Datasets
Models
Downloads: 1
Diff of
/tests/test_coverage.py
[000000]
..
[d7cf27]
Switch to unified view
| a | b/tests/test_coverage.py | ||
|---|---|---|---|
| 1 | import os |
||
| 2 | from itertools import product |
||
| 3 | |||
| 4 | import matplotlib |
||
| 5 | matplotlib.use('AGG') # pylint: disable= |
||
| 6 | |||
| 7 | import numpy as np |
||
| 8 | import pandas |
||
| 9 | import pkg_resources |
||
| 10 | import pytest |
||
| 11 | from pybedtools import BedTool |
||
| 12 | |||
| 13 | from janggu.data import Bioseq |
||
| 14 | from janggu.data import Cover |
||
| 15 | from janggu.data import Transpose |
||
| 16 | from janggu.data import GenomicIndexer |
||
| 17 | from janggu.data import plotGenomeTrack |
||
| 18 | from janggu.data import LineTrack |
||
| 19 | from janggu.data import SeqTrack |
||
| 20 | from janggu.data import HeatTrack |
||
| 21 | |||
| 22 | |||
| 23 | def test_channel_last_first(): |
||
| 24 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 25 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 26 | |||
| 27 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 28 | |||
| 29 | cover = Cover.create_from_bigwig( |
||
| 30 | 'test', |
||
| 31 | bigwigfiles=bwfile_, |
||
| 32 | resolution=1, |
||
| 33 | binsize=200, |
||
| 34 | roi=bed_file, |
||
| 35 | store_whole_genome=True, |
||
| 36 | storage='ndarray') |
||
| 37 | assert cover.shape == (100, 200, 1, 1) |
||
| 38 | assert cover[0].shape == (1, 200, 1, 1) |
||
| 39 | cover1 = cover |
||
| 40 | |||
| 41 | cover = Transpose(Cover.create_from_bigwig( |
||
| 42 | 'test', |
||
| 43 | bigwigfiles=bwfile_, |
||
| 44 | resolution=1, |
||
| 45 | binsize=200, |
||
| 46 | roi=bed_file, |
||
| 47 | store_whole_genome=True, |
||
| 48 | storage='ndarray'), axis=(0, 3, 2, 1)) |
||
| 49 | assert cover.shape == (100, 1, 1, 200) |
||
| 50 | assert cover[0].shape == (1, 1, 1, 200) |
||
| 51 | |||
| 52 | np.testing.assert_equal(cover1[0], np.transpose(cover[0], (0, 3, 2, 1))) |
||
| 53 | |||
| 54 | |||
| 55 | def test_cover_roi_binsize_padding(tmpdir): |
||
| 56 | |||
| 57 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 58 | bed_file = os.path.join(data_path, 'sample_equalsize.bed') |
||
| 59 | print(pandas.read_csv(bed_file, |
||
| 60 | sep='\t', header=None, |
||
| 61 | names=['chrom', 'start', 'end', |
||
| 62 | 'name', 'score', 'strand'])) |
||
| 63 | |||
| 64 | roi_file = os.path.join(data_path, "sample.bed") |
||
| 65 | roi = pandas.read_csv(roi_file, |
||
| 66 | sep='\t', header=None, |
||
| 67 | names=['chrom', 'start', 'end', |
||
| 68 | 'name', 'score', 'strand']) |
||
| 69 | |||
| 70 | roi.end.iloc[0] += 12 |
||
| 71 | roi.end.iloc[1] += 111 |
||
| 72 | print(roi) |
||
| 73 | |||
| 74 | with pytest.raises(ValueError): |
||
| 75 | # error due to binsize not being a multiple of resolution |
||
| 76 | Cover.create_from_bed('test', |
||
| 77 | bedfiles=bed_file, |
||
| 78 | roi=roi, binsize=30, |
||
| 79 | stepsize=30, |
||
| 80 | store_whole_genome=True, |
||
| 81 | cache=False, resolution=7) |
||
| 82 | |||
| 83 | with pytest.raises(ValueError): |
||
| 84 | # interval starts must align with resolution intervals |
||
| 85 | rroi = roi.copy() |
||
| 86 | rroi.start += 1 |
||
| 87 | Cover.create_from_bed('test', |
||
| 88 | bedfiles=bed_file, |
||
| 89 | roi=rroi, binsize=30, |
||
| 90 | stepsize=30, |
||
| 91 | store_whole_genome=True, |
||
| 92 | cache=False, resolution=30) |
||
| 93 | |||
| 94 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 95 | cov = Cover.create_from_bed('test', |
||
| 96 | bedfiles=bed_file, |
||
| 97 | roi=roi, binsize=300, |
||
| 98 | stepsize=300, |
||
| 99 | store_whole_genome=swg, |
||
| 100 | storage=store, |
||
| 101 | cache=False, resolution=10) |
||
| 102 | assert len(cov) == 68 |
||
| 103 | assert cov.shape == (68, 30, 1, 1) |
||
| 104 | [c for c in cov] |
||
| 105 | |||
| 106 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 107 | cov = Cover.create_from_bed('test', |
||
| 108 | bedfiles=bed_file, |
||
| 109 | roi=roi, binsize=300, |
||
| 110 | stepsize=300, |
||
| 111 | store_whole_genome=swg, |
||
| 112 | cache=False, resolution=3) |
||
| 113 | assert len(cov) == 68 |
||
| 114 | assert cov.shape == (68, 100, 1, 1) |
||
| 115 | [c for c in cov] |
||
| 116 | |||
| 117 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 118 | cov = Cover.create_from_bed('test', |
||
| 119 | bedfiles=bed_file, |
||
| 120 | roi=roi, binsize=300, |
||
| 121 | stepsize=300, |
||
| 122 | store_whole_genome=swg, |
||
| 123 | storage=store, |
||
| 124 | cache=False, resolution=3) |
||
| 125 | assert len(cov) == 68 |
||
| 126 | assert cov.shape == (68, 100, 1, 1) |
||
| 127 | [c for c in cov] |
||
| 128 | |||
| 129 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 130 | cov = Cover.create_from_bed('test', |
||
| 131 | bedfiles=bed_file, |
||
| 132 | roi=roi, binsize=300, |
||
| 133 | stepsize=300, |
||
| 134 | store_whole_genome=swg, |
||
| 135 | storage=store, |
||
| 136 | cache=False, resolution=3) |
||
| 137 | assert len(cov) == 68 |
||
| 138 | assert cov.shape == (68, 100, 1, 1) |
||
| 139 | [c for c in cov] |
||
| 140 | |||
| 141 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 142 | cov = Cover.create_from_bed('test', |
||
| 143 | bedfiles=bed_file, |
||
| 144 | roi=roi, binsize=300, |
||
| 145 | stepsize=300, |
||
| 146 | store_whole_genome=swg, |
||
| 147 | storage=store, |
||
| 148 | cache=False, resolution=100) |
||
| 149 | assert len(cov) == 68 |
||
| 150 | assert cov.shape == (68, 3, 1, 1) |
||
| 151 | [c for c in cov] |
||
| 152 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 153 | cov = Cover.create_from_bed('test', |
||
| 154 | bedfiles=bed_file, |
||
| 155 | roi=roi, binsize=300, |
||
| 156 | stepsize=300, |
||
| 157 | store_whole_genome=swg, |
||
| 158 | cache=False, resolution=100, |
||
| 159 | storage=store, |
||
| 160 | zero_padding=False) |
||
| 161 | assert len(cov) == 66 |
||
| 162 | assert cov.shape == (66, 3, 1, 1) |
||
| 163 | [c for c in cov] |
||
| 164 | |||
| 165 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 166 | |||
| 167 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 168 | cover = Cover.create_from_bigwig( |
||
| 169 | 'test', |
||
| 170 | bigwigfiles=bwfile_, |
||
| 171 | resolution=100, |
||
| 172 | binsize=300, |
||
| 173 | roi=roi, |
||
| 174 | storage=store, |
||
| 175 | store_whole_genome=swg) |
||
| 176 | assert len(cover) == 68 |
||
| 177 | assert cover.shape == (68, 3, 1, 1) |
||
| 178 | [c for c in cover] |
||
| 179 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 180 | cover = Cover.create_from_bigwig( |
||
| 181 | 'test', |
||
| 182 | bigwigfiles=bwfile_, |
||
| 183 | resolution=100, |
||
| 184 | binsize=300, |
||
| 185 | roi=roi, zero_padding=False, |
||
| 186 | storage=store, |
||
| 187 | store_whole_genome=swg) |
||
| 188 | assert len(cover) == 66 |
||
| 189 | assert cover.shape == (66, 3, 1, 1) |
||
| 190 | [c for c in cover] |
||
| 191 | |||
| 192 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 193 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 194 | cover = Cover.create_from_bam( |
||
| 195 | 'test', |
||
| 196 | bamfile_, |
||
| 197 | resolution=100, |
||
| 198 | binsize=300, |
||
| 199 | roi=roi, |
||
| 200 | stranded=False, |
||
| 201 | storage=store, |
||
| 202 | store_whole_genome=swg) |
||
| 203 | assert len(cover) == 68 |
||
| 204 | assert cover.shape == (68, 3, 1, 1) |
||
| 205 | [c for c in cover] |
||
| 206 | for swg, store in product([True, False], ['ndarray', 'sparse']): |
||
| 207 | cover = Cover.create_from_bam( |
||
| 208 | 'test', |
||
| 209 | bamfile_, |
||
| 210 | resolution=100, |
||
| 211 | binsize=300, |
||
| 212 | roi=roi, zero_padding=False, |
||
| 213 | stranded=False, |
||
| 214 | storage=store, |
||
| 215 | store_whole_genome=swg) |
||
| 216 | assert len(cover) == 66 |
||
| 217 | assert cover.shape == (66, 3, 1, 1) |
||
| 218 | [c for c in cover] |
||
| 219 | |||
| 220 | def test_cover_export_bigwig(tmpdir): |
||
| 221 | path = tmpdir.strpath |
||
| 222 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 223 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 224 | |||
| 225 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 226 | |||
| 227 | for resolution in [1, 50]: |
||
| 228 | for storage in [True, False]: |
||
| 229 | print('resolution=', resolution) |
||
| 230 | print('store_whole_genome', storage) |
||
| 231 | cover = Cover.create_from_bigwig( |
||
| 232 | 'test', |
||
| 233 | bigwigfiles=bwfile_, |
||
| 234 | resolution=resolution, |
||
| 235 | binsize=200, |
||
| 236 | roi=bed_file, |
||
| 237 | store_whole_genome=storage, |
||
| 238 | storage='ndarray') |
||
| 239 | |||
| 240 | cover.export_to_bigwig(output_dir=path) |
||
| 241 | |||
| 242 | cov2 = Cover.create_from_bigwig('test', |
||
| 243 | bigwigfiles='{path}/{name}.{sample}.bigwig'.format( |
||
| 244 | path=path, name=cover.name, |
||
| 245 | sample=cover.conditions[0]), |
||
| 246 | resolution=resolution, |
||
| 247 | binsize=200, |
||
| 248 | roi=bed_file, |
||
| 249 | store_whole_genome=storage, |
||
| 250 | storage='ndarray') |
||
| 251 | |||
| 252 | assert cover.shape == (100, 200 // resolution, 1, 1) |
||
| 253 | assert cover.shape == cov2.shape |
||
| 254 | np.testing.assert_allclose(cover[:].sum(), 1044.0 / resolution) |
||
| 255 | np.testing.assert_allclose(cov2[:].sum(), 1044.0 / resolution) |
||
| 256 | |||
| 257 | |||
| 258 | def test_bam_genomic_interval_access(): |
||
| 259 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 260 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 261 | |||
| 262 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 263 | |||
| 264 | for reso, shift, storage in product([1, 50], [0, 1], [True, False]): |
||
| 265 | cover = Cover.create_from_bam( |
||
| 266 | 'test', |
||
| 267 | bamfiles=bamfile_, |
||
| 268 | roi=bed_file, |
||
| 269 | flank=0, |
||
| 270 | storage='ndarray', |
||
| 271 | store_whole_genome=storage, |
||
| 272 | resolution=reso) |
||
| 273 | |||
| 274 | for i in range(len(cover)): |
||
| 275 | print('storage :',storage,'/ resolution :',reso,'/ shift :',shift) |
||
| 276 | |||
| 277 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 278 | cover.garray.resolution, |
||
| 279 | axis=1), cover[cover.gindexer[i]]) |
||
| 280 | |||
| 281 | chrom, start, end, strand = cover.gindexer[i].chrom, \ |
||
| 282 | cover.gindexer[i].start, \ |
||
| 283 | cover.gindexer[i].end, \ |
||
| 284 | cover.gindexer[i].strand |
||
| 285 | |||
| 286 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 287 | cover.garray.resolution, axis=1), |
||
| 288 | cover[chrom, start, end, strand]) |
||
| 289 | |||
| 290 | np.testing.assert_equal(cover[chrom, start, end, strand], |
||
| 291 | cover[chrom, start-1, end+1, strand][:, 1:-1, :, :]) |
||
| 292 | if shift != 0: |
||
| 293 | start += shift * reso |
||
| 294 | end += shift * reso |
||
| 295 | |||
| 296 | if strand != '-': |
||
| 297 | gicov = cover[chrom, start, end, strand][:, :(-shift*reso),:,:] |
||
| 298 | np.testing.assert_equal(cover[i][:, shift:,:, :], |
||
| 299 | gicov.reshape((1, gicov.shape[1]//reso, reso, 2, 1))[:, :, 0, :, :]) |
||
| 300 | else: |
||
| 301 | gicov = cover[chrom, start, end, strand][:, (shift*reso):,:,:] |
||
| 302 | np.testing.assert_equal(cover[i][:, :-shift,:, :], |
||
| 303 | gicov.reshape((1, gicov.shape[1]//reso, reso, 2, 1))[:, :, 0, :, :]) |
||
| 304 | |||
| 305 | |||
| 306 | def test_bigwig_genomic_interval_access(): |
||
| 307 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 308 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 309 | |||
| 310 | bamfile_ = os.path.join(data_path, "sample.bw") |
||
| 311 | |||
| 312 | for reso, shift, storage in product([1, 50], [0, 1], [True, False]): |
||
| 313 | cover = Cover.create_from_bigwig( |
||
| 314 | 'test', |
||
| 315 | bigwigfiles=bamfile_, |
||
| 316 | roi=bed_file, |
||
| 317 | flank=0, |
||
| 318 | storage='ndarray', |
||
| 319 | store_whole_genome=storage, |
||
| 320 | resolution=reso) |
||
| 321 | |||
| 322 | for i in range(len(cover)): |
||
| 323 | print('storage :',storage,'/ resolution :',reso,'/ shift :',shift) |
||
| 324 | |||
| 325 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 326 | cover.garray.resolution, |
||
| 327 | axis=1), cover[cover.gindexer[i]]) |
||
| 328 | |||
| 329 | chrom, start, end, strand = cover.gindexer[i].chrom, \ |
||
| 330 | cover.gindexer[i].start, \ |
||
| 331 | cover.gindexer[i].end, \ |
||
| 332 | cover.gindexer[i].strand |
||
| 333 | |||
| 334 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 335 | cover.garray.resolution, axis=1), |
||
| 336 | cover[chrom, start, end, strand]) |
||
| 337 | |||
| 338 | if shift != 0: |
||
| 339 | start += shift * reso |
||
| 340 | end += shift * reso |
||
| 341 | |||
| 342 | if strand != '-': |
||
| 343 | gicov = cover[chrom, start, end, strand][:, :(-shift*reso),:,:] |
||
| 344 | np.testing.assert_equal(cover[i][:, shift:,:, :], |
||
| 345 | gicov.reshape((1, gicov.shape[1]//reso, reso, 1, 1))[:, :, 0, :, :]) |
||
| 346 | else: |
||
| 347 | gicov = cover[chrom, start, end, strand][:, (shift*reso):,:,:] |
||
| 348 | np.testing.assert_equal(cover[i][:, :-shift,:, :], |
||
| 349 | gicov.reshape((1, gicov.shape[1]//reso, reso, 1, 1))[:, :, 0, :, :]) |
||
| 350 | |||
| 351 | |||
| 352 | def test_bed_genomic_interval_access(): |
||
| 353 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 354 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 355 | |||
| 356 | bamfile_ = os.path.join(data_path, "sample.bed") |
||
| 357 | |||
| 358 | |||
| 359 | for reso, shift, storage in product([1, 50], [0, 1], [True, False]): |
||
| 360 | cover = Cover.create_from_bed( |
||
| 361 | 'test', |
||
| 362 | bedfiles=bamfile_, |
||
| 363 | roi=bed_file, |
||
| 364 | flank=0, |
||
| 365 | storage='ndarray', |
||
| 366 | store_whole_genome=storage, |
||
| 367 | resolution=reso) |
||
| 368 | |||
| 369 | for i in range(len(cover)): |
||
| 370 | print('storage :',storage,'/ resolution :',reso,'/ shift :',shift) |
||
| 371 | |||
| 372 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 373 | cover.garray.resolution, |
||
| 374 | axis=1), cover[cover.gindexer[i]]) |
||
| 375 | |||
| 376 | chrom, start, end, strand = cover.gindexer[i].chrom, \ |
||
| 377 | cover.gindexer[i].start, \ |
||
| 378 | cover.gindexer[i].end, \ |
||
| 379 | cover.gindexer[i].strand |
||
| 380 | |||
| 381 | np.testing.assert_equal(np.repeat(cover[i], |
||
| 382 | cover.garray.resolution, axis=1), |
||
| 383 | cover[chrom, start, end, strand]) |
||
| 384 | |||
| 385 | if shift != 0: |
||
| 386 | start += shift * reso |
||
| 387 | end += shift * reso |
||
| 388 | |||
| 389 | if strand != '-': |
||
| 390 | gicov = cover[chrom, start, end, strand][:, :(-shift*reso),:,:] |
||
| 391 | np.testing.assert_equal(cover[i][:, shift:,:, :], |
||
| 392 | gicov.reshape((1, gicov.shape[1]//reso, reso, 1, 1))[:, :, 0, :, :]) |
||
| 393 | else: |
||
| 394 | gicov = cover[chrom, start, end, strand][:, (shift*reso):,:,:] |
||
| 395 | np.testing.assert_equal(cover[i][:, :-shift,:, :], |
||
| 396 | gicov.reshape((1, gicov.shape[1]//reso, reso, 1, 1))[:, :, 0, :, :]) |
||
| 397 | |||
| 398 | |||
| 399 | def test_bam_inferred_binsize(): |
||
| 400 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 401 | bed_file = os.path.join(data_path, "positive.bed") |
||
| 402 | |||
| 403 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 404 | |||
| 405 | cover = Cover.create_from_bam( |
||
| 406 | 'test', |
||
| 407 | bamfiles=bamfile_, |
||
| 408 | roi=bed_file, |
||
| 409 | flank=0, |
||
| 410 | storage='ndarray') |
||
| 411 | assert len(cover) == 25 |
||
| 412 | assert cover.shape == (25, 200, 2, 1) |
||
| 413 | |||
| 414 | |||
| 415 | def test_bigwig_inferred_binsize(): |
||
| 416 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 417 | bed_file = os.path.join(data_path, "positive.bed") |
||
| 418 | |||
| 419 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 420 | |||
| 421 | cover = Cover.create_from_bigwig( |
||
| 422 | 'test', |
||
| 423 | bigwigfiles=bwfile_, |
||
| 424 | resolution=1, |
||
| 425 | roi=bed_file, |
||
| 426 | storage='ndarray') |
||
| 427 | assert len(cover) == 25 |
||
| 428 | assert cover.shape == (25, 200, 1, 1) |
||
| 429 | |||
| 430 | |||
| 431 | def test_bed_unsync_roi_targets(): |
||
| 432 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 433 | bed_file = os.path.join(data_path, "positive.bed") |
||
| 434 | bed_shift_file = os.path.join(data_path, "positive_shift.bed") |
||
| 435 | |||
| 436 | cover = Cover.create_from_bed( |
||
| 437 | 'test', |
||
| 438 | bedfiles=bed_shift_file, |
||
| 439 | roi=bed_file, |
||
| 440 | resolution=None, |
||
| 441 | storage='ndarray') |
||
| 442 | assert len(cover) == 25 |
||
| 443 | assert cover.shape == (25, 1, 1, 1) |
||
| 444 | assert cover[:].sum() == 1 |
||
| 445 | |||
| 446 | cover = Cover.create_from_bed( |
||
| 447 | 'test', |
||
| 448 | bedfiles=bed_shift_file, |
||
| 449 | roi=bed_file, |
||
| 450 | resolution=50, |
||
| 451 | storage='ndarray') |
||
| 452 | assert len(cover) == 25 |
||
| 453 | assert cover.shape == (25, 4, 1, 1) |
||
| 454 | assert cover[:].sum() == 1 |
||
| 455 | |||
| 456 | |||
| 457 | cover = Cover.create_from_bed( |
||
| 458 | 'test', |
||
| 459 | bedfiles=bed_shift_file, |
||
| 460 | roi=bed_file, |
||
| 461 | resolution=50, |
||
| 462 | store_whole_genome=True, |
||
| 463 | storage='ndarray') |
||
| 464 | assert len(cover) == 25 |
||
| 465 | assert cover.shape == (25, 4, 1, 1) |
||
| 466 | assert cover[:].sum() == 1 |
||
| 467 | |||
| 468 | cover = Cover.create_from_bed( |
||
| 469 | 'test', |
||
| 470 | bedfiles=bed_shift_file, |
||
| 471 | roi=bed_file, |
||
| 472 | resolution=1, |
||
| 473 | store_whole_genome=False, |
||
| 474 | storage='ndarray') |
||
| 475 | assert len(cover) == 25 |
||
| 476 | assert cover.shape == (25, 200, 1, 1) |
||
| 477 | assert cover[0].sum() == 49 |
||
| 478 | |||
| 479 | cover = Cover.create_from_bed( |
||
| 480 | 'test', |
||
| 481 | bedfiles=bed_shift_file, |
||
| 482 | roi=bed_file, |
||
| 483 | resolution=1, |
||
| 484 | store_whole_genome=True, |
||
| 485 | storage='ndarray') |
||
| 486 | assert len(cover) == 25 |
||
| 487 | assert cover.shape == (25, 200, 1, 1) |
||
| 488 | assert cover[:].sum() == 49 |
||
| 489 | |||
| 490 | cover = Cover.create_from_bed( |
||
| 491 | 'test', |
||
| 492 | bedfiles=bed_shift_file, |
||
| 493 | roi=bed_file, |
||
| 494 | resolution=1, |
||
| 495 | store_whole_genome=True, |
||
| 496 | storage='ndarray', minoverlap=.5) |
||
| 497 | assert len(cover) == 25 |
||
| 498 | assert cover.shape == (25, 200, 1, 1) |
||
| 499 | assert cover[:].sum() == 0 |
||
| 500 | |||
| 501 | # check bed file loading without roi |
||
| 502 | cover_ = Cover.create_from_bed( |
||
| 503 | 'test', |
||
| 504 | bedfiles=bed_shift_file, |
||
| 505 | roi=None, |
||
| 506 | resolution=1, |
||
| 507 | store_whole_genome=True, |
||
| 508 | storage='ndarray', minoverlap=.5) |
||
| 509 | |||
| 510 | cover_.gindexer = cover.gindexer |
||
| 511 | assert len(cover) == 25 |
||
| 512 | assert cover.shape == (25, 200, 1, 1) |
||
| 513 | assert cover[:].sum() == 0 |
||
| 514 | |||
| 515 | def test_bed_inferred_binsize(): |
||
| 516 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 517 | bed_file = os.path.join(data_path, "positive.bed") |
||
| 518 | |||
| 519 | |||
| 520 | cover = Cover.create_from_bed( |
||
| 521 | 'test', |
||
| 522 | bedfiles=bed_file, |
||
| 523 | roi=bed_file, |
||
| 524 | resolution=1, |
||
| 525 | storage='ndarray') |
||
| 526 | assert len(cover) == 25 |
||
| 527 | assert cover.shape == (25, 200, 1, 1) |
||
| 528 | |||
| 529 | bed_file = os.path.join(data_path, "positive_gap.bed") |
||
| 530 | cover = Cover.create_from_bed( |
||
| 531 | 'test', |
||
| 532 | bedfiles=bed_file, |
||
| 533 | roi=bed_file, |
||
| 534 | resolution=1, |
||
| 535 | store_whole_genome=True, |
||
| 536 | storage='ndarray') |
||
| 537 | assert len(cover) == 2 |
||
| 538 | assert cover.shape == (2, 50, 1, 1) |
||
| 539 | |||
| 540 | def test_bed_overreaching_ends_whole_genome(): |
||
| 541 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 542 | bed_file = os.path.join(data_path, "bed_test.bed") |
||
| 543 | |||
| 544 | for store in ['ndarray', 'sparse']: |
||
| 545 | print(store) |
||
| 546 | cover = Cover.create_from_bed( |
||
| 547 | 'test', |
||
| 548 | bedfiles=bed_file, |
||
| 549 | roi=bed_file, |
||
| 550 | binsize=2, |
||
| 551 | flank=20, |
||
| 552 | resolution=1, |
||
| 553 | store_whole_genome=True, |
||
| 554 | storage=store) |
||
| 555 | assert len(cover) == 9 |
||
| 556 | assert cover.shape == (9, 2+2*20, 1, 1) |
||
| 557 | np.testing.assert_equal(cover[0].sum(), 18) |
||
| 558 | np.testing.assert_equal(cover[:].sum(), 9*18) |
||
| 559 | |||
| 560 | |||
| 561 | def test_bed_overreaching_ends_part_genome(): |
||
| 562 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 563 | bed_file = os.path.join(data_path, "bed_test.bed") |
||
| 564 | |||
| 565 | for store in ['ndarray', 'sparse']: |
||
| 566 | print(store) |
||
| 567 | cover = Cover.create_from_bed( |
||
| 568 | 'test', |
||
| 569 | bedfiles=bed_file, |
||
| 570 | roi=bed_file, |
||
| 571 | binsize=2, |
||
| 572 | flank=2, |
||
| 573 | resolution=1, |
||
| 574 | store_whole_genome=False, |
||
| 575 | storage=store) |
||
| 576 | assert len(cover) == 9 |
||
| 577 | assert cover.shape == (9, 2+2*2, 1, 1) |
||
| 578 | np.testing.assert_equal(cover[0].sum(), 4) |
||
| 579 | np.testing.assert_equal(cover[:].sum(), 6*7 + 8) |
||
| 580 | |||
| 581 | |||
| 582 | def test_bed_store_whole_genome_option(): |
||
| 583 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 584 | bed_file = os.path.join(data_path, "positive_shift.bed") |
||
| 585 | |||
| 586 | cover1 = Cover.create_from_bed( |
||
| 587 | 'test', |
||
| 588 | bedfiles=bed_file, |
||
| 589 | roi=bed_file, |
||
| 590 | store_whole_genome=True, |
||
| 591 | storage='ndarray') |
||
| 592 | cover2 = Cover.create_from_bed( |
||
| 593 | 'test2', |
||
| 594 | bedfiles=bed_file, |
||
| 595 | roi=bed_file, |
||
| 596 | store_whole_genome=False, |
||
| 597 | storage='ndarray') |
||
| 598 | |||
| 599 | assert len(cover1) == 1 |
||
| 600 | assert len(cover2) == len(cover1) |
||
| 601 | assert cover1.shape == (1, 49, 1, 1) |
||
| 602 | assert cover1.shape == cover2.shape |
||
| 603 | np.testing.assert_equal(cover1[:], np.ones(cover1.shape)) |
||
| 604 | np.testing.assert_equal(cover2[:], np.ones(cover1.shape)) |
||
| 605 | |||
| 606 | |||
| 607 | def test_bed_store_whole_genome_option_dataframe(tmpdir): |
||
| 608 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 609 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 610 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 611 | |||
| 612 | # as pd.dataframe |
||
| 613 | roi = pandas.read_csv(bed_file, |
||
| 614 | sep='\t', header=None, |
||
| 615 | names=['chrom', 'start', 'end', |
||
| 616 | 'name', 'score', 'strand']) |
||
| 617 | |||
| 618 | print(roi.head()) |
||
| 619 | cover1 = Cover.create_from_bed( |
||
| 620 | 'test', |
||
| 621 | bedfiles=bed_file, |
||
| 622 | roi=roi, |
||
| 623 | binsize=200, stepsize=200, |
||
| 624 | store_whole_genome=True, |
||
| 625 | cache=False, |
||
| 626 | storage='ndarray') |
||
| 627 | cover2 = Cover.create_from_bed( |
||
| 628 | 'test2', |
||
| 629 | bedfiles=bed_file, |
||
| 630 | roi=roi, |
||
| 631 | binsize=200, stepsize=200, |
||
| 632 | store_whole_genome=False, |
||
| 633 | cache=True, |
||
| 634 | storage='ndarray') |
||
| 635 | |||
| 636 | print(cover1.gindexer[0]) |
||
| 637 | assert len(cover1) == 100 |
||
| 638 | assert len(cover2) == len(cover1) |
||
| 639 | assert cover1.shape == (100, 200, 1, 1) |
||
| 640 | assert cover1.shape == cover2.shape |
||
| 641 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 642 | np.testing.assert_equal(cover1[:], np.ones(cover1.shape)) |
||
| 643 | |||
| 644 | # as bedtool |
||
| 645 | roi = BedTool(bed_file) |
||
| 646 | print(roi) |
||
| 647 | |||
| 648 | cover1 = Cover.create_from_bed( |
||
| 649 | 'test', |
||
| 650 | bedfiles=bed_file, |
||
| 651 | roi=roi, |
||
| 652 | binsize=200, stepsize=200, |
||
| 653 | store_whole_genome=True, |
||
| 654 | storage='ndarray') |
||
| 655 | cover2 = Cover.create_from_bed( |
||
| 656 | 'test2', |
||
| 657 | bedfiles=bed_file, |
||
| 658 | roi=roi, |
||
| 659 | binsize=200, stepsize=200, |
||
| 660 | store_whole_genome=False, |
||
| 661 | cache=True, |
||
| 662 | storage='ndarray') |
||
| 663 | |||
| 664 | assert len(cover1) == 100 |
||
| 665 | assert len(cover2) == len(cover1) |
||
| 666 | assert cover1.shape == (100, 200, 1, 1) |
||
| 667 | assert cover1.shape == cover2.shape |
||
| 668 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 669 | np.testing.assert_equal(cover1[:], np.ones(cover1.shape)) |
||
| 670 | |||
| 671 | # as interval list |
||
| 672 | roi = [iv for iv in BedTool(bed_file)] |
||
| 673 | print(roi) |
||
| 674 | |||
| 675 | cover1 = Cover.create_from_bed( |
||
| 676 | 'test', |
||
| 677 | bedfiles=bed_file, |
||
| 678 | roi=roi, |
||
| 679 | binsize=200, stepsize=200, |
||
| 680 | store_whole_genome=True, |
||
| 681 | storage='ndarray') |
||
| 682 | cover2 = Cover.create_from_bed( |
||
| 683 | 'test2', |
||
| 684 | bedfiles=bed_file, |
||
| 685 | roi=roi, |
||
| 686 | binsize=200, stepsize=200, |
||
| 687 | store_whole_genome=False, |
||
| 688 | cache=True, |
||
| 689 | storage='ndarray') |
||
| 690 | |||
| 691 | assert len(cover1) == 100 |
||
| 692 | assert len(cover2) == len(cover1) |
||
| 693 | assert cover1.shape == (100, 200, 1, 1) |
||
| 694 | assert cover1.shape == cover2.shape |
||
| 695 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 696 | np.testing.assert_equal(cover1[:], np.ones(cover1.shape)) |
||
| 697 | |||
| 698 | |||
| 699 | def test_bigwig_store_whole_genome_option(): |
||
| 700 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 701 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 702 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 703 | |||
| 704 | cover1 = Cover.create_from_bigwig( |
||
| 705 | 'test', |
||
| 706 | bigwigfiles=bwfile_, |
||
| 707 | roi=bed_file, |
||
| 708 | store_whole_genome=True, |
||
| 709 | binsize=200, stepsize=200, |
||
| 710 | storage='ndarray') |
||
| 711 | cover2 = Cover.create_from_bigwig( |
||
| 712 | 'test2', |
||
| 713 | bigwigfiles=bwfile_, |
||
| 714 | roi=bed_file, |
||
| 715 | store_whole_genome=False, |
||
| 716 | binsize=200, stepsize=200, |
||
| 717 | storage='ndarray') |
||
| 718 | cover3 = Cover.create_from_bigwig( |
||
| 719 | 'test3', |
||
| 720 | bigwigfiles=bwfile_, |
||
| 721 | roi=bed_file, |
||
| 722 | store_whole_genome=False, |
||
| 723 | binsize=200, stepsize=200, |
||
| 724 | nan_to_num=False, |
||
| 725 | storage='ndarray') |
||
| 726 | |||
| 727 | assert len(cover1) == 100 |
||
| 728 | assert len(cover2) == len(cover1) |
||
| 729 | assert cover1.shape == (100, 200, 1, 1) |
||
| 730 | assert cover1.shape == cover2.shape |
||
| 731 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 732 | assert cover1[:].sum() == 1044.0 |
||
| 733 | assert cover3[:].sum() == 1044.0 |
||
| 734 | |||
| 735 | |||
| 736 | def test_bigwig_store_whole_genome_option_dataframe(tmpdir): |
||
| 737 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 738 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 739 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 740 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 741 | |||
| 742 | # as dataframe |
||
| 743 | roi = pandas.read_csv(bed_file, |
||
| 744 | sep='\t', header=None, names=['chrom', 'start', 'end', 'name', 'score', 'strand']) |
||
| 745 | |||
| 746 | cover1 = Cover.create_from_bigwig( |
||
| 747 | 'test', |
||
| 748 | bigwigfiles=bwfile_, |
||
| 749 | roi=roi, |
||
| 750 | store_whole_genome=True, |
||
| 751 | binsize=200, stepsize=200, |
||
| 752 | storage='ndarray') |
||
| 753 | cover2 = Cover.create_from_bigwig( |
||
| 754 | 'test2', |
||
| 755 | bigwigfiles=bwfile_, |
||
| 756 | roi=roi, |
||
| 757 | store_whole_genome=False, |
||
| 758 | binsize=200, stepsize=200, |
||
| 759 | cache=True, |
||
| 760 | storage='ndarray') |
||
| 761 | cover3 = Cover.create_from_bigwig( |
||
| 762 | 'test3', |
||
| 763 | bigwigfiles=bwfile_, |
||
| 764 | roi=roi, |
||
| 765 | store_whole_genome=False, |
||
| 766 | binsize=200, stepsize=200, |
||
| 767 | nan_to_num=False, |
||
| 768 | storage='ndarray') |
||
| 769 | |||
| 770 | assert len(cover1) == 100 |
||
| 771 | assert len(cover2) == len(cover1) |
||
| 772 | assert cover1.shape == (100, 200, 1, 1) |
||
| 773 | assert cover1.shape == cover2.shape |
||
| 774 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 775 | assert cover1[:].sum() == 1044.0 |
||
| 776 | assert cover3[:].sum() == 1044.0 |
||
| 777 | |||
| 778 | # as bedtool |
||
| 779 | roi = BedTool(bed_file) |
||
| 780 | |||
| 781 | cover1 = Cover.create_from_bigwig( |
||
| 782 | 'test', |
||
| 783 | bigwigfiles=bwfile_, |
||
| 784 | roi=roi, |
||
| 785 | store_whole_genome=True, |
||
| 786 | binsize=200, stepsize=200, |
||
| 787 | storage='ndarray') |
||
| 788 | cover2 = Cover.create_from_bigwig( |
||
| 789 | 'test2', |
||
| 790 | bigwigfiles=bwfile_, |
||
| 791 | roi=roi, |
||
| 792 | store_whole_genome=False, |
||
| 793 | binsize=200, stepsize=200, |
||
| 794 | cache=True, |
||
| 795 | storage='ndarray') |
||
| 796 | cover3 = Cover.create_from_bigwig( |
||
| 797 | 'test3', |
||
| 798 | bigwigfiles=bwfile_, |
||
| 799 | roi=roi, |
||
| 800 | store_whole_genome=False, |
||
| 801 | binsize=200, stepsize=200, |
||
| 802 | nan_to_num=False, |
||
| 803 | storage='ndarray') |
||
| 804 | |||
| 805 | assert len(cover1) == 100 |
||
| 806 | assert len(cover2) == len(cover1) |
||
| 807 | assert cover1.shape == (100, 200, 1, 1) |
||
| 808 | assert cover1.shape == cover2.shape |
||
| 809 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 810 | assert cover1[:].sum() == 1044.0 |
||
| 811 | assert cover3[:].sum() == 1044.0 |
||
| 812 | |||
| 813 | # as list of intervals |
||
| 814 | roi = [iv for iv in roi] |
||
| 815 | |||
| 816 | cover1 = Cover.create_from_bigwig( |
||
| 817 | 'test', |
||
| 818 | bigwigfiles=bwfile_, |
||
| 819 | roi=roi, |
||
| 820 | store_whole_genome=True, |
||
| 821 | binsize=200, stepsize=200, |
||
| 822 | storage='ndarray') |
||
| 823 | cover2 = Cover.create_from_bigwig( |
||
| 824 | 'test2', |
||
| 825 | bigwigfiles=bwfile_, |
||
| 826 | roi=roi, |
||
| 827 | store_whole_genome=False, |
||
| 828 | binsize=200, stepsize=200, |
||
| 829 | cache=True, |
||
| 830 | storage='ndarray') |
||
| 831 | cover3 = Cover.create_from_bigwig( |
||
| 832 | 'test3', |
||
| 833 | bigwigfiles=bwfile_, |
||
| 834 | roi=roi, |
||
| 835 | store_whole_genome=False, |
||
| 836 | binsize=200, stepsize=200, |
||
| 837 | nan_to_num=False, |
||
| 838 | storage='ndarray') |
||
| 839 | |||
| 840 | assert len(cover1) == 100 |
||
| 841 | assert len(cover2) == len(cover1) |
||
| 842 | assert cover1.shape == (100, 200, 1, 1) |
||
| 843 | assert cover1.shape == cover2.shape |
||
| 844 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 845 | assert cover1[:].sum() == 1044.0 |
||
| 846 | assert cover3[:].sum() == 1044.0 |
||
| 847 | |||
| 848 | |||
| 849 | |||
| 850 | def test_bam_store_whole_genome_option_dataframe(tmpdir): |
||
| 851 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 852 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 853 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 854 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 855 | |||
| 856 | # as dataframe |
||
| 857 | roi = pandas.read_csv(bed_file, |
||
| 858 | sep='\t', header=None, names=['chrom', 'start', 'end', 'name', 'score', 'strand']) |
||
| 859 | |||
| 860 | cover1 = Cover.create_from_bam( |
||
| 861 | 'test', |
||
| 862 | bamfiles=bamfile_, |
||
| 863 | roi=roi, |
||
| 864 | store_whole_genome=True, |
||
| 865 | binsize=200, stepsize=200, |
||
| 866 | storage='ndarray') |
||
| 867 | cover2 = Cover.create_from_bam( |
||
| 868 | 'test2', |
||
| 869 | bamfiles=bamfile_, |
||
| 870 | roi=roi, |
||
| 871 | store_whole_genome=False, |
||
| 872 | binsize=200, stepsize=200, |
||
| 873 | cache=True, |
||
| 874 | storage='ndarray') |
||
| 875 | |||
| 876 | assert len(cover1) == 100 |
||
| 877 | assert len(cover2) == len(cover1) |
||
| 878 | assert cover1.shape == (100, 200, 2, 1) |
||
| 879 | assert cover1.shape == cover2.shape |
||
| 880 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 881 | assert cover1[:].sum() == 29. |
||
| 882 | |||
| 883 | # as bedtool |
||
| 884 | roi = BedTool(bed_file) |
||
| 885 | |||
| 886 | cover1 = Cover.create_from_bam( |
||
| 887 | 'test', |
||
| 888 | bamfiles=bamfile_, |
||
| 889 | roi=roi, |
||
| 890 | store_whole_genome=True, |
||
| 891 | binsize=200, stepsize=200, |
||
| 892 | storage='ndarray') |
||
| 893 | cover2 = Cover.create_from_bam( |
||
| 894 | 'test2', |
||
| 895 | bamfiles=bamfile_, |
||
| 896 | roi=roi, |
||
| 897 | store_whole_genome=False, |
||
| 898 | binsize=200, stepsize=200, |
||
| 899 | cache=True, |
||
| 900 | storage='ndarray') |
||
| 901 | |||
| 902 | assert len(cover1) == 100 |
||
| 903 | assert len(cover2) == len(cover1) |
||
| 904 | assert cover1.shape == (100, 200, 2, 1) |
||
| 905 | assert cover1.shape == cover2.shape |
||
| 906 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 907 | assert cover1[:].sum() == 29. |
||
| 908 | |||
| 909 | # as list of intervals |
||
| 910 | roi = [iv for iv in roi] |
||
| 911 | |||
| 912 | cover1 = Cover.create_from_bam( |
||
| 913 | 'test', |
||
| 914 | bamfiles=bamfile_, |
||
| 915 | roi=roi, |
||
| 916 | store_whole_genome=True, |
||
| 917 | binsize=200, stepsize=200, |
||
| 918 | storage='ndarray') |
||
| 919 | cover2 = Cover.create_from_bam( |
||
| 920 | 'test2', |
||
| 921 | bamfiles=bamfile_, |
||
| 922 | roi=roi, |
||
| 923 | store_whole_genome=False, |
||
| 924 | binsize=200, stepsize=200, |
||
| 925 | cache=True, |
||
| 926 | storage='ndarray') |
||
| 927 | |||
| 928 | assert len(cover1) == 100 |
||
| 929 | assert len(cover2) == len(cover1) |
||
| 930 | assert cover1.shape == (100, 200, 2, 1) |
||
| 931 | assert cover1.shape == cover2.shape |
||
| 932 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 933 | assert cover1[:].sum() == 29. |
||
| 934 | |||
| 935 | |||
| 936 | def test_bam_store_whole_genome_option(): |
||
| 937 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 938 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 939 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 940 | |||
| 941 | cover1 = Cover.create_from_bam( |
||
| 942 | 'test', |
||
| 943 | bamfiles=bamfile_, |
||
| 944 | roi=bed_file, |
||
| 945 | store_whole_genome=True, |
||
| 946 | binsize=200, stepsize=200, |
||
| 947 | storage='ndarray') |
||
| 948 | cover2 = Cover.create_from_bam( |
||
| 949 | 'test2', |
||
| 950 | bamfiles=bamfile_, |
||
| 951 | roi=bed_file, |
||
| 952 | store_whole_genome=False, |
||
| 953 | binsize=200, stepsize=200, |
||
| 954 | storage='ndarray') |
||
| 955 | |||
| 956 | assert len(cover1) == 100 |
||
| 957 | assert len(cover2) == len(cover1) |
||
| 958 | assert cover1.shape == (100, 200, 2, 1) |
||
| 959 | assert cover1.shape == cover2.shape |
||
| 960 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 961 | assert cover1[:].sum() == 29. |
||
| 962 | |||
| 963 | |||
| 964 | def test_cover_from_bam_sanity(): |
||
| 965 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 966 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 967 | |||
| 968 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 969 | cover = Cover.create_from_bam( |
||
| 970 | 'test', |
||
| 971 | bamfiles=bamfile_, |
||
| 972 | roi=bed_file, |
||
| 973 | binsize=200, stepsize=200, |
||
| 974 | flank=0, |
||
| 975 | storage='ndarray') |
||
| 976 | cover[0] |
||
| 977 | |||
| 978 | with pytest.raises(IndexError): |
||
| 979 | # not interable |
||
| 980 | cover[1.2] |
||
| 981 | |||
| 982 | cov2 = Cover.create_from_bam( |
||
| 983 | 'test', |
||
| 984 | bamfiles=bamfile_, |
||
| 985 | storage='ndarray', |
||
| 986 | store_whole_genome=True) |
||
| 987 | |||
| 988 | assert len(cover.gindexer) == len(cover.garray.handle['data']) |
||
| 989 | assert len(cov2.garray.handle) != len(cover.garray.handle['data']) |
||
| 990 | |||
| 991 | with pytest.raises(Exception): |
||
| 992 | # name must be a string |
||
| 993 | Cover.create_from_bam( |
||
| 994 | 1.2, |
||
| 995 | bamfiles=bamfile_, |
||
| 996 | roi=bed_file, |
||
| 997 | binsize=1, stepsize=1, |
||
| 998 | storage='ndarray') |
||
| 999 | |||
| 1000 | with pytest.raises(Exception): |
||
| 1001 | # bamfile does not exist |
||
| 1002 | Cover.create_from_bam( |
||
| 1003 | 'test', |
||
| 1004 | bamfiles="", |
||
| 1005 | roi=bed_file, |
||
| 1006 | binsize=1, stepsize=1, |
||
| 1007 | flank=-1, |
||
| 1008 | storage='ndarray') |
||
| 1009 | with pytest.raises(Exception): |
||
| 1010 | # bamfile does not exist |
||
| 1011 | Cover.create_from_bam( |
||
| 1012 | 'test', |
||
| 1013 | bamfiles=[], |
||
| 1014 | roi=bed_file, |
||
| 1015 | binsize=1, stepsize=1, |
||
| 1016 | flank=-1, |
||
| 1017 | storage='ndarray') |
||
| 1018 | with pytest.raises(Exception): |
||
| 1019 | Cover.create_from_bam( |
||
| 1020 | 'test', |
||
| 1021 | bamfiles=bamfile_, |
||
| 1022 | roi=bed_file, |
||
| 1023 | binsize=1, stepsize=1, |
||
| 1024 | flank=-1, |
||
| 1025 | storage='ndarray') |
||
| 1026 | with pytest.raises(Exception): |
||
| 1027 | Cover.create_from_bam( |
||
| 1028 | 'test', |
||
| 1029 | bamfiles=bamfile_, |
||
| 1030 | roi=bed_file, |
||
| 1031 | binsize=1, stepsize=-1, |
||
| 1032 | flank=0, |
||
| 1033 | storage='ndarray') |
||
| 1034 | with pytest.raises(Exception): |
||
| 1035 | Cover.create_from_bam( |
||
| 1036 | 'test', |
||
| 1037 | bamfiles=bamfile_, |
||
| 1038 | roi=bed_file, |
||
| 1039 | binsize=-1, stepsize=1, |
||
| 1040 | flank=0, |
||
| 1041 | storage='ndarray') |
||
| 1042 | |||
| 1043 | with pytest.warns(FutureWarning): |
||
| 1044 | Cover.create_from_bam( |
||
| 1045 | 'test', |
||
| 1046 | bamfiles=bamfile_, |
||
| 1047 | roi=bed_file, |
||
| 1048 | binsize=200, stepsize=200, |
||
| 1049 | storage='ndarray', |
||
| 1050 | overwrite=True) |
||
| 1051 | |||
| 1052 | with pytest.warns(FutureWarning): |
||
| 1053 | Cover.create_from_bam( |
||
| 1054 | 'test', |
||
| 1055 | bamfiles=bamfile_, |
||
| 1056 | roi=bed_file, |
||
| 1057 | binsize=200, stepsize=200, |
||
| 1058 | storage='ndarray', |
||
| 1059 | datatags=['asdf']) |
||
| 1060 | |||
| 1061 | |||
| 1062 | def test_cover_from_bigwig_sanity(): |
||
| 1063 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1064 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1065 | |||
| 1066 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 1067 | cover = Cover.create_from_bigwig( |
||
| 1068 | 'test', |
||
| 1069 | bigwigfiles=bwfile_, |
||
| 1070 | roi=bed_file, |
||
| 1071 | binsize=200, stepsize=50, |
||
| 1072 | resolution=50, |
||
| 1073 | flank=0, |
||
| 1074 | storage='ndarray') |
||
| 1075 | cover[0] |
||
| 1076 | assert len(cover.gindexer) == 394 |
||
| 1077 | assert len(cover.garray.handle['data']) == 394 |
||
| 1078 | |||
| 1079 | cover = Cover.create_from_bigwig( |
||
| 1080 | 'test', |
||
| 1081 | bigwigfiles=bwfile_, |
||
| 1082 | roi=bed_file, |
||
| 1083 | binsize=200, stepsize=50, |
||
| 1084 | resolution=50, |
||
| 1085 | flank=0, |
||
| 1086 | storage='ndarray', |
||
| 1087 | store_whole_genome=True) |
||
| 1088 | cover[0] |
||
| 1089 | assert len(cover.gindexer) == 394 |
||
| 1090 | assert len(cover.garray.handle) == 2 |
||
| 1091 | cov2 = Cover.create_from_bigwig( |
||
| 1092 | 'test', |
||
| 1093 | bigwigfiles=bwfile_, |
||
| 1094 | resolution=7, |
||
| 1095 | storage='ndarray', |
||
| 1096 | store_whole_genome=True) |
||
| 1097 | |||
| 1098 | assert len(cov2.garray.handle) == 2 |
||
| 1099 | assert cov2['chr1', 100, 200].shape == (1, 100, 1, 1) |
||
| 1100 | |||
| 1101 | with pytest.raises(Exception): |
||
| 1102 | cov2.shape |
||
| 1103 | with pytest.raises(Exception): |
||
| 1104 | cov2[0] |
||
| 1105 | |||
| 1106 | with pytest.raises(Exception): |
||
| 1107 | # name must be a string |
||
| 1108 | Cover.create_from_bigwig( |
||
| 1109 | 1.2, |
||
| 1110 | bigwigfiles=bwfile_, |
||
| 1111 | roi=bed_file, |
||
| 1112 | binsize=1, stepsize=1, |
||
| 1113 | storage='ndarray') |
||
| 1114 | |||
| 1115 | with pytest.raises(Exception): |
||
| 1116 | Cover.create_from_bigwig( |
||
| 1117 | 'test', |
||
| 1118 | bigwigfiles=bwfile_, |
||
| 1119 | roi=bed_file, |
||
| 1120 | binsize=1, stepsize=1, |
||
| 1121 | flank=-1, |
||
| 1122 | storage='ndarray') |
||
| 1123 | with pytest.raises(Exception): |
||
| 1124 | Cover.create_from_bigwig( |
||
| 1125 | 'test', |
||
| 1126 | bigwigfiles=bwfile_, |
||
| 1127 | roi=bed_file, |
||
| 1128 | binsize=1, stepsize=-1, |
||
| 1129 | flank=0, |
||
| 1130 | storage='ndarray') |
||
| 1131 | with pytest.raises(Exception): |
||
| 1132 | Cover.create_from_bigwig( |
||
| 1133 | 'test', |
||
| 1134 | bigwigfiles=bwfile_, |
||
| 1135 | roi=bed_file, |
||
| 1136 | binsize=-1, stepsize=1, |
||
| 1137 | flank=0, |
||
| 1138 | storage='ndarray') |
||
| 1139 | |||
| 1140 | with pytest.warns(FutureWarning): |
||
| 1141 | Cover.create_from_bigwig( |
||
| 1142 | 'test', |
||
| 1143 | bigwigfiles=bwfile_, |
||
| 1144 | roi=bed_file, |
||
| 1145 | binsize=200, stepsize=200, |
||
| 1146 | flank=0, |
||
| 1147 | storage='ndarray', |
||
| 1148 | overwrite=True) |
||
| 1149 | with pytest.warns(FutureWarning): |
||
| 1150 | Cover.create_from_bigwig( |
||
| 1151 | 'test', |
||
| 1152 | bigwigfiles=bwfile_, |
||
| 1153 | roi=bed_file, |
||
| 1154 | binsize=200, stepsize=200, |
||
| 1155 | storage='ndarray', |
||
| 1156 | datatags=['asdf']) |
||
| 1157 | |||
| 1158 | |||
| 1159 | def test_cover_from_bed_sanity(): |
||
| 1160 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1161 | bed_file = os.path.join(data_path, 'sample.bed') |
||
| 1162 | |||
| 1163 | bwfile_ = os.path.join(data_path, "scored_sample.bed") |
||
| 1164 | cover = Cover.create_from_bed( |
||
| 1165 | 'test', |
||
| 1166 | bedfiles=bwfile_, |
||
| 1167 | roi=bed_file, |
||
| 1168 | binsize=200, stepsize=50, |
||
| 1169 | resolution=50, |
||
| 1170 | flank=0, |
||
| 1171 | storage='ndarray') |
||
| 1172 | cover[0] |
||
| 1173 | Cover.create_from_bed( |
||
| 1174 | 'test', |
||
| 1175 | bedfiles=bwfile_, |
||
| 1176 | roi=bed_file, |
||
| 1177 | binsize=200, stepsize=50, |
||
| 1178 | resolution=50, |
||
| 1179 | storage='ndarray') |
||
| 1180 | |||
| 1181 | with pytest.raises(Exception): |
||
| 1182 | # name must be a string |
||
| 1183 | Cover.create_from_bed( |
||
| 1184 | 1.2, |
||
| 1185 | bedfiles=bwfile_, |
||
| 1186 | roi=bed_file, |
||
| 1187 | binsize=1, stepsize=1, |
||
| 1188 | storage='ndarray') |
||
| 1189 | |||
| 1190 | with pytest.raises(Exception): |
||
| 1191 | Cover.create_from_bed( |
||
| 1192 | 'test', |
||
| 1193 | bedfiles=bwfile_, |
||
| 1194 | roi=bed_file, |
||
| 1195 | binsize=1, stepsize=1, |
||
| 1196 | flank=-1, |
||
| 1197 | storage='ndarray') |
||
| 1198 | with pytest.raises(Exception): |
||
| 1199 | Cover.create_from_bed( |
||
| 1200 | 'test', |
||
| 1201 | bedfiles=bwfile_, |
||
| 1202 | roi=bed_file, |
||
| 1203 | binsize=1, stepsize=-1, |
||
| 1204 | flank=0, |
||
| 1205 | storage='ndarray') |
||
| 1206 | with pytest.raises(Exception): |
||
| 1207 | Cover.create_from_bed( |
||
| 1208 | 'test', |
||
| 1209 | bedfiles=bwfile_, |
||
| 1210 | roi=bed_file, |
||
| 1211 | binsize=-1, stepsize=1, |
||
| 1212 | flank=0, |
||
| 1213 | storage='ndarray') |
||
| 1214 | with pytest.raises(Exception): |
||
| 1215 | csvfile = os.path.join(data_path, 'ctcf_sample.csv') |
||
| 1216 | # must be a bed file |
||
| 1217 | Cover.create_from_bed( |
||
| 1218 | 'test', |
||
| 1219 | bedfiles=csvfile, |
||
| 1220 | roi=bed_file, |
||
| 1221 | binsize=1, stepsize=1, |
||
| 1222 | storage='ndarray') |
||
| 1223 | with pytest.warns(FutureWarning): |
||
| 1224 | Cover.create_from_bed( |
||
| 1225 | 'test', |
||
| 1226 | bedfiles=bwfile_, |
||
| 1227 | roi=bed_file, |
||
| 1228 | binsize=200, stepsize=200, |
||
| 1229 | flank=0, |
||
| 1230 | storage='ndarray', |
||
| 1231 | overwrite=True) |
||
| 1232 | with pytest.warns(FutureWarning): |
||
| 1233 | Cover.create_from_bed( |
||
| 1234 | 'test', |
||
| 1235 | bedfiles=bwfile_, |
||
| 1236 | roi=bed_file, |
||
| 1237 | binsize=200, stepsize=200, |
||
| 1238 | storage='ndarray', |
||
| 1239 | datatags=['asdf']) |
||
| 1240 | |||
| 1241 | |||
| 1242 | def test_cover_bam_unstranded(): |
||
| 1243 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1244 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 1245 | gsfile_ = os.path.join(data_path, 'sample.chrom.sizes') |
||
| 1246 | |||
| 1247 | content = pandas.read_csv(gsfile_, sep='\t', names=['chr', 'length'], |
||
| 1248 | index_col='chr') |
||
| 1249 | |||
| 1250 | gsize = content.to_dict()['length'] |
||
| 1251 | |||
| 1252 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1253 | |||
| 1254 | |||
| 1255 | cover = Cover.create_from_bam( |
||
| 1256 | "yeast_I_II_III.bam", |
||
| 1257 | bamfiles=bamfile_, |
||
| 1258 | roi=bed_file, |
||
| 1259 | binsize=200, stepsize=200, |
||
| 1260 | genomesize=gsize, |
||
| 1261 | stranded=False) |
||
| 1262 | |||
| 1263 | np.testing.assert_equal(len(cover), 100) |
||
| 1264 | np.testing.assert_equal(cover.shape, (100, 200, 1, 1)) |
||
| 1265 | |||
| 1266 | # the region is read relative to the forward strand |
||
| 1267 | # read on the reverse strand |
||
| 1268 | val = np.where(cover[4] == 1) |
||
| 1269 | np.testing.assert_equal(cover[4].sum(), 1.) |
||
| 1270 | np.testing.assert_equal(val[1][0], 179) # pos |
||
| 1271 | |||
| 1272 | # two reads on the forward strand |
||
| 1273 | val = np.where(cover[13] == 1) |
||
| 1274 | np.testing.assert_equal(cover[13].sum(), 2.) |
||
| 1275 | np.testing.assert_equal(val[1], np.asarray([162, 178])) # pos |
||
| 1276 | |||
| 1277 | # the region is read relative to the reverse strand |
||
| 1278 | # for index 50 |
||
| 1279 | # read on the reverse strand |
||
| 1280 | val = np.where(cover[52] == 1) |
||
| 1281 | np.testing.assert_equal(cover[52].sum(), 2.) |
||
| 1282 | np.testing.assert_equal(val[1], np.asarray([9, 89])) # pos |
||
| 1283 | |||
| 1284 | # two reads on the forward strand |
||
| 1285 | val = np.where(cover[96] == 1) |
||
| 1286 | np.testing.assert_equal(cover[96].sum(), 1.) |
||
| 1287 | np.testing.assert_equal(val[1], np.asarray([25])) # pos |
||
| 1288 | |||
| 1289 | |||
| 1290 | def test_cover_bam_paired_5pend(): |
||
| 1291 | # sample2.bam contains paired end examples, |
||
| 1292 | # unmapped examples, unmapped mate and low quality example |
||
| 1293 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1294 | bamfile_ = os.path.join(data_path, "sample2.bam") |
||
| 1295 | |||
| 1296 | cover = Cover.create_from_bam( |
||
| 1297 | "yeast_I_II_III.bam", |
||
| 1298 | bamfiles=bamfile_, |
||
| 1299 | stranded=False, |
||
| 1300 | pairedend='5pend', |
||
| 1301 | min_mapq=30, |
||
| 1302 | store_whole_genome=True) |
||
| 1303 | |||
| 1304 | assert cover.garray.handle['ref'].sum() == 4, cover.garray.handle['ref'] |
||
| 1305 | |||
| 1306 | # the read starts at index 6 and tlen is 39 |
||
| 1307 | assert cover.garray.handle['ref'][6, 0, 0] == 1 |
||
| 1308 | # another read maps to index 24 |
||
| 1309 | assert cover.garray.handle['ref'][24, 0, 0] == 1 |
||
| 1310 | |||
| 1311 | |||
| 1312 | def test_cover_bam_paired_midpoint(): |
||
| 1313 | # sample2.bam contains paired end examples, |
||
| 1314 | # unmapped examples, unmapped mate and low quality example |
||
| 1315 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1316 | bamfile_ = os.path.join(data_path, "sample2.bam") |
||
| 1317 | |||
| 1318 | |||
| 1319 | cover = Cover.create_from_bam( |
||
| 1320 | "yeast_I_II_III.bam", |
||
| 1321 | bamfiles=bamfile_, |
||
| 1322 | stranded=False, |
||
| 1323 | pairedend='midpoint', |
||
| 1324 | min_mapq=30, |
||
| 1325 | store_whole_genome=True) |
||
| 1326 | |||
| 1327 | assert cover.garray.handle['ref'].sum() == 2, cover.garray.handle['ref'] |
||
| 1328 | print(cover.garray.handle['ref']) |
||
| 1329 | # the read starts at index 6 and tlen is 39 |
||
| 1330 | assert cover.garray.handle['ref'][6 + 39//2, 0, 0] == 1 |
||
| 1331 | # another read maps to index 34 |
||
| 1332 | assert cover.garray.handle['ref'][34, 0, 0] == 1 |
||
| 1333 | |||
| 1334 | |||
| 1335 | def test_cover_bam_list(tmpdir): |
||
| 1336 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1337 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1338 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 1339 | |||
| 1340 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1341 | |||
| 1342 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1343 | # base pair binsize |
||
| 1344 | cover = Cover.create_from_bam( |
||
| 1345 | "yeast_I_II_III.bam", |
||
| 1346 | bamfiles=[bamfile_], |
||
| 1347 | roi=bed_file, |
||
| 1348 | conditions=['condition2'], |
||
| 1349 | normalizer='tpm', |
||
| 1350 | binsize=200, stepsize=200) |
||
| 1351 | |||
| 1352 | def test_cover_bam(tmpdir): |
||
| 1353 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1354 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1355 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 1356 | gsfile_ = os.path.join(data_path, 'sample.chrom.sizes') |
||
| 1357 | |||
| 1358 | content = pandas.read_csv(gsfile_, sep='\t', names=['chr', 'length'], |
||
| 1359 | index_col='chr') |
||
| 1360 | |||
| 1361 | gsize = content.to_dict()['length'] |
||
| 1362 | |||
| 1363 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1364 | |||
| 1365 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1366 | # base pair binsize |
||
| 1367 | cover = Cover.create_from_bam( |
||
| 1368 | "yeast_I_II_III.bam", |
||
| 1369 | bamfiles=bamfile_, |
||
| 1370 | roi=bed_file, |
||
| 1371 | binsize=200, stepsize=200, |
||
| 1372 | genomesize=gsize, |
||
| 1373 | storage=store, cache=True) |
||
| 1374 | |||
| 1375 | np.testing.assert_equal(len(cover), 100) |
||
| 1376 | np.testing.assert_equal(cover.shape, (100, 200, 2, 1)) |
||
| 1377 | |||
| 1378 | # the region is read relative to the forward strand |
||
| 1379 | # read on the reverse strand |
||
| 1380 | val = np.where(cover[4] == 1) |
||
| 1381 | np.testing.assert_equal(cover[4].sum(), 1.) |
||
| 1382 | np.testing.assert_equal(val[1][0], 179) # pos |
||
| 1383 | np.testing.assert_equal(val[2][0], 1) # strand |
||
| 1384 | |||
| 1385 | # two reads on the forward strand |
||
| 1386 | val = np.where(cover[13] == 1) |
||
| 1387 | np.testing.assert_equal(cover[13].sum(), 2.) |
||
| 1388 | np.testing.assert_equal(val[1], np.asarray([162, 178])) # pos |
||
| 1389 | np.testing.assert_equal(val[2], np.asarray([0, 0])) # strand |
||
| 1390 | |||
| 1391 | # the region is read relative to the reverse strand |
||
| 1392 | # for index 50 |
||
| 1393 | # read on the reverse strand |
||
| 1394 | val = np.where(cover[52] == 1) |
||
| 1395 | np.testing.assert_equal(cover[52].sum(), 2.) |
||
| 1396 | np.testing.assert_equal(val[1], np.asarray([9, 89])) # pos |
||
| 1397 | np.testing.assert_equal(val[2], np.asarray([0, 0])) # strand |
||
| 1398 | |||
| 1399 | # two reads on the forward strand |
||
| 1400 | val = np.where(cover[96] == 1) |
||
| 1401 | np.testing.assert_equal(cover[96].sum(), 1.) |
||
| 1402 | np.testing.assert_equal(val[1], np.asarray([25])) # pos |
||
| 1403 | np.testing.assert_equal(val[2], np.asarray([1])) # strand |
||
| 1404 | |||
| 1405 | |||
| 1406 | def test_load_bam_resolution10(tmpdir): |
||
| 1407 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1408 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1409 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 1410 | gsfile_ = os.path.join(data_path, 'sample.chrom.sizes') |
||
| 1411 | |||
| 1412 | content = pandas.read_csv(gsfile_, sep='\t', names=['chr', 'length'], |
||
| 1413 | index_col='chr') |
||
| 1414 | |||
| 1415 | gsize = content.to_dict()['length'] |
||
| 1416 | |||
| 1417 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1418 | |||
| 1419 | for store, store_genome in product(['ndarray', 'hdf5', 'sparse'], [True, False]): |
||
| 1420 | # base pair binsize |
||
| 1421 | cover = Cover.create_from_bam( |
||
| 1422 | "yeast_I_II_III.bam", |
||
| 1423 | bamfiles=bamfile_, |
||
| 1424 | roi=bed_file, |
||
| 1425 | binsize=200, stepsize=200, |
||
| 1426 | genomesize=gsize, |
||
| 1427 | resolution=10, |
||
| 1428 | store_whole_genome=store_genome, |
||
| 1429 | storage=store, cache=True) |
||
| 1430 | |||
| 1431 | np.testing.assert_equal(len(cover), 100) |
||
| 1432 | np.testing.assert_equal(cover.shape, (100, 20, 2, 1)) |
||
| 1433 | |||
| 1434 | # the region is read relative to the forward strand |
||
| 1435 | # read on the reverse strand |
||
| 1436 | val = np.where(cover[4] == 1) |
||
| 1437 | np.testing.assert_equal(cover[4].sum(), 1.) |
||
| 1438 | np.testing.assert_equal(val[1][0], 17) # pos |
||
| 1439 | np.testing.assert_equal(val[2][0], 1) # strand |
||
| 1440 | |||
| 1441 | # two reads on the forward strand |
||
| 1442 | val = np.where(cover[13] == 1) |
||
| 1443 | np.testing.assert_equal(cover[13].sum(), 2.) |
||
| 1444 | np.testing.assert_equal(val[1], np.asarray([16, 17])) # pos |
||
| 1445 | np.testing.assert_equal(val[2], np.asarray([0, 0])) # strand |
||
| 1446 | |||
| 1447 | # the region is read relative to the reverse strand |
||
| 1448 | # for index 50 |
||
| 1449 | # read on the reverse strand |
||
| 1450 | val = np.where(cover[52] == 1) |
||
| 1451 | np.testing.assert_equal(cover[52].sum(), 2.) |
||
| 1452 | np.testing.assert_equal(val[1], np.asarray([0, 8])) # pos |
||
| 1453 | np.testing.assert_equal(val[2], np.asarray([0, 0])) # strand |
||
| 1454 | |||
| 1455 | # two reads on the forward strand |
||
| 1456 | val = np.where(cover[96] == 1) |
||
| 1457 | np.testing.assert_equal(cover[96].sum(), 1.) |
||
| 1458 | np.testing.assert_equal(val[1], np.asarray([2])) # pos |
||
| 1459 | np.testing.assert_equal(val[2], np.asarray([1])) # strand |
||
| 1460 | |||
| 1461 | |||
| 1462 | def test_load_bam_resolutionNone(tmpdir): |
||
| 1463 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1464 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1465 | bamfile_ = os.path.join(data_path, "sample.bam") |
||
| 1466 | gsfile_ = os.path.join(data_path, 'sample.chrom.sizes') |
||
| 1467 | |||
| 1468 | content = pandas.read_csv(gsfile_, sep='\t', names=['chr', 'length'], |
||
| 1469 | index_col='chr') |
||
| 1470 | |||
| 1471 | gsize = content.to_dict()['length'] |
||
| 1472 | |||
| 1473 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1474 | |||
| 1475 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1476 | # base pair binsize |
||
| 1477 | cover1 = Cover.create_from_bam( |
||
| 1478 | "yeast_I_II_III.bam", |
||
| 1479 | bamfiles=bamfile_, |
||
| 1480 | roi=bed_file, |
||
| 1481 | binsize=200, stepsize=200, |
||
| 1482 | genomesize=gsize, |
||
| 1483 | resolution=1, |
||
| 1484 | storage=store, cache=True) |
||
| 1485 | cover = Cover.create_from_bam( |
||
| 1486 | "yeast_I_II_III.bam", |
||
| 1487 | bamfiles=bamfile_, |
||
| 1488 | roi=bed_file, |
||
| 1489 | binsize=200, stepsize=200, |
||
| 1490 | genomesize=gsize, |
||
| 1491 | resolution=None, |
||
| 1492 | storage=store, cache=True) |
||
| 1493 | |||
| 1494 | np.testing.assert_equal(len(cover), 100) |
||
| 1495 | np.testing.assert_equal(cover.shape, (100, 1, 2, 1)) |
||
| 1496 | |||
| 1497 | np.testing.assert_equal(cover1[:].sum(axis=1), cover[:].sum(axis=1)) |
||
| 1498 | |||
| 1499 | |||
| 1500 | def test_load_cover_bigwig_default(tmpdir): |
||
| 1501 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1502 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1503 | |||
| 1504 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 1505 | gsfile_ = os.path.join(data_path, 'sample.chrom.sizes') |
||
| 1506 | |||
| 1507 | gsize = pandas.read_csv(gsfile_, sep='\t', names=['chr', 'length'], |
||
| 1508 | index_col='chr').to_dict()['length'] |
||
| 1509 | |||
| 1510 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1511 | |||
| 1512 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1513 | # base pair binsize |
||
| 1514 | print(store) |
||
| 1515 | cover = Cover.create_from_bigwig( |
||
| 1516 | "cov", |
||
| 1517 | bigwigfiles=bwfile_, |
||
| 1518 | roi=bed_file, |
||
| 1519 | binsize=200, stepsize=200, |
||
| 1520 | genomesize=gsize, |
||
| 1521 | storage=store, |
||
| 1522 | store_whole_genome=True, |
||
| 1523 | cache=True) |
||
| 1524 | |||
| 1525 | np.testing.assert_equal(len(cover), 100) |
||
| 1526 | np.testing.assert_equal(cover.shape, (100, 200, 1, 1)) |
||
| 1527 | |||
| 1528 | # there is one read in the region |
||
| 1529 | np.testing.assert_allclose(cover[4].sum(), 36.) |
||
| 1530 | np.testing.assert_allclose(cover[52].sum(), 2*36.) |
||
| 1531 | |||
| 1532 | cover = Cover.create_from_bigwig( |
||
| 1533 | "cov", |
||
| 1534 | bigwigfiles=bwfile_, |
||
| 1535 | roi=bed_file, |
||
| 1536 | binsize=200, stepsize=200, |
||
| 1537 | genomesize=gsize, |
||
| 1538 | store_whole_genome=False, cache=True) |
||
| 1539 | |||
| 1540 | np.testing.assert_equal(len(cover), 100) |
||
| 1541 | np.testing.assert_equal(cover.shape, (100, 200, 1, 1)) |
||
| 1542 | |||
| 1543 | # there is one read in the region |
||
| 1544 | np.testing.assert_allclose(cover[4].sum(), 36.) |
||
| 1545 | np.testing.assert_allclose(cover[52].sum(), 2*36.) |
||
| 1546 | |||
| 1547 | def test_load_cover_bigwig_resolution1(tmpdir): |
||
| 1548 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1549 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1550 | |||
| 1551 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 1552 | |||
| 1553 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1554 | |||
| 1555 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1556 | # base pair binsize |
||
| 1557 | print(store) |
||
| 1558 | cover = Cover.create_from_bigwig( |
||
| 1559 | "cov", |
||
| 1560 | bigwigfiles=bwfile_, |
||
| 1561 | roi=bed_file, |
||
| 1562 | binsize=200, stepsize=200, |
||
| 1563 | resolution=1, |
||
| 1564 | storage=store, cache=True) |
||
| 1565 | |||
| 1566 | np.testing.assert_equal(len(cover), 100) |
||
| 1567 | np.testing.assert_equal(cover.shape, (100, 200, 1, 1)) |
||
| 1568 | |||
| 1569 | # there is one read in the region 4 |
||
| 1570 | np.testing.assert_allclose(cover[4].sum(), 36) |
||
| 1571 | np.testing.assert_equal(cover[4][0, :, 0, 0], |
||
| 1572 | np.asarray( |
||
| 1573 | [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1574 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1575 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1576 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1577 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1578 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1579 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1580 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1581 | 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., |
||
| 1582 | 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., |
||
| 1583 | 1., 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1584 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.])) |
||
| 1585 | # and two reads in region 52 |
||
| 1586 | np.testing.assert_allclose(cover[52].sum(), 2*36) |
||
| 1587 | np.testing.assert_equal(cover[52][0, :, 0, 0], |
||
| 1588 | np.asarray( |
||
| 1589 | [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., |
||
| 1590 | 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., |
||
| 1591 | 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., |
||
| 1592 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1593 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1594 | 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., |
||
| 1595 | 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., |
||
| 1596 | 1., 1., 1., 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1597 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1598 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1599 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., |
||
| 1600 | 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.])) |
||
| 1601 | |||
| 1602 | |||
| 1603 | |||
| 1604 | def test_load_cover_bigwig_resolutionNone(tmpdir): |
||
| 1605 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1606 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 1607 | |||
| 1608 | bwfile_ = os.path.join(data_path, "sample.bw") |
||
| 1609 | |||
| 1610 | bed_file = os.path.join(data_path, "sample.bed") |
||
| 1611 | |||
| 1612 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1613 | # base pair binsize |
||
| 1614 | print(store) |
||
| 1615 | cover1 = Cover.create_from_bigwig( |
||
| 1616 | "cov", |
||
| 1617 | bigwigfiles=bwfile_, |
||
| 1618 | roi=bed_file, |
||
| 1619 | binsize=200, stepsize=200, |
||
| 1620 | resolution=1, |
||
| 1621 | storage=store, cache=True) |
||
| 1622 | |||
| 1623 | cover = Cover.create_from_bigwig( |
||
| 1624 | "cov", |
||
| 1625 | bigwigfiles=bwfile_, |
||
| 1626 | roi=bed_file, |
||
| 1627 | binsize=200, stepsize=200, |
||
| 1628 | resolution=None, |
||
| 1629 | storage=store, cache=True, |
||
| 1630 | collapser='sum') |
||
| 1631 | np.testing.assert_equal(len(cover), 100) |
||
| 1632 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1633 | |||
| 1634 | np.testing.assert_equal(cover1[:].sum(axis=1), cover[:].sum(axis=1)) |
||
| 1635 | |||
| 1636 | |||
| 1637 | def test_load_cover_bed_binary(tmpdir): |
||
| 1638 | os.environ['JANGGU_OUTPUT'] = tmpdir.strpath |
||
| 1639 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1640 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1641 | 'resources/scored_sample.bed') |
||
| 1642 | |||
| 1643 | for store in ['ndarray', 'hdf5', 'sparse']: |
||
| 1644 | print('store', store) |
||
| 1645 | cover = Cover.create_from_bed( |
||
| 1646 | "cov", |
||
| 1647 | bedfiles=score_file, |
||
| 1648 | roi=bed_file, |
||
| 1649 | binsize=200, stepsize=200, |
||
| 1650 | resolution=200, |
||
| 1651 | storage=store, |
||
| 1652 | mode='binary', cache=True) |
||
| 1653 | np.testing.assert_equal(len(cover), 100) |
||
| 1654 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1655 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1656 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1657 | |||
| 1658 | cover = Cover.create_from_bed( |
||
| 1659 | "cov50", |
||
| 1660 | bedfiles=score_file, |
||
| 1661 | roi=bed_file, |
||
| 1662 | binsize=200, stepsize=200, |
||
| 1663 | storage=store, |
||
| 1664 | resolution=50, |
||
| 1665 | collapser='max', |
||
| 1666 | mode='binary', cache=True) |
||
| 1667 | np.testing.assert_equal(len(cover), 100) |
||
| 1668 | np.testing.assert_equal(cover.shape, (100, 4, 1, 1)) |
||
| 1669 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1670 | np.testing.assert_equal(cover[4].sum(), 4*1) |
||
| 1671 | |||
| 1672 | cover = Cover.create_from_bed( |
||
| 1673 | "cov50_firstdim", |
||
| 1674 | bedfiles=score_file, |
||
| 1675 | roi=bed_file, |
||
| 1676 | binsize=200, stepsize=200, |
||
| 1677 | storage=store, |
||
| 1678 | resolution=None, |
||
| 1679 | collapser='max', |
||
| 1680 | mode='binary', cache=True) |
||
| 1681 | np.testing.assert_equal(len(cover), 100) |
||
| 1682 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1683 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1684 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1685 | |||
| 1686 | cover = Cover.create_from_bed( |
||
| 1687 | "cov50_firstdim", |
||
| 1688 | bedfiles=score_file, |
||
| 1689 | roi=bed_file, |
||
| 1690 | binsize=200, stepsize=200, |
||
| 1691 | storage=store, |
||
| 1692 | store_whole_genome=True, |
||
| 1693 | resolution=200, |
||
| 1694 | collapser='max', |
||
| 1695 | mode='binary', cache=True) |
||
| 1696 | np.testing.assert_equal(len(cover), 100) |
||
| 1697 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1698 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1699 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1700 | |||
| 1701 | |||
| 1702 | def test_load_cover_bed_scored(): |
||
| 1703 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1704 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1705 | 'resources/scored_sample.bed') |
||
| 1706 | |||
| 1707 | for store in ['ndarray', 'sparse']: |
||
| 1708 | cover = Cover.create_from_bed( |
||
| 1709 | "cov", |
||
| 1710 | bedfiles=score_file, |
||
| 1711 | roi=bed_file, |
||
| 1712 | binsize=200, stepsize=200, |
||
| 1713 | resolution=200, |
||
| 1714 | storage=store, |
||
| 1715 | store_whole_genome=True, |
||
| 1716 | mode='score') |
||
| 1717 | |||
| 1718 | np.testing.assert_equal(len(cover), 100) |
||
| 1719 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1720 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1721 | np.testing.assert_equal(cover[4].sum(), 5) |
||
| 1722 | np.testing.assert_equal(cover[50].sum(), 0) |
||
| 1723 | np.testing.assert_equal(cover[54].sum(), 4) |
||
| 1724 | |||
| 1725 | cover = Cover.create_from_bed( |
||
| 1726 | "cov50", |
||
| 1727 | bedfiles=score_file, |
||
| 1728 | roi=bed_file, |
||
| 1729 | binsize=200, stepsize=200, |
||
| 1730 | storage=store, |
||
| 1731 | resolution=50, |
||
| 1732 | mode='score') |
||
| 1733 | |||
| 1734 | np.testing.assert_equal(len(cover), 100) |
||
| 1735 | np.testing.assert_equal(cover.shape, (100, 4, 1, 1)) |
||
| 1736 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1737 | np.testing.assert_equal(cover[4].sum(), 4*5) |
||
| 1738 | |||
| 1739 | cover = Cover.create_from_bed( |
||
| 1740 | "cov50", |
||
| 1741 | bedfiles=score_file, |
||
| 1742 | roi=bed_file, |
||
| 1743 | storage=store, |
||
| 1744 | resolution=None, |
||
| 1745 | binsize=200, stepsize=200, |
||
| 1746 | collapser='max', |
||
| 1747 | mode='score') |
||
| 1748 | |||
| 1749 | np.testing.assert_equal(len(cover), 100) |
||
| 1750 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1751 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1752 | np.testing.assert_equal(cover[4].sum(), 5) |
||
| 1753 | |||
| 1754 | |||
| 1755 | def test_load_cover_bed_categorical(): |
||
| 1756 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1757 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1758 | 'resources/scored_sample.bed') |
||
| 1759 | |||
| 1760 | with pytest.raises(ValueError): |
||
| 1761 | # Only one bed file allowed. |
||
| 1762 | cover = Cover.create_from_bed( |
||
| 1763 | "cov", |
||
| 1764 | bedfiles=[score_file] * 2, |
||
| 1765 | roi=bed_file, |
||
| 1766 | binsize=200, stepsize=200, |
||
| 1767 | resolution=200, |
||
| 1768 | mode='categorical') |
||
| 1769 | |||
| 1770 | for store in ['ndarray', 'sparse']: |
||
| 1771 | print(store) |
||
| 1772 | cover = Cover.create_from_bed( |
||
| 1773 | "cov", |
||
| 1774 | bedfiles=score_file, |
||
| 1775 | roi=bed_file, |
||
| 1776 | binsize=200, stepsize=200, |
||
| 1777 | resolution=200, |
||
| 1778 | storage=store, |
||
| 1779 | mode='categorical') |
||
| 1780 | |||
| 1781 | np.testing.assert_equal(len(cover), 100) |
||
| 1782 | np.testing.assert_equal(cover.shape, (100, 1, 1, 4)) |
||
| 1783 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1784 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1785 | np.testing.assert_equal(cover[4], [[[[0., 0., 0., 1.]]]]) |
||
| 1786 | |||
| 1787 | cover = Cover.create_from_bed( |
||
| 1788 | "cov50", |
||
| 1789 | bedfiles=score_file, |
||
| 1790 | roi=bed_file, |
||
| 1791 | binsize=200, stepsize=200, |
||
| 1792 | resolution=50, |
||
| 1793 | storage=store, |
||
| 1794 | mode='categorical') |
||
| 1795 | |||
| 1796 | np.testing.assert_equal(len(cover), 100) |
||
| 1797 | np.testing.assert_equal(cover.shape, (100, 4, 1, 4)) |
||
| 1798 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1799 | np.testing.assert_equal(cover[4].sum(), 4*1) |
||
| 1800 | |||
| 1801 | cover = Cover.create_from_bed( |
||
| 1802 | "cov50", |
||
| 1803 | bedfiles=score_file, |
||
| 1804 | roi=bed_file, |
||
| 1805 | resolution=None, |
||
| 1806 | binsize=200, stepsize=200, |
||
| 1807 | storage=store, |
||
| 1808 | collapser='max', |
||
| 1809 | mode='categorical') |
||
| 1810 | |||
| 1811 | np.testing.assert_equal(len(cover), 100) |
||
| 1812 | np.testing.assert_equal(cover.shape, (100, 1, 1, 4)) |
||
| 1813 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1814 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1815 | np.testing.assert_equal(cover[4], [[[[0., 0., 0., 1.]]]]) |
||
| 1816 | |||
| 1817 | |||
| 1818 | def test_load_cover_bed_score_category(): |
||
| 1819 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1820 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1821 | 'resources/scored_sample.bed') |
||
| 1822 | |||
| 1823 | with pytest.raises(ValueError): |
||
| 1824 | # Only one bed file allowed. |
||
| 1825 | cover = Cover.create_from_bed( |
||
| 1826 | "cov", |
||
| 1827 | bedfiles=[score_file] * 2, |
||
| 1828 | roi=bed_file, |
||
| 1829 | binsize=200, stepsize=200, |
||
| 1830 | resolution=200, |
||
| 1831 | mode='score_category') |
||
| 1832 | |||
| 1833 | for store in ['ndarray', 'sparse']: |
||
| 1834 | print(store) |
||
| 1835 | cover = Cover.create_from_bed( |
||
| 1836 | "cov", |
||
| 1837 | bedfiles=score_file, |
||
| 1838 | roi=bed_file, |
||
| 1839 | binsize=200, stepsize=200, |
||
| 1840 | resolution=200, |
||
| 1841 | storage=store, |
||
| 1842 | mode='score_category') |
||
| 1843 | |||
| 1844 | assert cover.conditions == ['1', '2', '4', '5'] |
||
| 1845 | np.testing.assert_equal(len(cover), 100) |
||
| 1846 | np.testing.assert_equal(cover.shape, (100, 1, 1, 4)) |
||
| 1847 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1848 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1849 | np.testing.assert_equal(cover[4], [[[[0., 0., 0., 1.]]]]) |
||
| 1850 | |||
| 1851 | cover = Cover.create_from_bed( |
||
| 1852 | "cov", |
||
| 1853 | bedfiles=score_file, |
||
| 1854 | roi=bed_file, |
||
| 1855 | binsize=200, stepsize=200, |
||
| 1856 | resolution=200, |
||
| 1857 | conditions=['1', '2', '4', '5'], |
||
| 1858 | storage=store, |
||
| 1859 | mode='score_category') |
||
| 1860 | |||
| 1861 | assert cover.conditions == ['1', '2', '4', '5'] |
||
| 1862 | np.testing.assert_equal(len(cover), 100) |
||
| 1863 | np.testing.assert_equal(cover.shape, (100, 1, 1, 4)) |
||
| 1864 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1865 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1866 | np.testing.assert_equal(cover[4], [[[[0., 0., 0., 1.]]]]) |
||
| 1867 | |||
| 1868 | cover = Cover.create_from_bed( |
||
| 1869 | "cov50", |
||
| 1870 | bedfiles=score_file, |
||
| 1871 | roi=bed_file, |
||
| 1872 | binsize=200, stepsize=200, |
||
| 1873 | resolution=50, |
||
| 1874 | storage=store, |
||
| 1875 | mode='score_category') |
||
| 1876 | |||
| 1877 | assert cover.conditions == ['1', '2', '4', '5'] |
||
| 1878 | np.testing.assert_equal(len(cover), 100) |
||
| 1879 | np.testing.assert_equal(cover.shape, (100, 4, 1, 4)) |
||
| 1880 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1881 | np.testing.assert_equal(cover[4].sum(), 4*1) |
||
| 1882 | |||
| 1883 | cover = Cover.create_from_bed( |
||
| 1884 | "cov50", |
||
| 1885 | bedfiles=score_file, |
||
| 1886 | roi=bed_file, |
||
| 1887 | resolution=None, |
||
| 1888 | binsize=200, stepsize=200, |
||
| 1889 | storage=store, |
||
| 1890 | collapser='max', |
||
| 1891 | mode='score_category') |
||
| 1892 | |||
| 1893 | assert cover.conditions == ['1', '2', '4', '5'] |
||
| 1894 | np.testing.assert_equal(len(cover), 100) |
||
| 1895 | np.testing.assert_equal(cover.shape, (100, 1, 1, 4)) |
||
| 1896 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1897 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1898 | np.testing.assert_equal(cover[4], [[[[0., 0., 0., 1.]]]]) |
||
| 1899 | |||
| 1900 | |||
| 1901 | def test_load_cover_bedgraph(): |
||
| 1902 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1903 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1904 | 'resources/sample.bedgraph') |
||
| 1905 | |||
| 1906 | for store in ['ndarray', 'sparse']: |
||
| 1907 | print(store) |
||
| 1908 | cover = Cover.create_from_bed( |
||
| 1909 | "cov", |
||
| 1910 | bedfiles=score_file, |
||
| 1911 | roi=bed_file, |
||
| 1912 | binsize=200, stepsize=200, |
||
| 1913 | resolution=200, |
||
| 1914 | storage=store, |
||
| 1915 | mode='bedgraph') |
||
| 1916 | |||
| 1917 | np.testing.assert_equal(len(cover), 100) |
||
| 1918 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1919 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1920 | np.testing.assert_equal(cover[4].sum(), .5) |
||
| 1921 | np.testing.assert_equal(cover[4], [[[[.5]]]]) |
||
| 1922 | |||
| 1923 | cover = Cover.create_from_bed( |
||
| 1924 | "cov50", |
||
| 1925 | bedfiles=score_file, |
||
| 1926 | roi=bed_file, |
||
| 1927 | binsize=200, stepsize=200, |
||
| 1928 | resolution=50, |
||
| 1929 | storage=store, |
||
| 1930 | mode='bedgraph') |
||
| 1931 | |||
| 1932 | np.testing.assert_equal(len(cover), 100) |
||
| 1933 | np.testing.assert_equal(cover.shape, (100, 4, 1, 1)) |
||
| 1934 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1935 | np.testing.assert_equal(cover[4].sum(), 4*.5) |
||
| 1936 | |||
| 1937 | cover = Cover.create_from_bed( |
||
| 1938 | "cov50", |
||
| 1939 | bedfiles=score_file, |
||
| 1940 | roi=bed_file, |
||
| 1941 | resolution=None, |
||
| 1942 | binsize=200, stepsize=200, |
||
| 1943 | storage=store, |
||
| 1944 | collapser='max', |
||
| 1945 | mode='bedgraph') |
||
| 1946 | |||
| 1947 | np.testing.assert_equal(len(cover), 100) |
||
| 1948 | np.testing.assert_equal(cover.shape, (100, 1, 1, 1)) |
||
| 1949 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1950 | np.testing.assert_equal(cover[4].sum(), .5) |
||
| 1951 | np.testing.assert_equal(cover[4], [[[[.5]]]]) |
||
| 1952 | |||
| 1953 | |||
| 1954 | def test_load_cover_bed_name_category(): |
||
| 1955 | bed_file = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 1956 | score_file = pkg_resources.resource_filename('janggu', |
||
| 1957 | 'resources/scored_sample.bed') |
||
| 1958 | |||
| 1959 | with pytest.raises(ValueError): |
||
| 1960 | # Only one bed file allowed. |
||
| 1961 | cover = Cover.create_from_bed( |
||
| 1962 | "cov", |
||
| 1963 | bedfiles=[score_file] * 2, |
||
| 1964 | roi=bed_file, |
||
| 1965 | binsize=200, stepsize=200, |
||
| 1966 | resolution=200, |
||
| 1967 | mode='name_category') |
||
| 1968 | |||
| 1969 | for store in ['ndarray', 'sparse']: |
||
| 1970 | print(store) |
||
| 1971 | cover = Cover.create_from_bed( |
||
| 1972 | "cov", |
||
| 1973 | bedfiles=score_file, |
||
| 1974 | roi=bed_file, |
||
| 1975 | binsize=200, stepsize=200, |
||
| 1976 | resolution=200, |
||
| 1977 | storage=store, |
||
| 1978 | mode='name_category') |
||
| 1979 | |||
| 1980 | assert cover.conditions == ['state1', 'state2'] |
||
| 1981 | np.testing.assert_equal(len(cover), 100) |
||
| 1982 | np.testing.assert_equal(cover.shape, (100, 1, 1, 2)) |
||
| 1983 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 1984 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 1985 | np.testing.assert_equal(cover[3], [[[[1., 0.]]]]) |
||
| 1986 | np.testing.assert_equal(cover[4], [[[[0., 1.]]]]) |
||
| 1987 | |||
| 1988 | cover = Cover.create_from_bed( |
||
| 1989 | "cov", |
||
| 1990 | bedfiles=score_file, |
||
| 1991 | roi=bed_file, |
||
| 1992 | binsize=200, stepsize=200, |
||
| 1993 | resolution=200, |
||
| 1994 | conditions=['state1', 'state2'], |
||
| 1995 | storage=store, |
||
| 1996 | mode='name_category') |
||
| 1997 | |||
| 1998 | assert cover.conditions == ['state1', 'state2'] |
||
| 1999 | np.testing.assert_equal(len(cover), 100) |
||
| 2000 | np.testing.assert_equal(cover.shape, (100, 1, 1, 2)) |
||
| 2001 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 2002 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 2003 | np.testing.assert_equal(cover[3], [[[[1., 0.]]]]) |
||
| 2004 | np.testing.assert_equal(cover[4], [[[[0., 1.]]]]) |
||
| 2005 | |||
| 2006 | cover = Cover.create_from_bed( |
||
| 2007 | "cov50", |
||
| 2008 | bedfiles=score_file, |
||
| 2009 | roi=bed_file, |
||
| 2010 | binsize=200, stepsize=200, |
||
| 2011 | resolution=50, |
||
| 2012 | storage=store, |
||
| 2013 | mode='name_category') |
||
| 2014 | |||
| 2015 | assert cover.conditions == ['state1', 'state2'] |
||
| 2016 | np.testing.assert_equal(len(cover), 100) |
||
| 2017 | np.testing.assert_equal(cover.shape, (100, 4, 1, 2)) |
||
| 2018 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 2019 | np.testing.assert_equal(cover[4].sum(), 4*1) |
||
| 2020 | |||
| 2021 | cover = Cover.create_from_bed( |
||
| 2022 | "cov50", |
||
| 2023 | bedfiles=score_file, |
||
| 2024 | roi=bed_file, |
||
| 2025 | resolution=None, |
||
| 2026 | binsize=200, stepsize=200, |
||
| 2027 | storage=store, |
||
| 2028 | collapser='max', |
||
| 2029 | mode='name_category') |
||
| 2030 | |||
| 2031 | assert cover.conditions == ['state1', 'state2'] |
||
| 2032 | np.testing.assert_equal(len(cover), 100) |
||
| 2033 | np.testing.assert_equal(cover.shape, (100, 1, 1, 2)) |
||
| 2034 | np.testing.assert_equal(cover[0].sum(), 0) |
||
| 2035 | np.testing.assert_equal(cover[4].sum(), 1) |
||
| 2036 | np.testing.assert_equal(cover[3], [[[[1., 0.]]]]) |
||
| 2037 | np.testing.assert_equal(cover[4], [[[[0., 1.]]]]) |
||
| 2038 | |||
| 2039 | |||
| 2040 | def test_filter_by_region(): |
||
| 2041 | |||
| 2042 | roi_file = pkg_resources.resource_filename('janggu', |
||
| 2043 | 'resources/bed_test.bed') |
||
| 2044 | |||
| 2045 | roi = GenomicIndexer.create_from_file(regions=roi_file, binsize=2, stepsize=2) |
||
| 2046 | np.testing.assert_equal(len(roi), 9) |
||
| 2047 | |||
| 2048 | np.testing.assert_equal((roi[0].chrom, roi[0].start, roi[0].end), ('chr1', 0, 2)) |
||
| 2049 | np.testing.assert_equal((roi[-1].chrom, roi[-1].start, roi[-1].end), ('chr1', 16, 18)) |
||
| 2050 | |||
| 2051 | test1 = roi.filter_by_region(include='chr1', start=0, end=18) |
||
| 2052 | |||
| 2053 | for i in range(len(test1)): |
||
| 2054 | np.testing.assert_equal(test1[i], roi[i]) |
||
| 2055 | |||
| 2056 | test2 = roi.filter_by_region(include='chr1', start=5, end=10) |
||
| 2057 | np.testing.assert_equal(len(test2), 3) |
||
| 2058 | np.testing.assert_equal((test2[0].chrom, test2[0].start, test2[0].end), ('chr1', 4, 6)) |
||
| 2059 | np.testing.assert_equal((test2[1].chrom, test2[1].start, test2[1].end), ('chr1', 6, 8)) |
||
| 2060 | np.testing.assert_equal((test2[2].chrom, test2[2].start, test2[2].end), ('chr1', 8, 10)) |
||
| 2061 | |||
| 2062 | test3 = roi.filter_by_region(include='chr1', start=5, end=11) |
||
| 2063 | np.testing.assert_equal(len(test3), 4) |
||
| 2064 | np.testing.assert_equal((test3[0].chrom, test3[0].start, test3[0].end), ('chr1', 4, 6)) |
||
| 2065 | np.testing.assert_equal((test3[1].chrom, test3[1].start, test3[1].end), ('chr1', 6, 8)) |
||
| 2066 | np.testing.assert_equal((test3[2].chrom, test3[2].start, test3[2].end), ('chr1', 8, 10)) |
||
| 2067 | np.testing.assert_equal((test3[3].chrom, test3[3].start, test3[3].end), ('chr1', 10, 12)) |
||
| 2068 | |||
| 2069 | test4 = roi.filter_by_region(include='chr1', start=6, end=10) |
||
| 2070 | np.testing.assert_equal(len(test4), 2) |
||
| 2071 | np.testing.assert_equal((test4[0].chrom, test4[0].start, test4[0].end), ('chr1', 6, 8)) |
||
| 2072 | np.testing.assert_equal((test4[1].chrom, test4[1].start, test4[1].end), ('chr1', 8, 10)) |
||
| 2073 | |||
| 2074 | test5 = roi.filter_by_region(include='chr1', start=6, end=11) |
||
| 2075 | np.testing.assert_equal(len(test5), 3) |
||
| 2076 | np.testing.assert_equal((test5[0].chrom, test5[0].start, test5[0].end), ('chr1', 6, 8)) |
||
| 2077 | np.testing.assert_equal((test5[1].chrom, test5[1].start, test5[1].end), ('chr1', 8, 10)) |
||
| 2078 | np.testing.assert_equal((test5[2].chrom, test5[2].start, test5[2].end), ('chr1', 10, 12)) |
||
| 2079 | |||
| 2080 | test6 = roi.filter_by_region(include='chr1', start=20, end=30) |
||
| 2081 | np.testing.assert_equal(len(test6), 0) |
||
| 2082 | |||
| 2083 | |||
| 2084 | def test_plotgenometracks_bigwigs(): |
||
| 2085 | |||
| 2086 | roi = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 2087 | |||
| 2088 | bw_file = pkg_resources.resource_filename('janggu', 'resources/sample.bw') |
||
| 2089 | |||
| 2090 | cover = Cover.create_from_bigwig('coverage2', |
||
| 2091 | bigwigfiles=bw_file, |
||
| 2092 | roi=roi, |
||
| 2093 | binsize=200, |
||
| 2094 | stepsize=200, |
||
| 2095 | resolution=50) |
||
| 2096 | |||
| 2097 | cover2 = Cover.create_from_bigwig('morecoverage', |
||
| 2098 | bigwigfiles=[bw_file] * 4, |
||
| 2099 | roi=roi, |
||
| 2100 | binsize=200, |
||
| 2101 | stepsize=200, |
||
| 2102 | resolution=50) |
||
| 2103 | |||
| 2104 | # line plots |
||
| 2105 | a = plotGenomeTrack([cover,cover2],'chr1',16000,18000) |
||
| 2106 | a = plotGenomeTrack(cover,'chr1',16000,18000) |
||
| 2107 | |||
| 2108 | a = plotGenomeTrack(LineTrack(cover),'chr1',16000,18000) |
||
| 2109 | |||
| 2110 | a = plotGenomeTrack([cover,cover2],'chr1',16000,18000, plottypes=['heatmap'] * 2) |
||
| 2111 | with pytest.raises(AssertionError): |
||
| 2112 | # differing number of plottypes and coverage objects raises an error |
||
| 2113 | a = plotGenomeTrack(cover,'chr1',16000,18000, plottypes=['heatmap'] * 2) |
||
| 2114 | with pytest.raises(ValueError): |
||
| 2115 | # coverage not a sequence |
||
| 2116 | a = plotGenomeTrack(cover,'chr1',16000,18000, plottypes=['seqplot']) |
||
| 2117 | with pytest.raises(ValueError): |
||
| 2118 | # coverage not a sequence |
||
| 2119 | a = plotGenomeTrack(cover2,'chr1',16000,18000, plottypes=['seqplot']) |
||
| 2120 | |||
| 2121 | |||
| 2122 | def test_plotgenometracks_bams(): |
||
| 2123 | |||
| 2124 | roi = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 2125 | |||
| 2126 | bw_file = pkg_resources.resource_filename('janggu', 'resources/sample.bam') |
||
| 2127 | |||
| 2128 | cover = Cover.create_from_bam('coverage', |
||
| 2129 | bamfiles=bw_file, |
||
| 2130 | roi=roi, |
||
| 2131 | binsize=200, |
||
| 2132 | stepsize=200, |
||
| 2133 | resolution=50) |
||
| 2134 | |||
| 2135 | # line plots |
||
| 2136 | a = plotGenomeTrack(cover,'chr1',16000,18000) |
||
| 2137 | |||
| 2138 | a = plotGenomeTrack([cover,cover],'chr1',16000,18000, plottypes=['heatmap'] * 2) |
||
| 2139 | |||
| 2140 | a = plotGenomeTrack([HeatTrack(cover), HeatTrack(cover)],'chr1',16000,18000) |
||
| 2141 | a = plotGenomeTrack([LineTrack(cover)],'chr1',16000,18000) |
||
| 2142 | |||
| 2143 | |||
| 2144 | def test_plotgenometracks_seqplot(): |
||
| 2145 | |||
| 2146 | roi = pkg_resources.resource_filename('janggu', 'resources/sample.bed') |
||
| 2147 | |||
| 2148 | refgenome = pkg_resources.resource_filename('janggu', |
||
| 2149 | 'resources/sample_genome.fa') |
||
| 2150 | |||
| 2151 | dna = Bioseq.create_from_refgenome('dna', refgenome=refgenome, |
||
| 2152 | storage='ndarray', |
||
| 2153 | roi=roi, order=1, |
||
| 2154 | store_whole_genome=True) |
||
| 2155 | |||
| 2156 | a = plotGenomeTrack(dna,'chr1',16000,18000, plottypes=['seqplot']) |
||
| 2157 | |||
| 2158 | a = plotGenomeTrack(SeqTrack(dna), 'chr1', 16000, 18000) |
||
| 2159 | |||
| 2160 | def test_padding_value_nan(): |
||
| 2161 | variantsfile = pkg_resources.resource_filename('janggu', 'resources/pseudo_snps.vcf') |
||
| 2162 | gindexer = GenomicIndexer.create_from_file(variantsfile, None, None) |
||
| 2163 | array = np.zeros((len(gindexer), 3)) |
||
| 2164 | |||
| 2165 | snpcov = Cover.create_from_array('snps', array, |
||
| 2166 | gindexer, |
||
| 2167 | store_whole_genome=True, |
||
| 2168 | padding_value=np.nan) |
||
| 2169 | |||
| 2170 | assert snpcov.shape == (6, 1, 1, 3) |
||
| 2171 | |||
| 2172 | np.testing.assert_equal(snpcov['pseudo1', 650, 670][0,:,0,0], |
||
| 2173 | np.array([np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, |
||
| 2174 | 0., np.nan, 0., np.nan, 0., 0., 0., |
||
| 2175 | np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan])) |
||
| 2176 | |||
| 2177 | snpcov = Cover.create_from_array('snps', array, |
||
| 2178 | gindexer, |
||
| 2179 | store_whole_genome=False, |
||
| 2180 | padding_value=np.nan) |
||
| 2181 | |||
| 2182 | assert snpcov.shape == (6, 1, 1, 3) |
||
| 2183 | |||
| 2184 | np.testing.assert_equal(snpcov['pseudo1', 650, 670][0,:,0,0], |
||
| 2185 | np.array([np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, |
||
| 2186 | 0., np.nan, 0., np.nan, 0., 0., 0., |
||
| 2187 | np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan])) |
||
| 2188 | |||
| 2189 | |||
| 2190 | def test_bedgraph(): |
||
| 2191 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2192 | bed_file = os.path.join(data_path, "positive.bed") |
||
| 2193 | bgfile_ = os.path.join(data_path, "positive.bedgraph") |
||
| 2194 | |||
| 2195 | cover1 = Cover.create_from_bed( |
||
| 2196 | 'test', |
||
| 2197 | bedfiles=bgfile_, |
||
| 2198 | roi=bed_file, |
||
| 2199 | mode='bedgraph', |
||
| 2200 | store_whole_genome=True) |
||
| 2201 | cover2 = Cover.create_from_bed( |
||
| 2202 | 'test2', |
||
| 2203 | bedfiles=bgfile_, |
||
| 2204 | roi=bed_file, |
||
| 2205 | mode='bedgraph', |
||
| 2206 | store_whole_genome=False) |
||
| 2207 | |||
| 2208 | assert len(cover1) == 25 |
||
| 2209 | assert len(cover2) == len(cover1) |
||
| 2210 | assert cover1.shape == (25, 200, 1, 1) |
||
| 2211 | assert cover1.shape == cover2.shape |
||
| 2212 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2213 | |||
| 2214 | def test_fulltilebigwig(): |
||
| 2215 | |||
| 2216 | import pkg_resources |
||
| 2217 | import os |
||
| 2218 | from janggu.data import Cover |
||
| 2219 | |||
| 2220 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2221 | roi = os.path.join(data_path, "sample_fulltile.bed") |
||
| 2222 | bwfile = os.path.join(data_path, "sample.bw") |
||
| 2223 | |||
| 2224 | cover1 = Cover.create_from_bigwig( |
||
| 2225 | 'test', |
||
| 2226 | bigwigfiles=bwfile, |
||
| 2227 | roi=roi, |
||
| 2228 | store_whole_genome=True) |
||
| 2229 | cover2 = Cover.create_from_bigwig( |
||
| 2230 | 'test2', |
||
| 2231 | bigwigfiles=bwfile, |
||
| 2232 | roi=roi, |
||
| 2233 | store_whole_genome=False) |
||
| 2234 | |||
| 2235 | assert len(cover1) == 2 |
||
| 2236 | assert len(cover2) == len(cover1) |
||
| 2237 | assert cover1.shape == (2, 30000, 1, 1) |
||
| 2238 | assert cover1.shape == cover2.shape |
||
| 2239 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2240 | |||
| 2241 | cover1 = Cover.create_from_bigwig( |
||
| 2242 | 'test', |
||
| 2243 | bigwigfiles=bwfile, |
||
| 2244 | roi=roi, binsize=200, |
||
| 2245 | store_whole_genome=True) |
||
| 2246 | cover2 = Cover.create_from_bigwig( |
||
| 2247 | 'test2', |
||
| 2248 | bigwigfiles=bwfile, |
||
| 2249 | roi=roi, binsize=200, |
||
| 2250 | store_whole_genome=False) |
||
| 2251 | |||
| 2252 | assert len(cover1) == 300 |
||
| 2253 | assert len(cover2) == len(cover1) |
||
| 2254 | assert cover1.shape == (300, 200, 1, 1) |
||
| 2255 | assert cover1.shape == cover2.shape |
||
| 2256 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2257 | |||
| 2258 | cover1 = Cover.create_from_bigwig( |
||
| 2259 | 'test', |
||
| 2260 | bigwigfiles=bwfile, |
||
| 2261 | roi=roi, binsize=200, |
||
| 2262 | flank=150, |
||
| 2263 | store_whole_genome=True) |
||
| 2264 | cover2 = Cover.create_from_bigwig( |
||
| 2265 | 'test2', |
||
| 2266 | bigwigfiles=bwfile, |
||
| 2267 | roi=roi, binsize=200, |
||
| 2268 | flank=150, |
||
| 2269 | store_whole_genome=False) |
||
| 2270 | |||
| 2271 | assert len(cover1) == 300 |
||
| 2272 | assert len(cover2) == len(cover1) |
||
| 2273 | assert cover1.shape == (300, 500, 1, 1) |
||
| 2274 | assert cover1.shape == cover2.shape |
||
| 2275 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2276 | |||
| 2277 | def test_fulltilebigwig2(): |
||
| 2278 | |||
| 2279 | import pkg_resources |
||
| 2280 | import os |
||
| 2281 | from janggu.data import Cover |
||
| 2282 | |||
| 2283 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2284 | roi = os.path.join(data_path, "sample_fulltile2.bed") |
||
| 2285 | bwfile = os.path.join(data_path, "sample.bw") |
||
| 2286 | |||
| 2287 | cover1 = Cover.create_from_bigwig( |
||
| 2288 | 'test', |
||
| 2289 | bigwigfiles=bwfile, |
||
| 2290 | roi=roi, |
||
| 2291 | store_whole_genome=True) |
||
| 2292 | cover2 = Cover.create_from_bigwig( |
||
| 2293 | 'test2', |
||
| 2294 | bigwigfiles=bwfile, |
||
| 2295 | roi=roi, |
||
| 2296 | store_whole_genome=False) |
||
| 2297 | |||
| 2298 | assert len(cover1) == 3 |
||
| 2299 | assert len(cover2) == len(cover1) |
||
| 2300 | assert cover1.shape == (3, 30000, 1, 1) |
||
| 2301 | assert cover1.shape == cover2.shape |
||
| 2302 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2303 | |||
| 2304 | cover1 = Cover.create_from_bigwig( |
||
| 2305 | 'test', |
||
| 2306 | bigwigfiles=bwfile, |
||
| 2307 | roi=roi, binsize=200, |
||
| 2308 | store_whole_genome=True) |
||
| 2309 | cover2 = Cover.create_from_bigwig( |
||
| 2310 | 'test2', |
||
| 2311 | bigwigfiles=bwfile, |
||
| 2312 | roi=roi, binsize=200, |
||
| 2313 | store_whole_genome=False) |
||
| 2314 | |||
| 2315 | assert len(cover1) == 450 |
||
| 2316 | assert len(cover2) == len(cover1) |
||
| 2317 | assert cover1.shape == (450, 200, 1, 1) |
||
| 2318 | assert cover1.shape == cover2.shape |
||
| 2319 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2320 | |||
| 2321 | cover1 = Cover.create_from_bigwig( |
||
| 2322 | 'test', |
||
| 2323 | bigwigfiles=bwfile, |
||
| 2324 | roi=roi, binsize=200, |
||
| 2325 | flank=150, |
||
| 2326 | store_whole_genome=True) |
||
| 2327 | cover2 = Cover.create_from_bigwig( |
||
| 2328 | 'test2', |
||
| 2329 | bigwigfiles=bwfile, |
||
| 2330 | roi=roi, binsize=200, |
||
| 2331 | flank=150, |
||
| 2332 | store_whole_genome=False) |
||
| 2333 | |||
| 2334 | assert len(cover1) == 450 |
||
| 2335 | assert len(cover2) == len(cover1) |
||
| 2336 | assert cover1.shape == (450, 500, 1, 1) |
||
| 2337 | assert cover1.shape == cover2.shape |
||
| 2338 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2339 | |||
| 2340 | |||
| 2341 | def test_fulltilebam(): |
||
| 2342 | |||
| 2343 | import pkg_resources |
||
| 2344 | import os |
||
| 2345 | from janggu.data import Cover |
||
| 2346 | |||
| 2347 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2348 | roi = os.path.join(data_path, "sample_fulltile.bed") |
||
| 2349 | bwfile = os.path.join(data_path, "sample.bam") |
||
| 2350 | |||
| 2351 | cover1 = Cover.create_from_bam( |
||
| 2352 | 'test', |
||
| 2353 | bamfiles=bwfile, |
||
| 2354 | roi=roi, |
||
| 2355 | stranded=False, |
||
| 2356 | store_whole_genome=True) |
||
| 2357 | cover2 = Cover.create_from_bam( |
||
| 2358 | 'test2', |
||
| 2359 | bamfiles=bwfile, |
||
| 2360 | stranded=False, |
||
| 2361 | roi=roi, |
||
| 2362 | store_whole_genome=False) |
||
| 2363 | |||
| 2364 | assert len(cover1) == 2 |
||
| 2365 | assert len(cover2) == len(cover1) |
||
| 2366 | assert cover1.shape == (2, 30000, 1, 1) |
||
| 2367 | assert cover1.shape == cover2.shape |
||
| 2368 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2369 | |||
| 2370 | cover1 = Cover.create_from_bam( |
||
| 2371 | 'test', |
||
| 2372 | bamfiles=bwfile, |
||
| 2373 | roi=roi, binsize=200, |
||
| 2374 | stranded=False, |
||
| 2375 | store_whole_genome=True) |
||
| 2376 | cover2 = Cover.create_from_bam( |
||
| 2377 | 'test2', |
||
| 2378 | bamfiles=bwfile, |
||
| 2379 | roi=roi, binsize=200, |
||
| 2380 | stranded=False, |
||
| 2381 | store_whole_genome=False) |
||
| 2382 | |||
| 2383 | assert len(cover1) == 300 |
||
| 2384 | assert len(cover2) == len(cover1) |
||
| 2385 | assert cover1.shape == (300, 200, 1, 1) |
||
| 2386 | assert cover1.shape == cover2.shape |
||
| 2387 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2388 | |||
| 2389 | cover1 = Cover.create_from_bam( |
||
| 2390 | 'test', |
||
| 2391 | bamfiles=bwfile, |
||
| 2392 | roi=roi, binsize=200, |
||
| 2393 | flank=150, |
||
| 2394 | stranded=False, |
||
| 2395 | store_whole_genome=True) |
||
| 2396 | cover2 = Cover.create_from_bam( |
||
| 2397 | 'test2', |
||
| 2398 | bamfiles=bwfile, |
||
| 2399 | roi=roi, binsize=200, |
||
| 2400 | flank=150, |
||
| 2401 | stranded=False, |
||
| 2402 | store_whole_genome=False) |
||
| 2403 | |||
| 2404 | assert len(cover1) == 300 |
||
| 2405 | assert len(cover2) == len(cover1) |
||
| 2406 | assert cover1.shape == (300, 500, 1, 1) |
||
| 2407 | assert cover1.shape == cover2.shape |
||
| 2408 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2409 | |||
| 2410 | def test_fulltilebam2(): |
||
| 2411 | |||
| 2412 | import pkg_resources |
||
| 2413 | import os |
||
| 2414 | from janggu.data import Cover |
||
| 2415 | |||
| 2416 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2417 | roi = os.path.join(data_path, "sample_fulltile2.bed") |
||
| 2418 | bwfile = os.path.join(data_path, "sample.bam") |
||
| 2419 | |||
| 2420 | cover1 = Cover.create_from_bam( |
||
| 2421 | 'test', |
||
| 2422 | bamfiles=bwfile, |
||
| 2423 | roi=roi, |
||
| 2424 | stranded=False, |
||
| 2425 | store_whole_genome=True) |
||
| 2426 | cover2 = Cover.create_from_bam( |
||
| 2427 | 'test2', |
||
| 2428 | bamfiles=bwfile, |
||
| 2429 | roi=roi, |
||
| 2430 | stranded=False, |
||
| 2431 | store_whole_genome=False) |
||
| 2432 | |||
| 2433 | assert len(cover1) == 3 |
||
| 2434 | assert len(cover2) == len(cover1) |
||
| 2435 | assert cover1.shape == (3, 30000, 1, 1) |
||
| 2436 | assert cover1.shape == cover2.shape |
||
| 2437 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2438 | |||
| 2439 | cover1 = Cover.create_from_bam( |
||
| 2440 | 'test', |
||
| 2441 | bamfiles=bwfile, |
||
| 2442 | roi=roi, binsize=200, |
||
| 2443 | stranded=False, |
||
| 2444 | store_whole_genome=True) |
||
| 2445 | cover2 = Cover.create_from_bam( |
||
| 2446 | 'test2', |
||
| 2447 | bamfiles=bwfile, |
||
| 2448 | roi=roi, binsize=200, |
||
| 2449 | stranded=False, |
||
| 2450 | store_whole_genome=False) |
||
| 2451 | |||
| 2452 | assert len(cover1) == 450 |
||
| 2453 | assert len(cover2) == len(cover1) |
||
| 2454 | assert cover1.shape == (450, 200, 1, 1) |
||
| 2455 | assert cover1.shape == cover2.shape |
||
| 2456 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2457 | |||
| 2458 | cover1 = Cover.create_from_bam( |
||
| 2459 | 'test', |
||
| 2460 | bamfiles=bwfile, |
||
| 2461 | roi=roi, binsize=200, |
||
| 2462 | flank=150, |
||
| 2463 | stranded=False, |
||
| 2464 | store_whole_genome=True) |
||
| 2465 | cover2 = Cover.create_from_bam( |
||
| 2466 | 'test2', |
||
| 2467 | bamfiles=bwfile, |
||
| 2468 | roi=roi, binsize=200, |
||
| 2469 | flank=150, |
||
| 2470 | stranded=False, |
||
| 2471 | store_whole_genome=False) |
||
| 2472 | |||
| 2473 | assert len(cover1) == 450 |
||
| 2474 | assert len(cover2) == len(cover1) |
||
| 2475 | assert cover1.shape == (450, 500, 1, 1) |
||
| 2476 | assert cover1.shape == cover2.shape |
||
| 2477 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2478 | |||
| 2479 | |||
| 2480 | def test_fulltilebed(): |
||
| 2481 | |||
| 2482 | import pkg_resources |
||
| 2483 | import os |
||
| 2484 | from janggu.data import Cover |
||
| 2485 | |||
| 2486 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2487 | roi = os.path.join(data_path, "sample_fulltile.bed") |
||
| 2488 | bwfile = os.path.join(data_path, "sample.bed") |
||
| 2489 | |||
| 2490 | cover1 = Cover.create_from_bed( |
||
| 2491 | 'test', |
||
| 2492 | bedfiles=bwfile, |
||
| 2493 | roi=roi, |
||
| 2494 | store_whole_genome=True) |
||
| 2495 | cover2 = Cover.create_from_bed( |
||
| 2496 | 'test2', |
||
| 2497 | bedfiles=bwfile, |
||
| 2498 | roi=roi, |
||
| 2499 | store_whole_genome=False) |
||
| 2500 | |||
| 2501 | assert len(cover1) == 2 |
||
| 2502 | assert len(cover2) == len(cover1) |
||
| 2503 | assert cover1.shape == (2, 30000, 1, 1) |
||
| 2504 | assert cover1.shape == cover2.shape |
||
| 2505 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2506 | |||
| 2507 | cover1 = Cover.create_from_bed( |
||
| 2508 | 'test', |
||
| 2509 | bedfiles=bwfile, |
||
| 2510 | roi=roi, binsize=200, |
||
| 2511 | store_whole_genome=True) |
||
| 2512 | cover2 = Cover.create_from_bed( |
||
| 2513 | 'test2', |
||
| 2514 | bedfiles=bwfile, |
||
| 2515 | roi=roi, binsize=200, |
||
| 2516 | store_whole_genome=False) |
||
| 2517 | |||
| 2518 | assert len(cover1) == 300 |
||
| 2519 | assert len(cover2) == len(cover1) |
||
| 2520 | assert cover1.shape == (300, 200, 1, 1) |
||
| 2521 | assert cover1.shape == cover2.shape |
||
| 2522 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2523 | |||
| 2524 | cover1 = Cover.create_from_bed( |
||
| 2525 | 'test', |
||
| 2526 | bedfiles=bwfile, |
||
| 2527 | roi=roi, binsize=200, |
||
| 2528 | flank=150, |
||
| 2529 | store_whole_genome=True) |
||
| 2530 | cover2 = Cover.create_from_bed( |
||
| 2531 | 'test2', |
||
| 2532 | bedfiles=bwfile, |
||
| 2533 | roi=roi, binsize=200, |
||
| 2534 | flank=150, |
||
| 2535 | store_whole_genome=False) |
||
| 2536 | |||
| 2537 | assert len(cover1) == 300 |
||
| 2538 | assert len(cover2) == len(cover1) |
||
| 2539 | assert cover1.shape == (300, 500, 1, 1) |
||
| 2540 | assert cover1.shape == cover2.shape |
||
| 2541 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2542 | |||
| 2543 | def test_fulltilebed2(): |
||
| 2544 | |||
| 2545 | import pkg_resources |
||
| 2546 | import os |
||
| 2547 | from janggu.data import Cover |
||
| 2548 | |||
| 2549 | data_path = pkg_resources.resource_filename('janggu', 'resources/') |
||
| 2550 | roi = os.path.join(data_path, "sample_fulltile2.bed") |
||
| 2551 | bwfile = os.path.join(data_path, "sample.bed") |
||
| 2552 | |||
| 2553 | cover1 = Cover.create_from_bed( |
||
| 2554 | 'test', |
||
| 2555 | bedfiles=bwfile, |
||
| 2556 | roi=roi, |
||
| 2557 | store_whole_genome=True) |
||
| 2558 | cover2 = Cover.create_from_bed( |
||
| 2559 | 'test2', |
||
| 2560 | bedfiles=bwfile, |
||
| 2561 | roi=roi, |
||
| 2562 | store_whole_genome=False) |
||
| 2563 | |||
| 2564 | assert len(cover1) == 3 |
||
| 2565 | assert len(cover2) == len(cover1) |
||
| 2566 | assert cover1.shape == (3, 30000, 1, 1) |
||
| 2567 | assert cover1.shape == cover2.shape |
||
| 2568 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2569 | |||
| 2570 | cover1 = Cover.create_from_bed( |
||
| 2571 | 'test', |
||
| 2572 | bedfiles=bwfile, |
||
| 2573 | roi=roi, binsize=200, |
||
| 2574 | store_whole_genome=True) |
||
| 2575 | cover2 = Cover.create_from_bed( |
||
| 2576 | 'test2', |
||
| 2577 | bedfiles=bwfile, |
||
| 2578 | roi=roi, binsize=200, |
||
| 2579 | store_whole_genome=False) |
||
| 2580 | |||
| 2581 | assert len(cover1) == 450 |
||
| 2582 | assert len(cover2) == len(cover1) |
||
| 2583 | assert cover1.shape == (450, 200, 1, 1) |
||
| 2584 | assert cover1.shape == cover2.shape |
||
| 2585 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2586 | |||
| 2587 | cover1 = Cover.create_from_bed( |
||
| 2588 | 'test', |
||
| 2589 | bedfiles=bwfile, |
||
| 2590 | roi=roi, binsize=200, |
||
| 2591 | flank=150, |
||
| 2592 | store_whole_genome=True) |
||
| 2593 | cover2 = Cover.create_from_bed( |
||
| 2594 | 'test2', |
||
| 2595 | bedfiles=bwfile, |
||
| 2596 | roi=roi, binsize=200, |
||
| 2597 | flank=150, |
||
| 2598 | store_whole_genome=False) |
||
| 2599 | |||
| 2600 | assert len(cover1) == 450 |
||
| 2601 | assert len(cover2) == len(cover1) |
||
| 2602 | assert cover1.shape == (450, 500, 1, 1) |
||
| 2603 | assert cover1.shape == cover2.shape |
||
| 2604 | np.testing.assert_equal(cover1[:], cover2[:]) |
||
| 2605 |