diff --git a/Dockerfile b/Dockerfile index 6a30dbde..70a67c35 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,22 +11,33 @@ # Inherit from base NVIDIA CUDA 10.1 image with CUDNN FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04 +RUN apt-get update && apt-get install -y \ + software-properties-common + RUN add-apt-repository ppa:deadsnakes/ppa + RUN apt-get update && apt-get install -y \ + python3.7 + + # Set python version to 3.6 RUN apt update && apt install -y \ - python3.6 \ rsync \ git \ python3-pip \ libz-dev \ vim \ - wget + wget \ + curl \ + python3.7-dev + +RUN ln -nsf /usr/bin/python3.7 /usr/bin/python -RUN ln -nsf /usr/bin/python3.6 /usr/bin/python +# Use python3.7 pip. Otherwise some packages won't be compatible. +RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.7 1 # Download 3rd party binaries RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bigWigToBedGraph /usr/local/bin # Download AtacWorks repo -RUN pip3 install atacworks==0.3.0 +RUN pip3 install atacworks==0.3.4 RUN pip3 install macs2==2.2.4 diff --git a/README.md b/README.md index 4bd7621e..da199477 100755 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ AtacWorks is a deep learning toolkit for coverage track denoising and peak calli * Ubuntu 16.04+ * CUDA 9.0+ -* Python 3.6.7+ +* Python 3.7.0+ * GCC 5+ * (Optional) A conda or virtualenv setup * Any NVIDIA GPU that supports CUDA 9.0+ diff --git a/atacworks/io/h5io.py b/atacworks/io/h5io.py index b2393edb..bba3d84b 100644 --- a/atacworks/io/h5io.py +++ b/atacworks/io/h5io.py @@ -26,7 +26,7 @@ def dict_to_h5(x, h5file, create_new=True, compression='lzf'): Only valid with create_new=True. """ - with h5py.File(h5file) as f: + with h5py.File(h5file, 'a') as f: if create_new: # Create new datasets for key in x.keys(): diff --git a/atacworks/io/peak2bw.py b/atacworks/io/peak2bw.py index 6b40f33d..e42dd74b 100755 --- a/atacworks/io/peak2bw.py +++ b/atacworks/io/peak2bw.py @@ -52,9 +52,9 @@ def peak2bw(input_file, sizesfile, out_dir): # Read input files _logger.info('Reading input file') # Skip first line if the file is narrowPeak - skip = False + skip = 0 if input_file.endswith("narrowPeak"): - skip = True + skip = 1 peaks = read_intervals(input_file, skip=skip) _logger.info('Read ' + str(len(peaks)) + ' peaks.') sizes = read_sizes(sizesfile) diff --git a/requirements.txt b/requirements.txt index e09c8ecb..b2000372 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,23 +8,22 @@ # license agreement from NVIDIA CORPORATION is strictly prohibited. # -configargparse~=0.15.2 +configargparse~=1.2.3 Cython~=0.29.13 -h5py~=2.10.0 -numpy~=1.17.0 -pandas~=1.0.0 +h5py~=3.1.0 +numpy~=1.19.4 +pandas~=1.2.0 pyBigWig~=0.3.17 -pytest~=5.4.3 -pyyaml~=5.3.0 -scikit-learn~=0.21.3 -scipy~=1.4.0 +pytest~=6.2.1 +pyyaml~=5.3.1 +scipy~=1.6.0 termcolor~=1.1.0 -torch~=1.2.0 -torchvision~=0.3.0 +torch~=1.7.1 +torchvision~=0.8.2 scikit-learn~=0.21.3 -configargparse~=0.15.2 -setuptools~=46.1.3 -sphinx~=2.3.1 -recommonmark~=0.6.0 -sphinx-rtd-theme~=0.4.3 -jupyterlab~=2.1.4 +setuptools~=51.1.1 +sphinx~=3.4.2 +recommonmark~=0.7.1 +sphinx-rtd-theme~=0.5.0 +jupyterlab~=3.0.0 + diff --git a/setup.cfg b/setup.cfg index 4317b1ea..0cd372ad 100644 --- a/setup.cfg +++ b/setup.cfg @@ -7,5 +7,5 @@ # license agreement from NVIDIA CORPORATION is strictly prohibited. [metadata] -version = 0.3.3 +version = 0.3.4 diff --git a/tests/expected_results/end-to-end/classification_metrics_log b/tests/expected_results/end-to-end/classification_metrics_log index d62dae1e..99e5316d 100644 --- a/tests/expected_results/end-to-end/classification_metrics_log +++ b/tests/expected_results/end-to-end/classification_metrics_log @@ -1,10 +1,10 @@ -INFO:2020-07-24 10:14:14,423:AtacWorks-calculate-metrics] Loading intervals -INFO:2020-07-24 10:14:14,425:AtacWorks-calculate-metrics] Loading labels for classification -INFO:2020-07-24 10:14:15,139:AtacWorks-calculate-metrics] Loading data for classification -INFO:2020-07-24 10:14:15,894:AtacWorks-calculate-metrics] Calculating per-threshold classification metrics -INFO:2020-07-24 10:14:20,130:AtacWorks-calculate-metrics] Calculating AUC metrics -INFO:2020-07-24 10:14:22,563:AtacWorks-calculate-metrics] Done! +INFO:2021-06-29 04:46:39,214:AtacWorks-calculate-metrics] Loading intervals +INFO:2021-06-29 04:46:39,216:AtacWorks-calculate-metrics] Loading labels for classification +INFO:2021-06-29 04:46:39,902:AtacWorks-calculate-metrics] Loading data for classification +INFO:2021-06-29 04:46:40,682:AtacWorks-calculate-metrics] Calculating per-threshold classification metrics +INFO:2021-06-29 04:46:43,972:AtacWorks-calculate-metrics] Calculating AUC metrics +INFO:2021-06-29 04:46:46,554:AtacWorks-calculate-metrics] Done! Bases per class in clean data: positive: 294990 | negative: 9689010 -Bases per class at threshold 0.5: positive: 1514137 | negative: 8469863 -Classification metrics at threshold 0.5 : recall: 0.8262 | precision: 0.1610 | specificity: 0.8689 | accuracy: 0.8676 | f1: 0.2694 -AUC metrics : auroc: 0.8475 | auprc: 0.1381 +Bases per class at threshold 0.5: positive: 1245708 | negative: 8738292 +Classification metrics at threshold 0.5 : recall: 0.9232 | precision: 0.2186 | specificity: 0.8995 | accuracy: 0.9002 | f1: 0.3535 +AUC metrics : auroc: 0.9113 | auprc: 0.2041 diff --git a/tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5 b/tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5 index 950395ab..4c6c0e23 100644 Binary files a/tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5 and b/tests/expected_results/end-to-end/evaluate_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.eval.h5 differ diff --git a/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph b/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph index fa2e6854..bd27f9e3 100644 --- a/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph +++ b/tests/expected_results/end-to-end/inference_latest/HSC_infer.peaks.bedGraph @@ -1,13803 +1,3825 @@ -chr3 59906 59907 1 -chr3 59908 60543 1 -chr3 60544 60545 1 -chr3 60546 60547 1 -chr3 63199 63200 1 -chr3 63201 63280 1 -chr3 63283 63284 1 -chr3 63287 63288 1 -chr3 63289 63290 1 -chr3 63291 63292 1 -chr3 63295 63296 1 -chr3 63297 63298 1 -chr3 63299 63300 1 -chr3 63301 63302 1 -chr3 63303 63304 1 -chr3 63305 63308 1 -chr3 63309 63312 1 -chr3 63313 63316 1 -chr3 63317 63935 1 -chr3 63936 63937 1 -chr3 66565 66767 1 -chr3 66768 66771 1 -chr3 66772 66773 1 -chr3 66774 66775 1 -chr3 66820 66823 1 -chr3 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9975469 226.0 +chr3 9975469 9975470 224.0 +chr3 9975470 9975472 223.0 +chr3 9975472 9975473 222.0 +chr3 9975473 9975474 220.0 +chr3 9975474 9975476 219.0 +chr3 9975476 9975477 218.0 +chr3 9975477 9975478 216.0 +chr3 9975478 9975479 215.0 +chr3 9975479 9975481 214.0 +chr3 9975481 9975482 212.0 +chr3 9975482 9975484 211.0 +chr3 9975484 9975485 209.0 +chr3 9975485 9975486 207.0 +chr3 9975486 9975488 205.0 +chr3 9975488 9975489 204.0 +chr3 9975489 9975490 201.0 +chr3 9975490 9975492 200.0 +chr3 9975492 9975493 198.0 +chr3 9975493 9975494 195.0 +chr3 9975494 9975496 193.0 +chr3 9975496 9975497 191.0 +chr3 9975497 9975498 189.0 +chr3 9975498 9975500 188.0 +chr3 9975500 9975501 186.0 +chr3 9975501 9975502 184.0 +chr3 9975502 9975504 183.0 +chr3 9975504 9975505 181.0 +chr3 9975505 9975506 179.0 +chr3 9975506 9975508 177.0 +chr3 9975508 9975509 175.0 +chr3 9975509 9975510 172.0 +chr3 9975510 9975512 170.0 +chr3 9975512 9975513 168.0 +chr3 9975513 9975514 166.0 +chr3 9975514 9975516 165.0 +chr3 9975516 9975517 164.0 +chr3 9975517 9975518 162.0 +chr3 9975518 9975520 160.0 +chr3 9975520 9975521 159.0 +chr3 9975521 9975522 156.0 +chr3 9975522 9975523 155.0 +chr3 9975523 9975524 154.0 +chr3 9975524 9975525 153.0 +chr3 9975525 9975526 151.0 +chr3 9975526 9975528 149.0 +chr3 9975528 9975529 148.0 +chr3 9975529 9975530 143.0 +chr3 9975530 9975532 142.0 +chr3 9975532 9975533 140.0 +chr3 9975533 9975534 138.0 +chr3 9975534 9975536 136.0 +chr3 9975536 9975537 135.0 +chr3 9975537 9975538 132.0 +chr3 9975538 9975540 130.0 +chr3 9975540 9975541 129.0 +chr3 9975541 9975542 126.0 +chr3 9975542 9975544 125.0 +chr3 9975544 9975545 123.0 +chr3 9975545 9975546 121.0 +chr3 9975546 9975548 120.0 +chr3 9975548 9975549 118.0 +chr3 9975549 9975550 116.0 +chr3 9975550 9975552 115.0 +chr3 9975552 9975553 113.0 +chr3 9975553 9975554 112.0 +chr3 9975554 9975556 110.0 +chr3 9975556 9975557 109.0 +chr3 9975557 9975558 107.0 +chr3 9975558 9975560 106.0 +chr3 9975560 9975561 105.0 +chr3 9975561 9975562 103.0 +chr3 9975562 9975564 102.0 +chr3 9975564 9975565 101.0 +chr3 9975565 9975566 99.0 +chr3 9975566 9975569 98.0 +chr3 9975569 9975570 97.0 +chr3 9975570 9975572 95.0 +chr3 9975572 9975573 94.0 +chr3 9975573 9975574 93.0 +chr3 9975574 9975576 92.0 +chr3 9975576 9975577 91.0 +chr3 9975577 9975578 90.0 +chr3 9975578 9975580 89.0 +chr3 9975580 9975581 88.0 +chr3 9975581 9975582 87.0 +chr3 9975582 9975585 84.0 +chr3 9975585 9975586 82.0 +chr3 9975586 9975589 81.0 +chr3 9975589 9975590 80.0 +chr3 9975590 9975592 79.0 +chr3 9975592 9975593 78.0 +chr3 9975593 9975596 77.0 +chr3 9975596 9975597 76.0 +chr3 9975597 9975598 75.0 +chr3 9975598 9975600 74.0 +chr3 9975600 9975602 73.0 +chr3 9975602 9975604 72.0 +chr3 9975604 9975605 71.0 +chr3 9975605 9975610 70.0 +chr3 9975610 9975612 69.0 +chr3 9975612 9975614 68.0 +chr3 9975614 9975617 67.0 +chr3 9975617 9975618 66.0 +chr3 9975618 9975621 65.0 +chr3 9975621 9975624 64.0 +chr3 9975624 9975626 62.0 +chr3 9975626 9975629 60.0 +chr3 9975629 9975632 59.0 +chr3 9975632 9975634 58.0 +chr3 9975634 9975635 57.0 +chr3 9975635 9975637 58.0 +chr3 9975637 9975642 57.0 +chr3 9975642 9975643 56.0 +chr3 9975643 9975644 57.0 +chr3 9975644 9975650 56.0 +chr3 9975650 9975653 55.0 +chr3 9975653 9975658 54.0 +chr3 9975658 9975659 53.0 +chr3 9975659 9975662 54.0 +chr3 9975662 9975670 53.0 +chr3 9975670 9975671 52.0 +chr3 9975671 9975672 53.0 +chr3 9975672 9975681 52.0 +chr3 9975681 9975685 51.0 +chr3 9975685 9975718 50.0 +chr3 9975718 9975719 49.0 +chr3 9975719 9975720 50.0 +chr3 9975720 9975721 49.0 +chr3 9975721 9975748 50.0 +chr3 9975748 9975754 51.0 +chr3 9975754 9975757 50.0 +chr3 9975757 9975760 51.0 +chr3 9975760 9975761 50.0 +chr3 9975761 9975781 51.0 +chr3 9975781 9975784 52.0 +chr3 9975784 9975785 51.0 +chr3 9975785 9975792 52.0 +chr3 9975792 9975793 51.0 +chr3 9975793 9975795 52.0 +chr3 9975795 9975799 51.0 +chr3 9975799 9975800 52.0 +chr3 9975800 9975801 51.0 +chr3 9975801 9975803 52.0 +chr3 9975803 9975809 51.0 +chr3 9975809 9975822 50.0 +chr3 9975822 9975830 49.0 +chr3 9975830 9975832 50.0 +chr3 9975832 9975839 49.0 +chr3 9975839 9975844 48.0 +chr3 9975844 9975849 47.0 +chr3 9975849 9975850 46.0 +chr3 9975850 9975852 47.0 +chr3 9975852 9975860 46.0 +chr3 9975860 9975874 45.0 +chr3 9975874 9975888 44.0 +chr3 9975888 9975899 43.0 +chr3 9975899 9975908 42.0 +chr3 9975908 9975917 41.0 +chr3 9975917 9975928 40.0 +chr3 9975928 9975940 39.0 +chr3 9975940 9975948 38.0 +chr3 9975948 9975957 37.0 +chr3 9975957 9975970 36.0 +chr3 9975970 9975978 35.0 +chr3 9975978 9975983 34.0 +chr3 9975983 9975991 33.0 +chr3 9975991 9976002 32.0 +chr3 9976002 9976010 31.0 +chr3 9976010 9976018 30.0 +chr3 9976018 9976026 29.0 +chr3 9976026 9976030 28.0 +chr3 9976030 9976038 27.0 +chr3 9976038 9976046 26.0 +chr3 9976046 9976051 25.0 +chr3 9976051 9976059 24.0 +chr3 9976059 9976063 23.0 +chr3 9976063 9976070 22.0 +chr3 9976070 9976076 21.0 +chr3 9976076 9976082 20.0 +chr3 9976082 9976089 19.0 +chr3 9976089 9976097 18.0 +chr3 9976097 9976105 17.0 +chr3 9976105 9976113 16.0 +chr3 9976113 9976121 15.0 +chr3 9976121 9976129 14.0 +chr3 9976129 9976135 13.0 +chr3 9976135 9976144 12.0 +chr3 9976144 9976154 11.0 +chr3 9976154 9976163 10.0 +chr3 9976163 9976173 9.0 +chr3 9976173 9976185 8.0 +chr3 9976185 9976197 7.0 +chr3 9976197 9976210 6.0 +chr3 9976210 9976228 5.0 +chr3 9976228 9976256 4.0 +chr3 9976256 9976301 3.0 +chr3 9976301 9976470 2.0 +chr3 9976470 9976609 1.0 +chr3 9976856 9976980 1.0 +chr3 9976980 9976982 2.0 +chr3 9976982 9976984 1.0 +chr3 9976984 9977024 2.0 +chr3 9977024 9977076 3.0 +chr3 9977076 9977112 4.0 +chr3 9977112 9977136 5.0 +chr3 9977136 9977156 6.0 +chr3 9977156 9977176 7.0 +chr3 9977176 9977188 8.0 +chr3 9977188 9977189 9.0 +chr3 9977189 9977200 8.0 +chr3 9977200 9977212 9.0 +chr3 9977212 9977213 10.0 +chr3 9977213 9977216 9.0 +chr3 9977216 9977256 10.0 +chr3 9977256 9977257 11.0 +chr3 9977257 9977260 10.0 +chr3 9977260 9977261 11.0 +chr3 9977261 9977264 10.0 +chr3 9977264 9977265 11.0 +chr3 9977265 9977268 10.0 +chr3 9977268 9977269 11.0 +chr3 9977269 9977272 10.0 +chr3 9977272 9977273 11.0 +chr3 9977273 9977276 10.0 +chr3 9977276 9977277 11.0 +chr3 9977277 9977280 10.0 +chr3 9977280 9977281 11.0 +chr3 9977281 9977325 10.0 +chr3 9977325 9977327 9.0 +chr3 9977327 9977329 10.0 +chr3 9977329 9977353 9.0 +chr3 9977353 9977354 8.0 +chr3 9977354 9977357 9.0 +chr3 9977357 9977377 8.0 +chr3 9977377 9977378 7.0 +chr3 9977378 9977381 8.0 +chr3 9977381 9977393 7.0 +chr3 9977393 9977405 6.0 +chr3 9977405 9977406 5.0 +chr3 9977406 9977408 6.0 +chr3 9977408 9977429 5.0 +chr3 9977429 9977430 4.0 +chr3 9977430 9977433 5.0 +chr3 9977433 9977442 4.0 +chr3 9977442 9977445 5.0 +chr3 9977445 9977446 4.0 +chr3 9977446 9977448 5.0 +chr3 9977448 9977501 4.0 +chr3 9977501 9977502 3.0 +chr3 9977502 9977503 4.0 +chr3 9977503 9977611 3.0 +chr3 9977611 9977613 2.0 +chr3 9977613 9977615 3.0 +chr3 9977615 9977671 2.0 +chr3 9977671 9977672 1.0 +chr3 9977672 9977675 2.0 +chr3 9977675 9977791 1.0 +chr3 9979505 9979601 1.0 +chr3 9979601 9979637 2.0 +chr3 9979637 9979689 3.0 +chr3 9979689 9979818 4.0 +chr3 9979818 9979821 3.0 +chr3 9979821 9980030 4.0 +chr3 9980030 9980074 3.0 +chr3 9980074 9980106 2.0 +chr3 9980106 9980170 1.0 +chr3 9982390 9982486 1.0 +chr3 9982486 9982526 2.0 +chr3 9982526 9982574 3.0 +chr3 9982574 9982575 4.0 +chr3 9982575 9982578 3.0 +chr3 9982578 9982904 4.0 +chr3 9982904 9982907 3.0 +chr3 9982907 9982908 4.0 +chr3 9982908 9982948 3.0 +chr3 9982948 9982951 2.0 +chr3 9982951 9982952 3.0 +chr3 9982952 9982980 2.0 +chr3 9982980 9983048 1.0 diff --git a/tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 b/tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 index b0f88c74..4d37349c 100644 Binary files a/tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 and b/tests/expected_results/end-to-end/inference_latest/bw2h5/HSC.5M.chr123.10mb.coverage.bw.denoise.h5 differ diff --git a/tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed b/tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed index 437e0f55..7779edee 100644 --- a/tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed +++ b/tests/expected_results/end-to-end/inference_latest/denoise.output.summary.bed @@ -1,3281 +1,1956 @@ #chrom start end len mean max relativesummit summit -chr3 59908 60543 635 5.2330708503723145 9.0 299 60207 -chr3 63201 63280 79 1.9240506887435913 3.0 63 63264 -chr3 63317 63935 618 4.631067752838135 6.0 302 63619 -chr3 66565 66767 202 5.99009895324707 10.0 174 66739 -chr3 66824 67505 681 7.13803243637085 11.0 357 67181 -chr3 68853 69507 654 10.38379192352295 21.0 239 69092 -chr3 72085 72157 72 2.069444417953491 4.0 64 72149 -chr3 72206 72321 115 8.069564819335938 10.0 111 72317 -chr3 72390 72497 107 7.532710075378418 9.0 0 72390 -chr3 72520 72647 127 2.3307087421417236 4.0 0 72520 -chr3 74050 74456 406 6.704433441162109 9.0 217 74267 -chr3 74847 74910 63 3.269841194152832 5.0 60 74907 -chr3 75240 75319 79 2.4556961059570312 4.0 0 75240 -chr3 77117 77194 77 3.5324676036834717 6.0 76 77193 -chr3 77203 77266 63 7.396825313568115 9.0 50 77253 -chr3 77454 77977 523 6.644359588623047 11.0 347 77801 -chr3 77988 78105 117 2.8974359035491943 5.0 0 77988 -chr3 79630 79709 79 1.9113924503326416 3.0 67 79697 -chr3 79822 80368 546 4.432234287261963 6.0 250 80072 -chr3 83628 83833 205 5.531707286834717 9.0 181 83809 -chr3 84392 85221 829 12.453558921813965 25.0 326 84718 -chr3 85529 86127 598 5.682274341583252 10.0 262 85791 -chr3 87785 88478 693 10.147186279296875 20.0 261 88046 -chr3 90072 90676 604 5.645695209503174 10.0 268 90340 -chr3 100767 101482 715 9.860139846801758 18.0 305 101072 -chr3 102172 102235 63 2.142857074737549 3.0 51 102223 -chr3 102372 102897 525 4.295238018035889 6.0 265 102637 -chr3 107513 107928 415 6.9566264152526855 10.0 215 107728 -chr3 107941 108068 127 2.385826826095581 4.0 0 107941 -chr3 109657 110291 634 5.261829853057861 9.0 266 109923 -chr3 112246 112825 579 5.804835796356201 10.0 251 112497 -chr3 113691 113766 75 3.440000057220459 5.0 63 113754 -chr3 113767 113832 65 7.046154022216797 8.0 41 113808 -chr3 115279 115876 597 5.6515913009643555 10.0 261 115540 -chr3 119030 119099 69 3.275362253189087 5.0 65 119095 -chr3 119100 119151 51 6.196078300476074 8.0 47 119147 -chr3 126573 126982 409 4.066014766693115 5.0 213 126786 -chr3 129938 130667 729 9.432098388671875 19.0 252 130190 -chr3 138632 139200 568 5.801056385040283 10.0 235 138867 -chr3 144498 144736 238 5.525209903717041 9.0 210 144708 -chr3 145324 146489 1165 16.865236282348633 30.0 333 145657 -chr3 147539 147614 75 1.9600000381469727 3.0 63 147602 -chr3 147771 148274 503 4.202783107757568 6.0 279 148050 -chr3 152947 153933 986 7.318458557128906 12.0 652 153599 -chr3 154802 154942 140 5.107142925262451 8.0 116 154918 -chr3 157948 158727 779 9.323492050170898 17.0 250 158198 -chr3 165892 166575 683 4.761346817016602 7.0 229 166121 -chr3 168245 168375 130 4.3692307472229 8.0 126 168371 -chr3 170653 170984 331 3.534743309020996 5.0 239 170892 -chr3 173855 173978 123 4.634146213531494 8.0 119 173974 -chr3 177926 178899 973 7.542651653289795 12.0 719 178645 -chr3 179093 179238 145 4.068965435028076 7.0 137 179230 -chr3 179243 180288 1045 6.342583656311035 10.0 102 179345 -chr3 185095 185675 580 11.193103790283203 21.0 228 185323 -chr3 187783 188543 760 12.427631378173828 25.0 253 188036 -chr3 190943 191089 146 5.18493127822876 9.0 143 191086 -chr3 192542 192613 71 3.380281686782837 5.0 63 192605 -chr3 193249 194019 770 13.48311710357666 27.0 409 193658 -chr3 194389 195367 978 5.691206455230713 11.0 947 195336 -chr3 195396 195483 87 8.954023361206055 11.0 0 195396 -chr3 195512 195611 99 3.5959596633911133 6.0 0 195512 -chr3 195987 196513 526 6.878326892852783 11.0 278 196265 -chr3 196659 196770 111 3.3963963985443115 5.0 83 196742 -chr3 197461 198280 819 27.33333396911621 52.0 282 197743 -chr3 198644 199582 938 5.420042514801025 9.0 33 198677 -chr3 201545 202352 807 351.540283203125 724.0 324 201869 -chr3 202917 203074 157 8.68152904510498 18.0 0 202917 -chr3 205474 206005 531 6.08474588394165 9.0 225 205699 -chr3 206274 206353 79 3.113924026489258 5.0 71 206345 -chr3 206354 206822 468 6.414529800415039 10.0 139 206493 -chr3 208851 209642 791 7.512010097503662 15.0 416 209267 -chr3 212542 213385 843 8.55160140991211 16.0 257 212799 -chr3 215286 215364 78 1.9358974695205688 3.0 62 215348 -chr3 215381 216000 619 4.3699517250061035 6.0 111 215492 -chr3 220982 221697 715 9.998600959777832 20.0 261 221243 -chr3 222786 222865 79 1.9113924503326416 3.0 67 222853 -chr3 223002 223524 522 4.312260627746582 6.0 266 223268 -chr3 225052 225195 143 5.07692289352417 8.0 119 225171 -chr3 231599 231720 121 4.504132270812988 8.0 118 231717 -chr3 233342 233675 333 6.3063063621521 9.0 237 233579 -chr3 233688 234364 676 6.677515029907227 11.0 358 234046 -chr3 235492 236256 764 9.736910820007324 18.0 271 235763 -chr3 238130 240000 1870 49.50481414794922 90.0 411 238541 -chr3 240269 240893 624 5.685897350311279 10.0 338 240607 -chr3 241360 242369 1009 9.523290634155273 15.0 343 241703 -chr3 244029 244240 211 5.834123134613037 10.0 210 244239 -chr3 244731 245612 881 7.203178405761719 12.0 356 245087 -chr3 251997 252881 884 8.150452613830566 13.0 245 252242 -chr3 253610 254678 1068 18.089887619018555 41.0 606 254216 -chr3 257846 258764 918 16.64379119873047 34.0 496 258342 -chr3 259477 260289 812 23.1798038482666 46.0 308 259785 -chr3 263338 264000 662 9.658610343933105 16.0 351 263689 -chr3 264414 264734 320 3.518749952316284 5.0 228 264642 -chr3 268572 268702 130 4.730769157409668 8.0 118 268690 -chr3 269979 270593 614 5.5488600730896 9.0 219 270198 -chr3 271594 272165 571 5.43082332611084 8.0 261 271855 -chr3 272526 273974 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b/tests/expected_results/end-to-end/model_latest/model_best.pth.tar index d1a15f0e..12b8285b 100644 Binary files a/tests/expected_results/end-to-end/model_latest/model_best.pth.tar and b/tests/expected_results/end-to-end/model_latest/model_best.pth.tar differ diff --git a/tests/expected_results/end-to-end/regression_metrics_log b/tests/expected_results/end-to-end/regression_metrics_log index fe2ce481..5e66021b 100644 --- a/tests/expected_results/end-to-end/regression_metrics_log +++ b/tests/expected_results/end-to-end/regression_metrics_log @@ -1,11 +1,11 @@ -INFO:2020-07-24 10:10:55,590:AtacWorks-calculate-metrics] Loading intervals -INFO:2020-07-24 10:10:55,592:AtacWorks-calculate-metrics] Loading labels for regression -INFO:2020-07-24 10:10:56,360:AtacWorks-calculate-metrics] Loading data for regression -INFO:2020-07-24 10:10:57,093:AtacWorks-calculate-metrics] Calculating metrics for regression -INFO:2020-07-24 10:11:02,252:AtacWorks-calculate-metrics] Loading labels for classification -INFO:2020-07-24 10:11:02,956:AtacWorks-calculate-metrics] Calculating metrics for regression in peaks -INFO:2020-07-24 10:11:02,995:AtacWorks-calculate-metrics] Calculating metrics for regression outside peaks -INFO:2020-07-24 10:11:04,480:AtacWorks-calculate-metrics] Done! -Regression metrics on full data : mse:329.1190 | corrcoef: 0.9539 | spearmancorrcoef: 0.4031 -Regression metrics in peaks : mse:10770.2969 | corrcoef: 0.9485 | spearmancorrcoef: 0.8116 -Regression metrics outside peaks : mse:11.2286 | corrcoef: 0.4128 | spearmancorrcoef: 0.3315 +INFO:2021-06-29 04:38:48,240:AtacWorks-calculate-metrics] Loading intervals +INFO:2021-06-29 04:38:48,242:AtacWorks-calculate-metrics] Loading labels for regression +INFO:2021-06-29 04:38:48,995:AtacWorks-calculate-metrics] Loading data for regression +INFO:2021-06-29 04:38:49,712:AtacWorks-calculate-metrics] Calculating metrics for regression +INFO:2021-06-29 04:38:54,432:AtacWorks-calculate-metrics] Loading labels for classification +INFO:2021-06-29 04:38:55,133:AtacWorks-calculate-metrics] Calculating metrics for regression in peaks +INFO:2021-06-29 04:38:55,181:AtacWorks-calculate-metrics] Calculating metrics for regression outside peaks +INFO:2021-06-29 04:38:56,968:AtacWorks-calculate-metrics] Done! +Regression metrics on full data : mse:766.2310 | corrcoef: 0.9627 | spearmancorrcoef: 0.4117 +Regression metrics in peaks : mse:25640.6914 | corrcoef: 0.9647 | spearmancorrcoef: 0.8133 +Regression metrics outside peaks : mse: 8.9072 | corrcoef: 0.3981 | spearmancorrcoef: 0.3397 diff --git a/tests/io/test_h5io.py b/tests/io/test_h5io.py index 9c39ac50..77ef7217 100644 --- a/tests/io/test_h5io.py +++ b/tests/io/test_h5io.py @@ -52,7 +52,7 @@ def test_h5_to_array(tmpdir): input_dict = {"features": np.array([0, 1, 2, 3]), "scores": np.array([1, 2, 1, 1])} h5file = os.path.join(tmpdir, "h5file.h5") - with h5py.File(h5file) as f: + with h5py.File(h5file, 'w') as f: for key in input_dict.keys(): f.create_dataset(key, data=input_dict[key])