalid letter: {}", letter),
}
}
fn get_node_sequence<'a>(
sequence_map: &'a HashMap<String, String>,
node: &(String, Orientation),
) -> String {
let (id, orientation) = node;
let seq = sequence_map.get(id).expect("sequence not found");
match orientation {
Orientation::Forward => seq.clone(),
Orientation::Reverse => seq.chars().map(letter_complement).rev().collect::<String>(),
}
}
fn compute_sequence_occurrences_rolling_hash(sequence: &str, pattern: &str) -> Vec<usize> {
let chars = sequence.chars().map(letter_to_number).collect::<Vec<_>>();
@ -191,7 +270,6 @@ fn compute_sequence_occurrences_rolling_hash(sequence: &str, pattern: &str) -> V
let pattern_hash = rl.hash_pattern(&pattern.chars().map(letter_to_number).collect::<Vec<_>>());
for i in 0..pattern.len() {
// println!("Adding letter: {}", chars[i]);
rl.add_last(chars[i]);
}
@ -242,23 +320,8 @@ fn compute_sequences(
let mut sequence = String::new();
for node in path {
let (id, orientation) = node;
let seq = sequence_map.get(&id).expect("sequence not found");
match orientation {
Orientation::Forward => sequence.push_str(seq),
Orientation::Reverse => sequence.push_str(
&seq.chars()
.map(|c| match c {
'A' => 'T',
'T' => 'A',
'C' => 'G',
'G' => 'C',
_ => panic!("Invalid letter: {}", c),
})
.rev()
.collect::<String>(),
),
}
let piece = get_node_sequence(sequence_map, &node);
sequence.push_str(&piece);
}
sequences.push(sequence);
@ -285,6 +348,7 @@ fn compute_orientation_histogram(graph: &impl Graph<(String, Orientation)>) {
for (orientation, count) in orientation_histogram.iter() {
println!("- {:?}: {}", orientation, count);
}
println!();
}
fn compute_ccs<V>(graph: &AdjacencyGraph<V>) -> Vec<Vec<V>>
@ -307,6 +371,7 @@ where
for (size, count) in hist.iter() {
println!("- {}: {}", size, count);
}
println!();
ccs
}
@ -333,10 +398,12 @@ where
graph.edges().len(),
edge_types.len()
);
println!("Edge types histogram (type/count):");
for (edge_type, count) in histogram.iter() {
println!("- {:?}: {}", edge_type, count);
}
println!();
edge_types
}
@ -447,35 +514,34 @@ where
for (degree, count) in histogram.iter() {
println!("- {}: {}", degree, count);
}
println!("In-degrees histogram (degree/count):");
for (degree, count) in histogram_in.iter() {
println!("- {}: {}", degree, count);
}
println!("Out-degrees histogram (degree/count):");
for (degree, count) in histogram_out.iter() {
println!("- {}: {}", degree, count);
}
println!();
let mut node_degrees = BTreeMap::new();
for node in graph.nodes() {
node_degrees.insert(
node.clone(),
NodeDegree {
degree: *vertices_degrees.get(&node).expect("node already computed"),
in_degree: *vertices_in_degrees
.get(&node)
.expect("node already computed"),
out_degree: *vertices_out_degrees
.get(&node)
.expect("node already computed"),
},
);
}
node_degrees
graph
.nodes()
.iter()
.map(|node| {
(
node.clone(),
NodeDegree {
degree: *vertices_degrees.get(node).expect("node already computed"),
in_degree: *vertices_in_degrees
.get(node)
.expect("node already computed"),
out_degree: *vertices_out_degrees
.get(node)
.expect("node already computed"),
},
)
})
.collect()
}
// fn compute_compact_graph<V>(graph: &mut UndirectedGraph<V>) -> UndirectedGraph<V>

19
src/rolling_hash/mod.rs
Unescape Escape View File

@ -66,9 +66,10 @@ where
};
// Shift lhs to the right by the difference in offsets
let shifted_lhs = (lhs.hash
* wrapping_pow_correct(self.alphabet_size, rhs.offset - lhs.offset))
% self.modulus;
let shifted_lhs = (lhs.hash.wrapping_mul(wrapping_pow_correct(
self.alphabet_size,
rhs.offset - lhs.offset,
))) % self.modulus;
shifted_lhs == rhs.hash
}
@ -100,7 +101,11 @@ where
// wrapping_pow_correct(self.alphabet_size, i),
// self.hash
// );
self.hash += value.into() * wrapping_pow_correct(self.alphabet_size, i);
self.hash = self.hash.wrapping_add(
value
.into()
.wrapping_mul(wrapping_pow_correct(self.alphabet_size, i)),
);
}
pub fn remove_first(&mut self) {
@ -108,7 +113,11 @@ where
let i = self.offset;
self.hash -= value.into() * wrapping_pow_correct(self.alphabet_size, i);
self.hash = self.hash.wrapping_sub(
value
.into()
.wrapping_mul(wrapping_pow_correct(self.alphabet_size, i)),
);
self.offset += 1;
}

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