├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── graphs ├── Benchmark.py ├── bedgraph_stats.csv ├── find_stats.py ├── generate_graphs.py ├── make_benchmarks.py ├── runHelix.pbs ├── run_benchmark.sh ├── v-1_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ ├── run_time_results.txt │ │ ├── values_indexed.png │ │ └── values_indexed.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── format_results.sh ├── v1_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt ├── v2_graphs │ ├── ENCFF050CCI │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF321FZQ │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF376VCU │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF384CMP │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF631HEX │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF643WMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ ├── ENCFF770CQD │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt │ └── ENCFF847JMY │ │ ├── interval_error.png │ │ ├── interval_error_results.txt │ │ ├── interval_run_time.png │ │ ├── interval_runtime_results.txt │ │ ├── pyBG_app._bin=int_size10_table.png │ │ ├── pyBG_app._bin=int_size20_table.png │ │ ├── pyBG_app._bin=int_size5_table.png │ │ ├── pyBW_app._table.png │ │ ├── run_time.png │ │ └── run_time_results.txt └── v3_graphs │ ├── ENCFF000KYT │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF000LAB │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF050CCI │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF321FZQ │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF376VCU │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF384CMP │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF631HEX │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF643WMY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF726XVA │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF770CQD │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF847JMY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ ├── ENCFF877IHY │ ├── interval_error.png │ ├── interval_error_results.txt │ ├── interval_run_time.png │ ├── interval_runtime_results.txt │ ├── interval_runtime_table.png │ ├── pyBG_app._bin=int_size10_table.png │ ├── pyBG_app._bin=int_size20_table.png │ ├── pyBG_app._bin=int_size5_table.png │ ├── pyBW_app._table.png │ ├── run_time.png │ └── run_time_results.txt │ └── runtime_table.png ├── pyBedGraph ├── BedGraph.py ├── Chrom_Data.py ├── Chrom_Data_Complete.py ├── __init__.py ├── ignore_missing_bp.c ├── ignore_missing_bp.pyx ├── include_missing_bp.c ├── include_missing_bp.pyx ├── util.c └── util.pyx ├── setup.py └── test ├── default.conf ├── extensive_test.py ├── make_test_files.py ├── run_tests.sh ├── test.py └── test_files ├── README.py ├── custom_intervals.txt ├── hg38.chrom.sizes ├── mm10.chrom.sizes ├── myChrom.sizes ├── random_test.bedGraph ├── random_test.bigWig └── test_intervals.txt /.gitignore: -------------------------------------------------------------------------------- 1 | * 2 | 3 | !.gitignore 4 | !LICENSE 5 | !MANIFEST.in 6 | !README.md 7 | 8 | !setup.py 9 | !pyBedGraph/ 10 | !pyBedGraph/*.py 11 | !pyBedGraph/*.c 12 | !pyBedGraph/*.pyx 13 | !pyBedGraph/data/ 14 | !pyBedGraph/data/chrom_sizes/ 15 | !pyBedGraph/data/chrom_sizes/*.sizes 16 | !test/ 17 | !test/test_files/ 18 | !test/test_files/* 19 | test/test_files/ENCFF* 20 | !test/*.py 21 | !test/*.sh 22 | !test/*.conf 23 | !graphs/ 24 | !graphs/* 25 | !graphs/v-1_graphs/** 26 | !graphs/v1_graphs/** 27 | !graphs/v2_graphs/** 28 | !graphs/v3_graphs/** 29 | graphs/log.txt 30 | *.swp 31 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: python 2 | python: 3 | - "3.6" # current default Python on Travis CI 4 | - "3.7" 5 | - "3.8" 6 | install: 7 | - pip3 install . 8 | script: cd test && ./run_tests.sh 9 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 Henry Zhang 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | 23 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | recursive-include pyBedGraph *.pyx 2 | recursive-include pyBedGraph *.c 3 | 4 | exclude pyBedGraph/Benchmark.py 5 | exclude test/* 6 | -------------------------------------------------------------------------------- /graphs/bedgraph_stats.csv: -------------------------------------------------------------------------------- 1 | name,total_coverage,num_samples,avg_chrom_value,avg_interval_value,avg_interval_size,num_intervals 2 | ENCFF000LAB,210608995,1630090340.0,7.739889457238045,21.538977756401824,35.24505226454014,5975562 3 | ENCFF000KYT,92406732,322750781.0,3.4927193507936196,19.66172022650371,110.60276750095454,835483 4 | ENCFF877IHY,20123179,8761394.066806199,0.4353881693745406,3.034348777491196,9.982607112525697,2015824 5 | ENCFF847JMY,248938446,151998660.6238633,0.6105873281777588,10.630235756349464,45.25007502645239,5501393 6 | ENCFF726XVA,19608719,12518585.256433686,0.6384193305250427,3.676645306087061,6.349268523606348,3088343 7 | ENCFF631HEX,248956422,15656403528.159958,62.88812878327741,365.0918083567748,64.41452907971231,3864911 8 | ENCFF321FZQ,248945843,163851013.2315499,0.6581793504041354,1.4681227345066048,6.666052301388891,37345318 9 | ENCFF050CCI,248946328,163025562.69535866,0.6548622910210536,2.406267180648243,19.27405595605373,12916136 10 | ENCFF770CQD,195371622,77326009.20251197,0.3957893598411747,1.5743921128320995,25.90048711654685,7543164 11 | ENCFF376VCU,195371552,101739760.25504415,0.5207501256633522,1.0197289833832917,26.44760851190099,7387116 12 | ENCFF643WMY,195371517,109424808.9942997,0.5600857825877438,1.267956079299403,30.17742510729299,6474095 13 | ENCFF384CMP,195371615,112424350.33019583,0.5754385064083942,1.154285227763735,32.12539983763957,6081531 14 | -------------------------------------------------------------------------------- /graphs/find_stats.py: -------------------------------------------------------------------------------- 1 | from pyBedGraph import BedGraph 2 | import os 3 | import csv 4 | 5 | FOLDER_LOC = '/media/hirow/extra/jax/data/pybedgraph' 6 | 7 | stats = [] 8 | 9 | for folder in os.listdir(FOLDER_LOC): 10 | for filename in os.listdir(f'{FOLDER_LOC}/{folder}'): 11 | print(folder, filename) 12 | bedgraph = BedGraph(f'/media/hirow/extra/jax/data/chrom_sizes/{folder}.chrom.sizes', f'{FOLDER_LOC}/{folder}/{filename}', 'chr1') 13 | sample_name = filename.split('.')[0] 14 | sample = {} 15 | sample['name'] = sample_name 16 | chrom = bedgraph.chromosome_map['chr1'] 17 | 18 | sample['total_coverage'] = chrom.total_coverage 19 | sample['num_samples'] = chrom.num_samples 20 | sample['avg_chrom_value'] = chrom.avg_chrom_value 21 | sample['avg_interval_value'] = chrom.avg_interval_value 22 | sample['avg_interval_size'] = chrom.avg_interval_size 23 | sample['num_intervals'] = chrom.num_intervals 24 | 25 | stats.append(sample) 26 | 27 | csv_columns = list(stats[0].keys()) 28 | 29 | with open('bedgraph_stats.csv', 'w') as csv_file: 30 | writer = csv.DictWriter(csv_file, fieldnames=csv_columns) 31 | writer.writeheader() 32 | for data in stats: 33 | writer.writerow(data) 34 | -------------------------------------------------------------------------------- /graphs/runHelix.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Maximum hours 3 | #PBS -l walltime=10:00:00 4 | 5 | # Max memory 6 | #PBS -l mem=16G 7 | #PBS -l vmem=16G 8 | 9 | # email for begin, aborts, ends 10 | #PBS -m bae 11 | #PBS -M henry.zhang@jax.org 12 | 13 | # job name 14 | #PBS -N pyBedGraph_benchmark 15 | 16 | # standard out 17 | #PBS -o log.txt 18 | 19 | # adds stderr to stdout 20 | #PBS -j oe 21 | 22 | # verify options and abort if error 23 | #PBS -w e 24 | 25 | cd ${PBS_O_WORKDIR} 26 | cd "pyBedGraph/graphs" 27 | 28 | # Load modules 29 | module load python/3.6.6 30 | 31 | ./run_benchmark.sh 32 | -------------------------------------------------------------------------------- /graphs/run_benchmark.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ "$#" -ne 2 ]; then 4 | echo "You must enter exactly 2 command line arguments: 5 | 6 | 1 - Folder location of bedgraph files 7 | 2 - chrom size file abbreviation (ex: mm10, hg38)" 8 | exit 1 9 | fi 10 | 11 | chrom_size="/media/hirow/extra/jax/data/chrom_sizes/$2.chrom.sizes" 12 | if [ ! -f $chrom_size ]; then 13 | echo "$chrom_size does not exist" 14 | exit 1 15 | fi 16 | 17 | files=$(find "$1/$2" -type f -name "*.bigWig") 18 | echo "Number of files found in \"$1/$2\": $(ls -1 "$1"/"$2" | wc -l)" 19 | 20 | for file in ${files[*]} 21 | do 22 | file=$(basename "${file%.*}") 23 | echo "Running benchmark for $file" 24 | python3 make_benchmarks.py "$chrom_size" "$1/$2/$file.bigWig" 25 | if [[ $? -ne 0 ]]; 26 | then 27 | exit 1 28 | fi 29 | done 30 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF050CCI/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF050CCI/interval_error.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF050CCI/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF050CCI/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF050CCI/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 1.5948657989501953 1.7763009071350098 1.7982800006866455 1.6831672191619873 2.1965997219085693 2.2986299991607666 1.829296588897705 1.8453962802886963 1.809152603149414 4 | pyBW app. 5 | 1.6009516716003418 1.7007668018341064 1.6810095310211182 2.002182960510254 2.0181655883789062 2.4937357902526855 2.317692995071411 1.9501478672027588 1.7051055431365967 6 | pyBG exact 7 | 0.0019507408142089844 0.0009245872497558594 0.0012061595916748047 0.0014650821685791016 0.0017383098602294922 0.003459453582763672 0.005476951599121094 0.007044792175292969 0.008141756057739258 8 | pyBG app. bin=int_size/5 9 | 0.0016367435455322266 0.0014333724975585938 0.0013730525970458984 0.0013370513916015625 0.0018224716186523438 0.001692056655883789 0.001611948013305664 0.0015168190002441406 0.0014684200286865234 10 | pyBG app. bin=int_size/10 11 | 0.0019850730895996094 0.0017745494842529297 0.0021343231201171875 0.0022983551025390625 0.002121448516845703 0.002008676528930664 0.0018668174743652344 0.0017914772033691406 0.0017044544219970703 12 | pyBG app. bin=int_size/20 13 | 0.002418994903564453 0.002206087112426758 0.0020148754119873047 0.0024187564849853516 0.002322673797607422 0.002561330795288086 0.002432584762573242 0.0023488998413085938 0.002306222915649414 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF050CCI/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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800000 900000 1000000 2 | pyBW exact 3 | 19.798956871032715 34.74007248878479 66.34702253341675 81.31721949577332 98.18077278137207 120.15814256668091 125.63749766349792 147.28676223754883 177.91932082176208 184.65336108207703 4 | pyBW app. 5 | 23.00829768180847 35.06188154220581 54.792882680892944 72.95014595985413 91.30922436714172 118.02662873268127 125.05263447761536 152.50234246253967 161.2505555152893 190.86514163017273 6 | pyBG exact 7 | 0.027274131774902344 0.05374598503112793 0.0803365707397461 0.10666656494140625 0.13325810432434082 0.15948486328125 0.186173677444458 0.21239185333251953 0.23912763595581055 0.26595163345336914 8 | pyBG app. bin=100 9 | 0.010768413543701172 0.016228675842285156 0.024538516998291016 0.03303670883178711 0.04128408432006836 0.04981637001037598 0.06042027473449707 0.06598973274230957 0.07612299919128418 0.08232307434082031 10 | pyBG app. bin=50 11 | 0.01348567008972168 0.02544403076171875 0.03749203681945801 0.049981117248535156 0.06328177452087402 0.07509899139404297 0.0878605842590332 0.10039258003234863 0.11599326133728027 0.12696123123168945 12 | pyBG app. bin=25 13 | 0.018364906311035156 0.03543519973754883 0.05197024345397949 0.06911659240722656 0.08690738677978516 0.10394120216369629 0.12004446983337402 0.13944339752197266 0.15195369720458984 0.1686701774597168 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF321FZQ/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF321FZQ/interval_error.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF321FZQ/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF321FZQ/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF321FZQ/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 1.9813964366912842 1.942075252532959 2.4152474403381348 2.5540108680725098 2.0965874195098877 2.6166577339172363 1.9067223072052002 2.2427096366882324 2.2720541954040527 4 | pyBW app. 5 | 1.8783679008483887 1.997908592224121 3.2374491691589355 3.523993730545044 2.5125584602355957 2.065262794494629 1.9931302070617676 1.9091417789459229 1.979278326034546 6 | pyBG exact 7 | 0.002422332763671875 0.0016520023345947266 0.002712726593017578 0.0041599273681640625 0.005686283111572266 0.009144067764282227 0.012307405471801758 0.015520334243774414 0.018729448318481445 8 | pyBG app. bin=int_size/5 9 | 0.001253366470336914 0.0013043880462646484 0.0012989044189453125 0.0013244152069091797 0.00128173828125 0.0011856555938720703 0.0011241436004638672 0.0010657310485839844 0.0009992122650146484 10 | pyBG app. bin=int_size/10 11 | 0.0014677047729492188 0.0014033317565917969 0.0014865398406982422 0.0015480518341064453 0.0016696453094482422 0.0014255046844482422 0.0013346672058105469 0.0012888908386230469 0.001280069351196289 12 | pyBG app. bin=int_size/20 13 | 0.0037469863891601562 0.0017952919006347656 0.001894235610961914 0.0018208026885986328 0.0017156600952148438 0.0018787384033203125 0.0017364025115966797 0.001678466796875 0.0016248226165771484 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF321FZQ/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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800000 900000 1000000 2 | pyBW exact 3 | 19.05256462097168 33.09868049621582 52.185669898986816 69.23033833503723 90.5621030330658 103.04808139801025 118.79857087135315 160.66217184066772 191.39047265052795 227.06593585014343 4 | pyBW app. 5 | 20.304131031036377 37.293089389801025 55.774425745010376 75.60859799385071 95.32740306854248 114.46595239639282 132.3446502685547 167.24434399604797 250.211106300354 291.27741956710815 6 | pyBG exact 7 | 0.04339241981506348 0.08633995056152344 0.12842369079589844 0.1713707447052002 0.21417641639709473 0.2571852207183838 0.2998363971710205 0.3428938388824463 0.38567423820495605 0.4288506507873535 8 | pyBG app. bin=100 9 | 0.011082887649536133 0.015972137451171875 0.023755311965942383 0.03204488754272461 0.04075026512145996 0.04834151268005371 0.056894779205322266 0.06414103507995605 0.0735468864440918 0.08020472526550293 10 | pyBG app. bin=50 11 | 0.013501167297363281 0.024929285049438477 0.0378110408782959 0.049932241439819336 0.0628056526184082 0.07549595832824707 0.08938145637512207 0.1059417724609375 0.11398863792419434 0.12564802169799805 12 | pyBG app. bin=25 13 | 0.01645684242248535 0.03182411193847656 0.04807615280151367 0.06321072578430176 0.07934880256652832 0.0951690673828125 0.11120271682739258 0.12682247161865234 0.1427614688873291 0.16175103187561035 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF376VCU/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF376VCU/interval_error.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF376VCU/interval_run_time.png: -------------------------------------------------------------------------------- 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0.0064563751220703125 8 | pyBG app. bin=int_size/5 9 | 0.002134084701538086 0.0014231204986572266 0.0013201236724853516 0.001232147216796875 0.0011982917785644531 0.0011398792266845703 0.0010988712310791016 0.0009679794311523438 0.0009477138519287109 10 | pyBG app. bin=int_size/10 11 | 0.0019183158874511719 0.0016489028930664062 0.0015556812286376953 0.0014805793762207031 0.0014259815216064453 0.0013310909271240234 0.001275777816772461 0.0012333393096923828 0.00116729736328125 12 | pyBG app. bin=int_size/20 13 | 0.002379179000854492 0.0022127628326416016 0.0019266605377197266 0.0018715858459472656 0.0018358230590820312 0.0018069744110107422 0.0016884803771972656 0.0016210079193115234 0.0015685558319091797 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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800000 900000 1000000 2 | pyBW exact 3 | 15.594137907028198 29.374537706375122 47.775927782058716 65.42411136627197 78.43937182426453 94.33032631874084 106.6914656162262 131.6691710948944 138.0487072467804 154.71098399162292 4 | pyBW app. 5 | 16.828280448913574 28.975358486175537 47.58720064163208 62.57395815849304 77.66221904754639 93.22247004508972 109.98133683204651 129.84473609924316 144.94649696350098 152.07468724250793 6 | pyBG exact 7 | 0.024185657501220703 0.04749178886413574 0.07047748565673828 0.0938720703125 0.11739420890808105 0.14049553871154785 0.16381120681762695 0.18775629997253418 0.21029090881347656 0.23400378227233887 8 | pyBG app. bin=100 9 | 0.014047384262084961 0.016672134399414062 0.02466750144958496 0.033535003662109375 0.042916059494018555 0.050687313079833984 0.05968284606933594 0.06718277931213379 0.07573485374450684 0.08451199531555176 10 | pyBG app. bin=50 11 | 0.0131683349609375 0.023677587509155273 0.035761117935180664 0.04802227020263672 0.05971550941467285 0.07287192344665527 0.08637833595275879 0.09749555587768555 0.10991859436035156 0.12481260299682617 12 | pyBG app. bin=25 13 | 0.016544818878173828 0.03223252296447754 0.04847240447998047 0.06615471839904785 0.0823976993560791 0.0963752269744873 0.11194181442260742 0.12805819511413574 0.1439673900604248 0.15999555587768555 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF376VCU/values_indexed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF376VCU/values_indexed.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF376VCU/values_indexed.txt: -------------------------------------------------------------------------------- 1 | 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 2 | 5809370 5454620 5176188 4956956 4776393 4638054 4533845 4450400 4383900 4338896 4305475 4279860 4281089 4285012 4291272 4304072 4330325 4357208 4387469 4428236 4468637 4518320 4568725 4621248 4680869 4732536 4794455 4853840 4916647 4987290 5053007 5122080 5186959 5267354 5347682 5417528 5490725 5574718 5656628 5724464 5800873 5883500 5982155 6047832 6128243 6206270 6294525 6382776 6464426 6557478 6636534 6725960 6815172 6895678 6983285 7067648 7161620 7247906 7342775 7425336 7515320 7603450 7704519 7781864 7875715 7951424 8052200 8152196 8251370 8338874 8423880 8513360 8597822 8697174 8794733 8895860 8996340 9076212 9180383 9256352 9351564 9455180 9550045 9667016 9738533 9827408 9945530 10021856 10111272 10221310 10302089 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3000 4000 5000 2 | pyBW exact 3 | 1.5372860431671143 1.8280651569366455 1.6855413913726807 1.7893180847167969 1.6977362632751465 1.6927967071533203 1.698319435119629 1.6839001178741455 1.9763059616088867 4 | pyBW app. 5 | 1.5437452793121338 1.8660478591918945 1.6421568393707275 1.9282162189483643 1.785780906677246 1.7311162948608398 1.7369048595428467 1.5966613292694092 1.6179418563842773 6 | pyBG exact 7 | 0.0017316341400146484 0.0007739067077636719 0.0009305477142333984 0.001079559326171875 0.0012278556823730469 0.002104520797729492 0.002952098846435547 0.004289865493774414 0.005548000335693359 8 | pyBG app. bin=int_size/5 9 | 0.002068758010864258 0.002018451690673828 0.0018649101257324219 0.0018987655639648438 0.0017282962799072266 0.0015957355499267578 0.001493215560913086 0.0013580322265625 0.0012664794921875 10 | pyBG app. bin=int_size/10 11 | 0.0019850730895996094 0.002379179000854492 0.0015861988067626953 0.0015614032745361328 0.0014922618865966797 0.0013890266418457031 0.0013356208801269531 0.0013306140899658203 0.0012323856353759766 12 | pyBG app. bin=int_size/20 13 | 0.0024361610412597656 0.0021774768829345703 0.0019676685333251953 0.0019307136535644531 0.0018825531005859375 0.0017359256744384766 0.0016646385192871094 0.001603841781616211 0.0016512870788574219 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF384CMP/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- 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145.4091181755066 161.08408546447754 171.9333016872406 6 | pyBG exact 7 | 0.02267932891845703 0.044977664947509766 0.06705546379089355 0.0892181396484375 0.11119794845581055 0.13387203216552734 0.15577125549316406 0.17787432670593262 0.19988727569580078 0.22264647483825684 8 | pyBG app. bin=100 9 | 0.010066986083984375 0.014167308807373047 0.02060532569885254 0.02709031105041504 0.03408646583557129 0.04167580604553223 0.04810786247253418 0.05493450164794922 0.0623471736907959 0.06819343566894531 10 | pyBG app. bin=50 11 | 0.012832164764404297 0.02284383773803711 0.0346372127532959 0.04643678665161133 0.05808305740356445 0.06924867630004883 0.08051705360412598 0.09186053276062012 0.10354328155517578 0.11497116088867188 12 | pyBG app. bin=25 13 | 0.01652050018310547 0.032143354415893555 0.048391103744506836 0.06390213966369629 0.08027529716491699 0.09618949890136719 0.11190104484558105 0.12901544570922852 0.14615106582641602 0.16219091415405273 14 | 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0 0 0 0 0 47 35 20 11 7 | pyBG app. bin=int_size/5 8 | percent_error 0.016001145433790703 0.03200065011120534 0.03934994816088677 0.041418933037503186 0.04414349280312875 0.060199051516001044 0.04220701984461759 0.048658984139223975 0.04464596064482097 9 | ms_error 0.479894533080972 1.4630282049339478 3.4560035639885203 6.844281585444953 9.509247455550149 18.6303604448678 26.81736658403331 33.5903998152727 35.010659777306685 10 | abs_error 0.28937636717963977 0.5661009458664582 0.9113115379864104 1.2018135117189743 1.4342481697822846 1.9644503636586876 2.1678477180359703 2.2360564257280346 2.2695575550238005 11 | num_actual_0 125 175 140 108 63 25 29 18 11 12 | pyBG app. bin=int_size/10 13 | percent_error 0.005207809953740135 0.011083341573131364 0.012971538491243098 0.016000074566041203 0.014500481777352903 0.01745134614137202 0.019370206614146006 0.019684175655230632 0.023042826252759434 14 | ms_error 0.06075905265203753 0.14539537887522652 0.35247561164544505 0.5817603259971095 0.8931241485897781 2.367863619236691 4.204117629501685 4.917927139090445 5.662209960255119 15 | abs_error 0.08329319898488723 0.16760081819040665 0.2841661039057015 0.3809236282350843 0.46396357040077457 0.7305472820604082 0.914459014374731 0.9920684108110992 1.0355018071387525 16 | num_actual_0 59 89 76 57 37 13 17 9 9 17 | pyBG app. bin=int_size/20 18 | percent_error 0.0015783194361759726 0.00321848518250887 0.0038188344340448926 0.0046331731763854704 0.005225502559787084 0.0060203545414500475 0.006402656601662395 0.007754650404444401 0.009939852870363293 19 | ms_error 0.007413180357993553 0.014526787978338795 0.038049570788166905 0.05739882691985253 0.08775110580856031 0.22034804148119155 0.37413092734444975 0.6340800248452444 0.7396574234531049 20 | abs_error 0.021609553572695558 0.04444024153892301 0.08613844333277076 0.11670181896947845 0.14387893930493073 0.23684368362120012 0.30447390226551424 0.3697006894204321 0.4186901963257466 21 | num_actual_0 25 46 37 26 17 5 11 4 3 22 | 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1.6632053852081299 6 | pyBG exact 7 | 0.0012621879577636719 0.0006632804870605469 0.0007336139678955078 0.000812530517578125 0.0008907318115234375 0.001260995864868164 0.0015532970428466797 0.0018758773803710938 0.002231121063232422 8 | pyBG app. bin=int_size/5 9 | 0.001996278762817383 0.0016927719116210938 0.0016117095947265625 0.001650094985961914 0.0017278194427490234 0.0017964839935302734 0.0014467239379882812 0.001363515853881836 0.0012772083282470703 10 | pyBG app. bin=int_size/10 11 | 0.0019943714141845703 0.001758575439453125 0.0018069744110107422 0.001680135726928711 0.0017197132110595703 0.0017650127410888672 0.001779317855834961 0.001687765121459961 0.0015971660614013672 12 | pyBG app. bin=int_size/20 13 | 0.0024747848510742188 0.0022394657135009766 0.0019826889038085938 0.002117156982421875 0.002155780792236328 0.0020055770874023438 0.00205230712890625 0.002053976058959961 0.0019905567169189453 14 | 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-------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF631HEX/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 19.33808398246765 38.78543972969055 58.0387122631073 77.39090728759766 97.07964825630188 120.84044361114502 159.4645824432373 166.668555021286 196.10916352272034 209.71325659751892 4 | pyBW app. 5 | 20.090290784835815 39.02413201332092 58.17812919616699 76.70329093933105 96.78039908409119 116.39877605438232 152.28250551223755 172.08817172050476 189.44585371017456 210.49219727516174 6 | pyBG exact 7 | 1.7887895107269287 3.187974452972412 4.272586345672607 5.810789108276367 7.9159204959869385 10.050431251525879 11.608693361282349 14.770535707473755 17.389095067977905 21.047636032104492 8 | pyBG app. bin=100 9 | 0.01248931884765625 0.019364595413208008 0.030059814453125 0.040209054946899414 0.05321383476257324 0.05881619453430176 0.0749361515045166 0.07769942283630371 0.08022856712341309 0.08905482292175293 10 | pyBG app. bin=50 11 | 0.016924381256103516 0.028434038162231445 0.04041767120361328 0.05437326431274414 0.06734633445739746 0.08227086067199707 0.0964503288269043 0.10845828056335449 0.12608075141906738 0.13775181770324707 12 | pyBG app. bin=25 13 | 0.018720149993896484 0.03460335731506348 0.05170011520385742 0.07049059867858887 0.08773922920227051 0.10665392875671387 0.1256237030029297 0.14236235618591309 0.15967249870300293 0.17777085304260254 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF643WMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF643WMY/interval_error.png 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1.6631286144256592 6 | pyBG exact 7 | 0.0017437934875488281 0.000774383544921875 0.0009496212005615234 0.0011026859283447266 0.0012640953063964844 0.0021750926971435547 0.0031478404998779297 0.0045680999755859375 0.005822181701660156 8 | pyBG app. bin=int_size/5 9 | 0.002339601516723633 0.002755403518676758 0.0014579296112060547 0.0012753009796142578 0.0012023448944091797 0.001146554946899414 0.0010974407196044922 0.0009942054748535156 0.0009834766387939453 10 | pyBG app. bin=int_size/10 11 | 0.0018792152404785156 0.0017366409301757812 0.00159454345703125 0.0015544891357421875 0.001495361328125 0.0013477802276611328 0.0012819766998291016 0.0012383460998535156 0.0011866092681884766 12 | pyBG app. bin=int_size/20 13 | 0.0023641586303710938 0.0021491050720214844 0.0019664764404296875 0.00199127197265625 0.0018634796142578125 0.0016946792602539062 0.0016138553619384766 0.0015537738800048828 0.0015060901641845703 14 | 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-------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF643WMY/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 18.316174268722534 36.27020859718323 50.875311613082886 69.16397476196289 88.5446367263794 102.40772914886475 122.60736680030823 152.90104603767395 165.22707724571228 177.1432683467865 4 | pyBW app. 5 | 18.84094548225403 35.37746047973633 54.75072526931763 69.94125056266785 89.68451762199402 104.01172590255737 127.00806927680969 145.15350651741028 152.6485559940338 182.6434588432312 6 | pyBG exact 7 | 0.022955656051635742 0.04562258720397949 0.06756877899169922 0.09043693542480469 0.11293745040893555 0.13500642776489258 0.15772223472595215 0.18038272857666016 0.20267009735107422 0.22502756118774414 8 | pyBG app. bin=100 9 | 0.011157035827636719 0.021162033081054688 0.03057861328125 0.04055905342102051 0.05115866661071777 0.059029340744018555 0.06901955604553223 0.0813138484954834 0.08817601203918457 0.09745478630065918 10 | pyBG app. bin=50 11 | 0.018934011459350586 0.03146052360534668 0.04708981513977051 0.06372809410095215 0.07845616340637207 0.09445810317993164 0.11032485961914062 0.12643885612487793 0.1419219970703125 0.15732407569885254 12 | pyBG app. bin=25 13 | 0.01810622215270996 0.03435778617858887 0.05131220817565918 0.07103514671325684 0.09000301361083984 0.10724449157714844 0.1212773323059082 0.13897275924682617 0.1569685935974121 0.17282676696777344 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF770CQD/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF770CQD/interval_error.png 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1.8802595138549805 6 | pyBG exact 7 | 0.0017838478088378906 0.0008370876312255859 0.0010499954223632812 0.0012357234954833984 0.001428842544555664 0.002490520477294922 0.0038025379180908203 0.005721330642700195 0.0067064762115478516 8 | pyBG app. bin=int_size/5 9 | 0.0016376972198486328 0.001430511474609375 0.0013535022735595703 0.0013229846954345703 0.0012831687927246094 0.0011355876922607422 0.0010759830474853516 0.0010001659393310547 0.0009350776672363281 10 | pyBG app. bin=int_size/10 11 | 0.0023343563079833984 0.0017769336700439453 0.0016427040100097656 0.0015926361083984375 0.0015096664428710938 0.0014140605926513672 0.0018856525421142578 0.0033867359161376953 0.001728057861328125 12 | pyBG app. bin=int_size/20 13 | 0.0024080276489257812 0.0037622451782226562 0.0025200843811035156 0.0020270347595214844 0.0018775463104248047 0.0017647743225097656 0.0017087459564208984 0.0016651153564453125 0.002245187759399414 14 | 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-------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF770CQD/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 18.839476108551025 36.95874762535095 55.26872372627258 70.92704153060913 91.4594829082489 98.90621376037598 116.2219672203064 132.6059501171112 148.4392249584198 166.7127239704132 4 | pyBW app. 5 | 19.362516403198242 38.440064907073975 52.29002237319946 71.01817226409912 91.23634719848633 110.2642753124237 115.35388588905334 131.5977909564972 148.8433392047882 165.84490036964417 6 | pyBG exact 7 | 0.024800777435302734 0.051788330078125 0.07528209686279297 0.1009984016418457 0.12602019309997559 0.14794564247131348 0.16431617736816406 0.1882779598236084 0.20991873741149902 0.23248958587646484 8 | pyBG app. bin=100 9 | 0.010149240493774414 0.014191150665283203 0.019919872283935547 0.027448654174804688 0.037598609924316406 0.04141497611999512 0.05058002471923828 0.05449628829956055 0.06193828582763672 0.07027387619018555 10 | pyBG app. bin=50 11 | 0.012948751449584961 0.024049758911132812 0.03699231147766113 0.04760599136352539 0.059108734130859375 0.06996345520019531 0.08224225044250488 0.09488749504089355 0.10535860061645508 0.11794066429138184 12 | pyBG app. bin=25 13 | 0.017345905303955078 0.03323960304260254 0.050260066986083984 0.06591057777404785 0.0818634033203125 0.1047217845916748 0.11858201026916504 0.13918828964233398 0.14715790748596191 0.16339945793151855 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF847JMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v-1_graphs/ENCFF847JMY/interval_error.png 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1.7644634246826172 6 | pyBG exact 7 | 0.0013151168823242188 0.0006964206695556641 0.0008273124694824219 0.0009315013885498047 0.0010521411895751953 0.0016052722930908203 0.002054929733276367 0.002658843994140625 0.0034983158111572266 8 | pyBG app. bin=int_size/5 9 | 0.0017309188842773438 0.001798391342163086 0.0022056102752685547 0.0020902156829833984 0.0015635490417480469 0.0011000633239746094 0.001070261001586914 0.0010330677032470703 0.0010790824890136719 10 | pyBG app. bin=int_size/10 11 | 0.0032701492309570312 0.004108428955078125 0.0017628669738769531 0.002010345458984375 0.0014681816101074219 0.0012667179107666016 0.0012264251708984375 0.0012440681457519531 0.0012204647064208984 12 | pyBG app. bin=int_size/20 13 | 0.0035533905029296875 0.00263214111328125 0.002093076705932617 0.002117156982421875 0.0018618106842041016 0.0016641616821289062 0.0015835762023925781 0.0015423297882080078 0.0014874935150146484 14 | 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-------------------------------------------------------------------------------- /graphs/v-1_graphs/ENCFF847JMY/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 15.288001298904419 31.65485119819641 54.66478753089905 73.81391453742981 91.03133368492126 96.65535616874695 97.33534502983093 113.45415234565735 133.72681617736816 146.12200736999512 4 | pyBW app. 5 | 16.337255716323853 31.33069610595703 52.704243898391724 68.1120970249176 80.08354830741882 112.66581654548645 98.01744198799133 114.10399222373962 131.10386729240417 147.61071610450745 6 | pyBG exact 7 | 1.2599186897277832 1.0737578868865967 1.092677354812622 2.1873645782470703 2.2093234062194824 2.1938281059265137 2.722900867462158 3.259439706802368 3.796720504760742 3.8194680213928223 8 | pyBG app. bin=100 9 | 0.011567354202270508 0.022028207778930664 0.03152799606323242 0.04177570343017578 0.05275774002075195 0.06284952163696289 0.07273221015930176 0.08368444442749023 0.09394288063049316 0.10445284843444824 10 | pyBG app. bin=50 11 | 0.014734983444213867 0.02738165855407715 0.04089093208312988 0.05495572090148926 0.06830883026123047 0.08227396011352539 0.09673118591308594 0.11105465888977051 0.12540864944458008 0.13790202140808105 12 | pyBG app. bin=25 13 | 0.020595073699951172 0.035646677017211914 0.05268597602844238 0.07359075546264648 0.10004162788391113 0.11887335777282715 0.14385342597961426 0.14098596572875977 0.15885663032531738 0.1756129264831543 14 | -------------------------------------------------------------------------------- /graphs/v-1_graphs/format_results.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | sed -i -e 's/pyBigWig_exact /pyBW exact\n/g' $1/* 4 | sed -i -e 's/pyBigWig_approx /pyBW app.\n/g' $1/* 5 | sed -i -e 's/pyBigWig_approx/pyBW app./g' $1/* 6 | sed -i -e 's/pyBedGraph_exact /pyBG exact\n/g' $1/* 7 | sed -i -e 's/pBG approx./pyBG app./g' $1/* 8 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF050CCI/interval_error.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF050CCI/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 0.5811326503753662 0.5897583961486816 0.5978219509124756 0.6077773571014404 0.6188442707061768 0.6496067047119141 0.6794848442077637 0.7105615139007568 0.739180326461792 4 | pyBW app. 5 | 0.5840606689453125 0.5934443473815918 0.6040520668029785 0.6110084056854248 1.1393330097198486 1.1422276496887207 1.1477456092834473 1.1349396705627441 1.1387875080108643 6 | pyBG exact 7 | 0.0023627281188964844 0.002629995346069336 0.003004789352416992 0.0032422542572021484 0.0035254955291748047 0.004464626312255859 0.0052487850189208984 0.006089925765991211 0.006904125213623047 8 | pyBG app. bin=int_size/5 9 | 0.0012390613555908203 0.0010883808135986328 0.0010635852813720703 0.0009887218475341797 0.0009627342224121094 0.0008802413940429688 0.0008902549743652344 0.0007643699645996094 0.0007302761077880859 10 | pyBG app. bin=int_size/10 11 | 0.0015268325805664062 0.001336812973022461 0.0012311935424804688 0.0012326240539550781 0.0011661052703857422 0.001094818115234375 0.0011565685272216797 0.0009980201721191406 0.0009856224060058594 12 | pyBG app. bin=int_size/20 13 | 0.0018725395202636719 0.0017666816711425781 0.001531362533569336 0.0015053749084472656 0.0014424324035644531 0.0013649463653564453 0.0013797283172607422 0.0013496875762939453 0.0012521743774414062 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF050CCI/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/pyBG_app._bin=int_size20_table.png: 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https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF050CCI/pyBW_app._table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF050CCI/run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF050CCI/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 5.949225664138794 11.936779022216797 17.887224674224854 23.843714952468872 29.765455722808838 35.7209050655365 41.62929105758667 47.44882369041443 53.29787802696228 59.26465892791748 4 | pyBW app. 5 | 6.002312660217285 12.033823490142822 18.021657705307007 24.012705326080322 29.974560737609863 35.94641876220703 41.92200255393982 47.81545639038086 53.696086406707764 59.648796796798706 6 | pyBG exact 7 | 0.028717994689941406 0.056722402572631836 0.0833275318145752 0.10935354232788086 0.13552331924438477 0.1614246368408203 0.18636178970336914 0.21311616897583008 0.23839950561523438 0.2657358646392822 8 | pyBG app. bin=100 9 | 0.009128570556640625 0.01892852783203125 0.02847456932067871 0.037537336349487305 0.04630446434020996 0.05661916732788086 0.06533336639404297 0.07428741455078125 0.0833139419555664 0.09254932403564453 10 | pyBG app. bin=50 11 | 0.011612653732299805 0.02245306968688965 0.03513932228088379 0.04664111137390137 0.05745840072631836 0.06890416145324707 0.08006763458251953 0.09189748764038086 0.10347628593444824 0.11289548873901367 12 | pyBG app. bin=25 13 | 0.014441728591918945 0.029119253158569336 0.04223322868347168 0.055999755859375 0.07040905952453613 0.08371186256408691 0.09666180610656738 0.11062860488891602 0.12348294258117676 0.13704490661621094 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF321FZQ/interval_error.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF321FZQ/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 0.5927941799163818 0.6098828315734863 0.6319849491119385 0.6567795276641846 0.6791679859161377 0.766026496887207 0.8469960689544678 0.9322965145111084 1.0165824890136719 4 | pyBW app. 5 | 0.5978972911834717 0.6153719425201416 1.2709345817565918 1.2755680084228516 1.2776944637298584 1.2531120777130127 1.2536201477050781 1.2580578327178955 1.2597169876098633 6 | pyBG exact 7 | 0.0028913021087646484 0.003437519073486328 0.00412440299987793 0.004818916320800781 0.0053462982177734375 0.007681608200073242 0.00984334945678711 0.01256704330444336 0.0150604248046875 8 | pyBG app. bin=int_size/5 9 | 0.0012907981872558594 0.001130819320678711 0.0010907649993896484 0.000997781753540039 0.0009768009185791016 0.0009028911590576172 0.0008082389831542969 0.0007688999176025391 0.0007262229919433594 10 | pyBG app. bin=int_size/10 11 | 0.001550436019897461 0.0013668537139892578 0.0012276172637939453 0.0012097358703613281 0.0011832714080810547 0.0011014938354492188 0.0010318756103515625 0.0010006427764892578 0.0009386539459228516 12 | pyBG app. bin=int_size/20 13 | 0.0019085407257080078 0.0017478466033935547 0.0016133785247802734 0.0014939308166503906 0.0015053749084472656 0.0014083385467529297 0.0013833045959472656 0.001325368881225586 0.0012631416320800781 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF321FZQ/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF321FZQ/pyBW_app._table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF321FZQ/run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF321FZQ/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 6.306811809539795 12.606421947479248 18.85970640182495 25.156485319137573 31.42676067352295 37.80121922492981 44.04736518859863 50.29187345504761 56.492533922195435 62.87085795402527 4 | pyBW app. 5 | 12.644474744796753 25.303398609161377 37.99331021308899 50.64139699935913 63.312384843826294 75.96312832832336 88.6771650314331 101.28574109077454 113.90395331382751 126.58746480941772 6 | pyBG exact 7 | 0.04004025459289551 0.07862973213195801 0.11577367782592773 0.1531050205230713 0.19015049934387207 0.2275981903076172 0.26303958892822266 0.29948902130126953 0.3359334468841553 0.3732144832611084 8 | pyBG app. bin=100 9 | 0.009192705154418945 0.01851201057434082 0.028254032135009766 0.03917670249938965 0.04718279838562012 0.056559085845947266 0.06565451622009277 0.07478857040405273 0.08362364768981934 0.09205222129821777 10 | pyBG app. bin=50 11 | 0.0118255615234375 0.023088693618774414 0.03489065170288086 0.04591774940490723 0.05812358856201172 0.06903815269470215 0.08003115653991699 0.09120678901672363 0.10171222686767578 0.11505436897277832 12 | pyBG app. bin=25 13 | 0.014404773712158203 0.028806209564208984 0.0443110466003418 0.057914018630981445 0.07102584838867188 0.0847620964050293 0.09839415550231934 0.11269474029541016 0.12381458282470703 0.1389451026916504 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF376VCU/interval_error.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF376VCU/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 0.5528011322021484 0.5581092834472656 0.5660269260406494 0.5728228092193604 0.5805439949035645 0.6015830039978027 0.6255266666412354 0.6479196548461914 0.669177770614624 4 | pyBW app. 5 | 0.5542042255401611 0.5600800514221191 0.566664457321167 0.57489013671875 1.0596718788146973 1.061594009399414 1.0672073364257812 1.1169157028198242 1.118311882019043 6 | pyBG exact 7 | 0.002079486846923828 0.00247955322265625 0.002771139144897461 0.0030143260955810547 0.003258228302001953 0.0039288997650146484 0.0046155452728271484 0.005227804183959961 0.005827188491821289 8 | pyBG app. bin=int_size/5 9 | 0.0011928081512451172 0.0010738372802734375 0.0010807514190673828 0.000997781753540039 0.0009732246398925781 0.0008375644683837891 0.0008306503295898438 0.0007259845733642578 0.0006916522979736328 10 | pyBG app. bin=int_size/10 11 | 0.001489400863647461 0.0012879371643066406 0.0012156963348388672 0.0012176036834716797 0.0011627674102783203 0.001062154769897461 0.0011668205261230469 0.0009250640869140625 0.0008771419525146484 12 | pyBG app. bin=int_size/20 13 | 0.0018506050109863281 0.0016694068908691406 0.0015015602111816406 0.0014653205871582031 0.0014190673828125 0.0013432502746582031 0.0012884140014648438 0.0012371540069580078 0.0012171268463134766 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF376VCU/pyBW_app._table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF376VCU/run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF376VCU/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 5.618337869644165 11.222501516342163 16.80812978744507 22.41913414001465 28.02916669845581 33.61992955207825 39.18348264694214 44.767627000808716 50.35418915748596 55.952465534210205 4 | pyBW app. 5 | 5.637825965881348 11.293111085891724 16.86077880859375 22.47714591026306 28.086614847183228 33.71267533302307 39.31841850280762 44.90207767486572 50.490121603012085 56.13388156890869 6 | pyBG exact 7 | 0.027211666107177734 0.0535125732421875 0.079498291015625 0.1044623851776123 0.12982845306396484 0.15468502044677734 0.1794757843017578 0.20325708389282227 0.2277235984802246 0.25401926040649414 8 | pyBG app. bin=100 9 | 0.008756875991821289 0.01825237274169922 0.028294801712036133 0.037271738052368164 0.04672574996948242 0.053873300552368164 0.06455659866333008 0.07183647155761719 0.08071398735046387 0.08877086639404297 10 | pyBG app. bin=50 11 | 0.01124262809753418 0.02225470542907715 0.034116506576538086 0.04601168632507324 0.056456804275512695 0.06807613372802734 0.07898116111755371 0.09046578407287598 0.09971427917480469 0.11062264442443848 12 | pyBG app. bin=25 13 | 0.014039039611816406 0.02891373634338379 0.04263448715209961 0.056276559829711914 0.06928658485412598 0.08395028114318848 0.09727883338928223 0.10912656784057617 0.12229228019714355 0.13535594940185547 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF384CMP/interval_error.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF384CMP/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 0.537132740020752 0.5427706241607666 0.5460119247436523 0.5513653755187988 0.5582675933837891 0.5759499073028564 0.5945336818695068 0.6119832992553711 0.628864049911499 4 | pyBW app. 5 | 0.5365719795227051 0.5434813499450684 0.5485734939575195 0.5530679225921631 1.0500741004943848 1.0524649620056152 1.0568397045135498 1.1021537780761719 1.10443115234375 6 | pyBG exact 7 | 0.0020074844360351562 0.002498149871826172 0.002816915512084961 0.0029773712158203125 0.003142833709716797 0.003810405731201172 0.004354000091552734 0.0048370361328125 0.005332231521606445 8 | pyBG app. bin=int_size/5 9 | 0.0011925697326660156 0.0010597705841064453 0.001012563705444336 0.0009710788726806641 0.0009739398956298828 0.0008349418640136719 0.0007679462432861328 0.0007205009460449219 0.0006809234619140625 10 | pyBG app. bin=int_size/10 11 | 0.0014870166778564453 0.0012888908386230469 0.001264333724975586 0.001180410385131836 0.0012142658233642578 0.0010650157928466797 0.0010361671447753906 0.0009307861328125 0.0008933544158935547 12 | pyBG app. bin=int_size/20 13 | 0.0019066333770751953 0.0016791820526123047 0.0014934539794921875 0.0014557838439941406 0.0014467239379882812 0.001344919204711914 0.0012965202331542969 0.0012459754943847656 0.001192331314086914 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF384CMP/pyBW_app._table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF384CMP/run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF384CMP/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 5.456228017807007 10.879177570343018 16.290369033813477 21.714656591415405 27.129868030548096 32.536200523376465 37.94447588920593 43.29699492454529 48.653578996658325 54.09262657165527 4 | pyBW app. 5 | 5.476881980895996 10.936261892318726 16.344602823257446 21.790096044540405 27.23683452606201 32.627732038497925 38.03930616378784 43.425684213638306 48.8477578163147 54.245107889175415 6 | pyBG exact 7 | 0.02730393409729004 0.05386185646057129 0.07916522026062012 0.10407829284667969 0.1290736198425293 0.15397906303405762 0.17757844924926758 0.20214223861694336 0.22707271575927734 0.2517423629760742 8 | pyBG app. bin=100 9 | 0.009129762649536133 0.018274307250976562 0.027750492095947266 0.03679656982421875 0.04523110389709473 0.055167436599731445 0.06363892555236816 0.07201886177062988 0.08088850975036621 0.08910131454467773 10 | pyBG app. bin=50 11 | 0.011260509490966797 0.02210402488708496 0.03427886962890625 0.04609227180480957 0.05691933631896973 0.06807947158813477 0.07883620262145996 0.0899209976196289 0.10051369667053223 0.11115908622741699 12 | pyBG app. bin=25 13 | 0.014397144317626953 0.028079986572265625 0.042200565338134766 0.056318044662475586 0.06989574432373047 0.0819249153137207 0.09634757041931152 0.11070442199707031 0.12279248237609863 0.13591361045837402 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF631HEX/interval_error.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/interval_error_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW app. 3 | percent_error 0.0 0.0 0.0 0.0 0.0 0.12876640013742785 0.07785801815751618 0.05238072679784191 0.048515713881948634 4 | ms_error 0.0 0.0 0.0 0.0 0.0 231.13894663391608 97.2997835721028 54.82365323179074 32.974266962041206 5 | abs_error 0.0 0.0 0.0 0.0 0.0 5.647237902973561 3.8141163969057614 2.8118334027315357 2.2619828554318007 6 | not_included 0 0 0 0 0 47 35 20 11 7 | pyBG app. bin=int_size/5 8 | percent_error 0.016001145433790685 0.03200065011120516 0.03934994816088682 0.041418933037503186 0.04414349280312872 0.06019905151600105 0.04220701984461768 0.04865898413922402 0.044645960644820994 9 | ms_error 0.47989453308097135 1.4630282049339458 3.4560035639885376 6.844281585444935 9.509247455550156 18.630360444867712 26.817366584033397 33.590399815272896 35.01065977730675 10 | abs_error 0.2893763671796415 0.5661009458664523 0.9113115379864098 1.201813511718973 1.4342481697822835 1.9644503636586872 2.1678477180359774 2.236056425728039 2.2695575550238094 11 | not_included 125 175 140 108 63 25 29 18 11 12 | pyBG app. bin=int_size/10 13 | percent_error 0.0052078099537400755 0.011083341573131303 0.012971538491242933 0.016000074566041154 0.014500481777352947 0.017451346141371976 0.01937020661414598 0.019684175655230642 0.02304282625275945 14 | ms_error 0.06075905265203717 0.14539537887522727 0.3524756116454443 0.5817603259971141 0.8931241485897852 2.367863619236688 4.20411762950166 4.9179271390904375 5.662209960255094 15 | abs_error 0.08329319898488097 0.16760081819040873 0.28416610390569724 0.380923628235082 0.4639635704007741 0.7305472820604069 0.9144590143747282 0.9920684108110996 1.0355018071387514 16 | not_included 59 89 76 57 37 13 17 9 9 17 | pyBG app. bin=int_size/20 18 | percent_error 0.0015783194361759726 0.0032184851825088415 0.003818834434044845 0.004633173176385403 0.005225502559786976 0.006020354541450076 0.006402656601662388 0.007754650404444381 0.009939852870363267 19 | ms_error 0.00741318035799358 0.014526787978338621 0.038049570788167085 0.057398826919852784 0.08775110580856091 0.2203480414811962 0.37413092734445047 0.6340800248452477 0.7396574234531016 20 | abs_error 0.021609553572695485 0.04444024153892039 0.08613844333277279 0.11670181896947857 0.14387893930492893 0.23684368362120012 0.30447390226551413 0.3697006894204313 0.4186901963257447 21 | not_included 25 46 37 26 17 5 11 4 3 22 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF631HEX/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 1.1707627773284912 1.1743125915527344 1.1790306568145752 1.1803882122039795 1.184683084487915 1.1942241191864014 1.20438814163208 1.2147107124328613 1.2232656478881836 4 | pyBW app. 5 | 1.1708378791809082 1.1762065887451172 1.178551435470581 1.181581735610962 1.182539463043213 1.038295030593872 1.0416083335876465 1.0423438549041748 1.042612075805664 6 | pyBG exact 7 | 0.0013937950134277344 0.0020904541015625 0.0023543834686279297 0.0025527477264404297 0.00274658203125 0.0030400753021240234 0.0034093856811523438 0.00365447998046875 0.0038862228393554688 8 | pyBG app. bin=int_size/5 9 | 0.0012485980987548828 0.0010976791381835938 0.001033782958984375 0.0010046958923339844 0.001009225845336914 0.0009210109710693359 0.0008039474487304688 0.0007584095001220703 0.0007255077362060547 10 | pyBG app. bin=int_size/10 11 | 0.0015521049499511719 0.0013909339904785156 0.001293182373046875 0.0012366771697998047 0.001191854476928711 0.00110626220703125 0.0010797977447509766 0.0009837150573730469 0.0009245872497558594 12 | pyBG app. bin=int_size/20 13 | 0.0019457340240478516 0.0017426013946533203 0.001542806625366211 0.0014925003051757812 0.0014600753784179688 0.001369476318359375 0.0013377666473388672 0.0015683174133300781 0.0012488365173339844 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF631HEX/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF631HEX/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF631HEX/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.17350149154663086 0.1948413848876953 0.21573829650878906 8 | pyBG app. bin=100 9 | 0.00916600227355957 0.018804311752319336 0.02889871597290039 0.03847956657409668 0.04802083969116211 0.05750584602355957 0.06626629829406738 0.0751495361328125 0.08465242385864258 0.0934438705444336 10 | pyBG app. bin=50 11 | 0.01180720329284668 0.023580074310302734 0.035143136978149414 0.04742264747619629 0.05869340896606445 0.06958389282226562 0.08096528053283691 0.09289336204528809 0.10488200187683105 0.11504101753234863 12 | pyBG app. bin=25 13 | 0.014614582061767578 0.028887033462524414 0.04294466972351074 0.05702662467956543 0.07061338424682617 0.08410477638244629 0.09773778915405273 0.11073160171508789 0.1257185935974121 0.138624906539917 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF643WMY/interval_error.png: -------------------------------------------------------------------------------- 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| 0.5504586696624756 0.5558180809020996 0.5630149841308594 0.5680351257324219 1.0654127597808838 1.0648713111877441 1.0711588859558105 1.1084046363830566 1.1100058555603027 6 | pyBG exact 7 | 0.002118349075317383 0.0025136470794677734 0.0028493404388427734 0.0030317306518554688 0.003283262252807617 0.003887176513671875 0.004499912261962891 0.004995584487915039 0.005525350570678711 8 | pyBG app. bin=int_size/5 9 | 0.0011985301971435547 0.0010745525360107422 0.0010235309600830078 0.0009758472442626953 0.000942230224609375 0.00083160400390625 0.0007781982421875 0.0007817745208740234 0.0007107257843017578 10 | pyBG app. bin=int_size/10 11 | 0.0014917850494384766 0.0013396739959716797 0.0012145042419433594 0.0011858940124511719 0.001176595687866211 0.0010640621185302734 0.0009999275207519531 0.0009312629699707031 0.000885009765625 12 | pyBG app. bin=int_size/20 13 | 0.00188446044921875 0.0016894340515136719 0.001573324203491211 0.0014810562133789062 0.001466512680053711 0.0013704299926757812 0.0013127326965332031 0.0012462139129638672 0.0012159347534179688 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF643WMY/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF643WMY/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF643WMY/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF643WMY/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.20667147636413574 0.23084163665771484 0.25672054290771484 8 | pyBG app. bin=100 9 | 0.00892782211303711 0.018158435821533203 0.0272219181060791 0.03765249252319336 0.04524970054626465 0.05403542518615723 0.06383514404296875 0.07250547409057617 0.08115887641906738 0.08953070640563965 10 | pyBG app. bin=50 11 | 0.011414051055908203 0.022235870361328125 0.03418374061584473 0.04518890380859375 0.05736851692199707 0.06915688514709473 0.07913517951965332 0.09147953987121582 0.10082268714904785 0.11152052879333496 12 | pyBG app. bin=25 13 | 0.014428138732910156 0.028119325637817383 0.04208564758300781 0.05608534812927246 0.07014203071594238 0.08281612396240234 0.09684872627258301 0.10982203483581543 0.12325024604797363 0.13695597648620605 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF770CQD/interval_error.png: -------------------------------------------------------------------------------- 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0.5154404640197754 0.5206749439239502 0.5265791416168213 0.5350019931793213 1.041017770767212 1.0441334247589111 1.051501750946045 1.1009924411773682 1.1017940044403076 6 | pyBG exact 7 | 0.0020427703857421875 0.0025565624237060547 0.002846240997314453 0.0031480789184570312 0.0032892227172851562 0.00403594970703125 0.0046808719635009766 0.005340576171875 0.005961179733276367 8 | pyBG app. bin=int_size/5 9 | 0.0011866092681884766 0.0010836124420166016 0.00101470947265625 0.0009710788726806641 0.0009410381317138672 0.0008332729339599609 0.0008270740509033203 0.0007240772247314453 0.0006794929504394531 10 | pyBG app. bin=int_size/10 11 | 0.001506805419921875 0.0012979507446289062 0.0012090206146240234 0.00121307373046875 0.0011970996856689453 0.001074075698852539 0.0009789466857910156 0.0009772777557373047 0.0009694099426269531 12 | pyBG app. bin=int_size/20 13 | 0.0018465518951416016 0.0016748905181884766 0.0015120506286621094 0.0015151500701904297 0.0014069080352783203 0.0013539791107177734 0.0013308525085449219 0.0012402534484863281 0.0011858940124511719 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF770CQD/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF770CQD/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF770CQD/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF770CQD/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.17992687225341797 0.2070925235748291 0.2302253246307373 0.25539517402648926 8 | pyBG app. bin=100 9 | 0.007721662521362305 0.015269041061401367 0.02287912368774414 0.030518054962158203 0.03843045234680176 0.0456540584564209 0.05421614646911621 0.06087183952331543 0.06856822967529297 0.07595944404602051 10 | pyBG app. bin=50 11 | 0.012134552001953125 0.024287700653076172 0.03560209274291992 0.048362016677856445 0.05948591232299805 0.07197928428649902 0.08268189430236816 0.09428787231445312 0.10589790344238281 0.11778855323791504 12 | pyBG app. bin=25 13 | 0.01492166519165039 0.02959609031677246 0.04438924789428711 0.05912947654724121 0.07387232780456543 0.08870887756347656 0.10328149795532227 0.11804890632629395 0.13914752006530762 0.14801335334777832 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF847JMY/interval_error.png: -------------------------------------------------------------------------------- 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0.5588469505310059 0.5641355514526367 0.5694608688354492 0.5733652114868164 0.5784187316894531 1.1126272678375244 1.1150765419006348 1.117136001586914 1.1190361976623535 6 | pyBG exact 7 | 0.0014913082122802734 0.002020120620727539 0.002357959747314453 0.0026895999908447266 0.0028493404388427734 0.0033483505249023438 0.0037810802459716797 0.004099607467651367 0.0044879913330078125 8 | pyBG app. bin=int_size/5 9 | 0.0012688636779785156 0.0010921955108642578 0.001035451889038086 0.0009906291961669922 0.0009715557098388672 0.0008876323699951172 0.0008528232574462891 0.0008087158203125 0.0007257461547851562 10 | pyBG app. bin=int_size/10 11 | 0.001537322998046875 0.0013382434844970703 0.0012421607971191406 0.0012476444244384766 0.0011708736419677734 0.0011036396026611328 0.0010385513305664062 0.0009741783142089844 0.0009710788726806641 12 | pyBG app. bin=int_size/20 13 | 0.0018956661224365234 0.0017354488372802734 0.0015404224395751953 0.0014843940734863281 0.00144195556640625 0.0013737678527832031 0.0013282299041748047 0.0013661384582519531 0.0012691020965576172 14 | -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF847JMY/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF847JMY/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v1_graphs/ENCFF847JMY/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v1_graphs/ENCFF847JMY/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.17263007164001465 0.19307971000671387 0.21496820449829102 8 | pyBG app. bin=100 9 | 0.009157896041870117 0.019413232803344727 0.028615713119506836 0.03777027130126953 0.04789161682128906 0.056535959243774414 0.06620073318481445 0.07489609718322754 0.08479905128479004 0.0923924446105957 10 | pyBG app. bin=50 11 | 0.011269330978393555 0.022713422775268555 0.035021066665649414 0.04635357856750488 0.05821037292480469 0.06946849822998047 0.08037972450256348 0.091461181640625 0.1039280891418457 0.11454033851623535 12 | pyBG app. bin=25 13 | 0.014537334442138672 0.028635501861572266 0.04288768768310547 0.05643630027770996 0.07008910179138184 0.08415818214416504 0.09861159324645996 0.11097931861877441 0.12493395805358887 0.13713860511779785 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF050CCI/interval_error.png: -------------------------------------------------------------------------------- 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| 0.5856785774230957 0.5954287052154541 0.6045799255371094 0.6101453304290771 1.1381781101226807 1.1443712711334229 1.1470143795013428 1.1341602802276611 1.1354453563690186 6 | pyBG exact 7 | 0.0023124217987060547 0.0026090145111083984 0.0030508041381835938 0.0034329891204833984 0.003584623336791992 0.004544496536254883 0.0052947998046875 0.006131410598754883 0.006948947906494141 8 | pyBG app. bin=int_size/5 9 | 0.001277923583984375 0.00109100341796875 0.0010349750518798828 0.0010008811950683594 0.0009703636169433594 0.0009260177612304688 0.0008113384246826172 0.0007643699645996094 0.0007297992706298828 10 | pyBG app. bin=int_size/10 11 | 0.0015451908111572266 0.0014023780822753906 0.0012733936309814453 0.0011954307556152344 0.0012178421020507812 0.0011379718780517578 0.001035928726196289 0.0010297298431396484 0.0009260177612304688 12 | pyBG app. bin=int_size/20 13 | 0.0019307136535644531 0.0017368793487548828 0.0015423297882080078 0.0014851093292236328 0.001458883285522461 0.0014233589172363281 0.0013477802276611328 0.0012965202331542969 0.00127410888671875 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF050CCI/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF050CCI/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF050CCI/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF050CCI/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.18880152702331543 0.21213912963867188 0.23861002922058105 0.26445937156677246 8 | pyBG app. bin=100 9 | 0.009128093719482422 0.018939733505249023 0.02846837043762207 0.038375139236450195 0.04746723175048828 0.05681037902832031 0.06661558151245117 0.07475423812866211 0.08358502388000488 0.09238910675048828 10 | pyBG app. bin=50 11 | 0.011636495590209961 0.02259063720703125 0.035077810287475586 0.046514034271240234 0.05772042274475098 0.06919384002685547 0.07998895645141602 0.09084701538085938 0.10229730606079102 0.11363911628723145 12 | pyBG app. bin=25 13 | 0.014501571655273438 0.029157400131225586 0.04232931137084961 0.05660438537597656 0.07042670249938965 0.08392858505249023 0.09782743453979492 0.11036086082458496 0.1234278678894043 0.13694310188293457 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF321FZQ/interval_error.png: -------------------------------------------------------------------------------- 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| 0.5960533618927002 0.614931583404541 1.2757036685943604 1.279642105102539 1.280066728591919 1.25657057762146 1.2596759796142578 1.261023759841919 1.2642347812652588 6 | pyBG exact 7 | 0.0028123855590820312 0.00342559814453125 0.0041577816009521484 0.004796743392944336 0.0053920745849609375 0.007796764373779297 0.009813547134399414 0.012632131576538086 0.015025854110717773 8 | pyBG app. bin=int_size/5 9 | 0.0012357234954833984 0.0010924339294433594 0.0011067390441894531 0.0009989738464355469 0.000972747802734375 0.0008788108825683594 0.00086212158203125 0.0007641315460205078 0.0007264614105224609 10 | pyBG app. bin=int_size/10 11 | 0.0015647411346435547 0.0013751983642578125 0.0012333393096923828 0.0012097358703613281 0.0011792182922363281 0.0011219978332519531 0.001096963882446289 0.0010190010070800781 0.0009398460388183594 12 | pyBG app. bin=int_size/20 13 | 0.0019037723541259766 0.0017290115356445312 0.0015430450439453125 0.0015342235565185547 0.0014483928680419922 0.0013704299926757812 0.0013744831085205078 0.0013093948364257812 0.0012497901916503906 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF321FZQ/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF321FZQ/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF321FZQ/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF321FZQ/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.26233363151550293 0.2991526126861572 0.3365364074707031 0.37444591522216797 8 | pyBG app. bin=100 9 | 0.009130477905273438 0.018561124801635742 0.028518199920654297 0.038378238677978516 0.0465083122253418 0.05654120445251465 0.06531023979187012 0.07498693466186523 0.08310914039611816 0.09175705909729004 10 | pyBG app. bin=50 11 | 0.011545658111572266 0.02260899543762207 0.03482961654663086 0.04664134979248047 0.057587385177612305 0.06889629364013672 0.08037519454956055 0.09063339233398438 0.10174012184143066 0.1143639087677002 12 | pyBG app. bin=25 13 | 0.01417851448059082 0.028580427169799805 0.042710304260253906 0.05758500099182129 0.0703592300415039 0.08340072631835938 0.09731292724609375 0.11148190498352051 0.1235494613647461 0.13672924041748047 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF376VCU/interval_error.png: -------------------------------------------------------------------------------- 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0.5558023452758789 0.56363844871521 0.5685920715332031 0.5774519443511963 1.0621647834777832 1.0625951290130615 1.0682373046875 1.1171166896820068 1.1180496215820312 6 | pyBG exact 7 | 0.0021071434020996094 0.002489328384399414 0.002864837646484375 0.0031003952026367188 0.0032668113708496094 0.003949165344238281 0.004583120346069336 0.005275726318359375 0.005792140960693359 8 | pyBG app. bin=int_size/5 9 | 0.0011866092681884766 0.0010983943939208984 0.001020193099975586 0.0009648799896240234 0.0009367465972900391 0.0008230209350585938 0.0007736682891845703 0.0007195472717285156 0.0006873607635498047 10 | pyBG app. bin=int_size/10 11 | 0.0014948844909667969 0.001287698745727539 0.0012118816375732422 0.001172780990600586 0.0012083053588867188 0.0010776519775390625 0.0009868144989013672 0.0010058879852294922 0.0008804798126220703 12 | pyBG app. bin=int_size/20 13 | 0.001903533935546875 0.0016629695892333984 0.0014965534210205078 0.0014612674713134766 0.0014202594757080078 0.0013446807861328125 0.0013070106506347656 0.0012392997741699219 0.0012135505676269531 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF376VCU/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF376VCU/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.17918634414672852 0.2037200927734375 0.22972416877746582 0.25349926948547363 8 | pyBG app. bin=100 9 | 0.008862972259521484 0.01863384246826172 0.026485919952392578 0.03691363334655762 0.04536914825439453 0.05462908744812012 0.06348252296447754 0.07205820083618164 0.08104491233825684 0.08891439437866211 10 | pyBG app. bin=50 11 | 0.011245489120483398 0.023137569427490234 0.033944129943847656 0.04545783996582031 0.05682992935180664 0.06844258308410645 0.07854390144348145 0.08775949478149414 0.09969902038574219 0.11042428016662598 12 | pyBG app. bin=25 13 | 0.014292478561401367 0.027959585189819336 0.04202723503112793 0.05577206611633301 0.06944513320922852 0.0840303897857666 0.09644484519958496 0.11030745506286621 0.1225590705871582 0.1359720230102539 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF384CMP/interval_error.png: -------------------------------------------------------------------------------- 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| 0.5370528697967529 0.5440936088562012 0.5479636192321777 0.5529539585113525 1.0509300231933594 1.0534985065460205 1.0580005645751953 1.1043403148651123 1.1050889492034912 6 | pyBG exact 7 | 0.0020020008087158203 0.0023849010467529297 0.00270843505859375 0.002974987030029297 0.0031294822692871094 0.0037059783935546875 0.004225969314575195 0.004806995391845703 0.005225658416748047 8 | pyBG app. bin=int_size/5 9 | 0.0011692047119140625 0.0010685920715332031 0.0010786056518554688 0.0009627342224121094 0.0009341239929199219 0.0008282661437988281 0.0007658004760742188 0.0007207393646240234 0.0007240772247314453 10 | pyBG app. bin=int_size/10 11 | 0.0014755725860595703 0.0012984275817871094 0.001199960708618164 0.001207113265991211 0.0011439323425292969 0.0010576248168945312 0.0009884834289550781 0.0009264945983886719 0.0008769035339355469 12 | pyBG app. bin=int_size/20 13 | 0.0019192695617675781 0.0017046928405761719 0.0014882087707519531 0.001463174819946289 0.0014162063598632812 0.001394033432006836 0.0012879371643066406 0.001245737075805664 0.001195669174194336 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF384CMP/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF384CMP/pyBG_app._bin=int_size20_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF384CMP/pyBG_app._bin=int_size20_table.png -------------------------------------------------------------------------------- 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0.20078229904174805 0.22359585762023926 0.25011372566223145 8 | pyBG app. bin=100 9 | 0.008995294570922852 0.018373966217041016 0.02824091911315918 0.03670930862426758 0.04516339302062988 0.054007530212402344 0.06368470191955566 0.07310771942138672 0.08104896545410156 0.08929038047790527 10 | pyBG app. bin=50 11 | 0.011234521865844727 0.022150754928588867 0.03439474105834961 0.04603075981140137 0.05698060989379883 0.0681459903717041 0.07897615432739258 0.0906226634979248 0.10060596466064453 0.11086511611938477 12 | pyBG app. bin=25 13 | 0.014379262924194336 0.028021574020385742 0.04308152198791504 0.056372642517089844 0.06983613967895508 0.08315849304199219 0.0966494083404541 0.11103177070617676 0.12256669998168945 0.13646507263183594 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF631HEX/interval_error.png: -------------------------------------------------------------------------------- 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0.10387141011686013 0.09816046402632692 9 | ms_error 19.801345221108345 76.18342899667009 223.18716366958833 255.62819296069225 351.0043689901836 558.8871785779764 579.332470373631 445.3002891759267 484.35998256474306 10 | abs_error 2.121644219365344 4.278055799895717 6.19978989398143 6.696647044859457 7.149764902378392 8.024119547078646 8.025117234017737 7.739019715270722 7.688265054062722 11 | num_actual_0 0 0 0 0 0 0 0 0 0 12 | pyBG app. bin=int_size/10 13 | percent_error 0.024141603187292627 0.04776400445408301 0.0635019866494578 0.06573456351145245 0.06620851649857476 0.06365315331888886 0.06177845325305535 0.05869037380224074 0.05789607069984799 14 | ms_error 4.581510840219182 16.99707310993781 48.07322264511279 74.88560556248079 95.25904541943409 139.19619602348226 150.44589914011763 147.79285359579964 130.3157283490106 15 | abs_error 0.9803708740598002 2.0546822964263396 2.9950418781453543 3.3893219643585444 3.6482416642473465 4.1228644409487565 4.260252408297479 4.202491538003842 4.180648099990175 16 | num_actual_0 0 0 0 0 0 0 0 0 0 17 | pyBG app. bin=int_size/20 18 | percent_error 0.012701448552153627 0.02438336383874296 0.03347966571844321 0.03221619287285299 0.034632737619723755 0.033357913695324905 0.03330187513162387 0.03250335376391498 0.03233042183718962 19 | ms_error 0.8764053318036982 3.638503200593556 10.432959050276695 14.460117659787656 19.59620399332631 33.65705680124935 31.893181528170558 35.97543586032977 36.534068210900365 20 | abs_error 0.4153824316379486 0.9508379627214073 1.412426260097917 1.487512945691792 1.758771281757108 2.072495710387166 2.144438735157976 2.1651943753484573 2.2216510699169834 21 | num_actual_0 0 0 0 0 0 0 0 0 0 22 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF631HEX/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF631HEX/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF631HEX/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2000 3000 4000 5000 2 | pyBW exact 3 | 1.1760172843933105 1.1742939949035645 1.177239179611206 1.180619716644287 1.183706521987915 1.1961607933044434 1.2055118083953857 1.2132914066314697 1.2224276065826416 4 | pyBW app. 5 | 1.172050952911377 1.1753554344177246 1.178415060043335 1.1811802387237549 1.1839685440063477 1.0383479595184326 1.0394926071166992 1.0412583351135254 1.0429601669311523 6 | pyBG exact 7 | 0.0013539791107177734 0.0020482540130615234 0.0023741722106933594 0.0024728775024414062 0.0026273727416992188 0.0029735565185546875 0.0032622814178466797 0.0035414695739746094 0.003813028335571289 8 | pyBG app. bin=int_size/5 9 | 0.0012433528900146484 0.001087188720703125 0.001087188720703125 0.0009922981262207031 0.0010263919830322266 0.001001119613647461 0.0008177757263183594 0.0008389949798583984 0.0007302761077880859 10 | pyBG app. bin=int_size/10 11 | 0.0015358924865722656 0.001356363296508789 0.0012373924255371094 0.0012030601501464844 0.001180410385131836 0.0010883808135986328 0.0014126300811767578 0.0009927749633789062 0.0009310245513916016 12 | pyBG app. bin=int_size/20 13 | 0.0018856525421142578 0.001745462417602539 0.001577615737915039 0.0014750957489013672 0.0014309883117675781 0.0013725757598876953 0.0013649463653564453 0.0012943744659423828 0.001294851303100586 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF631HEX/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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900000 1000000 2 | pyBW exact 3 | 11.757296800613403 23.487826347351074 35.213833808898926 46.92534017562866 58.65961766242981 70.36232829093933 82.03286027908325 93.76965570449829 105.45544052124023 117.18299269676208 4 | pyBW app. 5 | 12.517224073410034 23.485045671463013 35.21711802482605 46.939773082733154 58.64679408073425 70.4024727344513 82.0419499874115 93.78708577156067 105.49841237068176 117.22831225395203 6 | pyBG exact 7 | 0.022737741470336914 0.04455924034118652 0.06695389747619629 0.08822345733642578 0.10903215408325195 0.13030743598937988 0.1500248908996582 0.17122125625610352 0.19165730476379395 0.21219658851623535 8 | pyBG app. bin=100 9 | 0.009146451950073242 0.01934671401977539 0.0293886661529541 0.038048744201660156 0.047948598861694336 0.05694079399108887 0.06586098670959473 0.07599616050720215 0.08271980285644531 0.09293913841247559 10 | pyBG app. bin=50 11 | 0.011548280715942383 0.02319931983947754 0.03511929512023926 0.04593801498413086 0.05784106254577637 0.06921696662902832 0.08046865463256836 0.09116291999816895 0.10406017303466797 0.11359214782714844 12 | pyBG app. bin=25 13 | 0.014470815658569336 0.02863764762878418 0.04235100746154785 0.05692458152770996 0.07034730911254883 0.08404994010925293 0.09698939323425293 0.11039090156555176 0.12383008003234863 0.13695359230041504 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF643WMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF643WMY/interval_error.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF643WMY/interval_run_time.png: -------------------------------------------------------------------------------- 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0.005419254302978516 8 | pyBG app. bin=int_size/5 9 | 0.0011932849884033203 0.0010650157928466797 0.0010085105895996094 0.0009675025939941406 0.0009343624114990234 0.0008246898651123047 0.0007662773132324219 0.0007190704345703125 0.0006852149963378906 10 | pyBG app. bin=int_size/10 11 | 0.0014901161193847656 0.0012836456298828125 0.001216888427734375 0.0011649131774902344 0.0011489391326904297 0.0010547637939453125 0.000990152359008789 0.0009908676147460938 0.0008714199066162109 12 | pyBG app. bin=int_size/20 13 | 0.0018985271453857422 0.0016589164733886719 0.0015177726745605469 0.0014693737030029297 0.0014450550079345703 0.0013439655303955078 0.0013129711151123047 0.0012538433074951172 0.0011775493621826172 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF643WMY/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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900000 1000000 2 | pyBW exact 3 | 5.5642735958099365 11.144207954406738 16.7071692943573 22.2135808467865 27.758116960525513 33.339584827423096 38.86592221260071 44.378937005996704 49.9425151348114 55.55098581314087 4 | pyBW app. 5 | 8.785006523132324 11.186121702194214 16.74503493309021 22.288835525512695 27.82994508743286 33.42647957801819 38.95932674407959 44.472187757492065 50.063963890075684 55.65474033355713 6 | pyBG exact 7 | 0.02722787857055664 0.053899288177490234 0.07947111129760742 0.10288715362548828 0.12751317024230957 0.15194964408874512 0.17681026458740234 0.20250558853149414 0.22575640678405762 0.25128984451293945 8 | pyBG app. bin=100 9 | 0.008824348449707031 0.017801523208618164 0.02759528160095215 0.03696703910827637 0.0458073616027832 0.05440878868103027 0.06320810317993164 0.07207655906677246 0.08121109008789062 0.08868837356567383 10 | pyBG app. bin=50 11 | 0.011211156845092773 0.022156238555908203 0.035223960876464844 0.045082807540893555 0.0570068359375 0.06867694854736328 0.07896041870117188 0.08951950073242188 0.09984397888183594 0.11190366744995117 12 | pyBG app. bin=25 13 | 0.014292001724243164 0.027914762496948242 0.04237008094787598 0.05589723587036133 0.0696108341217041 0.08301854133605957 0.09598326683044434 0.10923933982849121 0.12246179580688477 0.13691377639770508 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF770CQD/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF770CQD/interval_error.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF770CQD/interval_run_time.png: -------------------------------------------------------------------------------- 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0.0058858394622802734 8 | pyBG app. bin=int_size/5 9 | 0.0012290477752685547 0.0011005401611328125 0.0010485649108886719 0.0009684562683105469 0.0010466575622558594 0.000827789306640625 0.0007975101470947266 0.0007512569427490234 0.0006866455078125 10 | pyBG app. bin=int_size/10 11 | 0.0014774799346923828 0.0013086795806884766 0.00122833251953125 0.0012102127075195312 0.0011610984802246094 0.0010592937469482422 0.0010080337524414062 0.00091552734375 0.00086212158203125 12 | pyBG app. bin=int_size/20 13 | 0.0018584728240966797 0.0016658306121826172 0.001588582992553711 0.0014545917510986328 0.0014154911041259766 0.0013763904571533203 0.0013077259063720703 0.001252889633178711 0.0011878013610839844 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF770CQD/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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900000 1000000 2 | pyBW exact 3 | 5.242838144302368 10.481489658355713 15.726719379425049 20.95887589454651 26.190995931625366 31.436304569244385 36.6186728477478 41.803746700286865 47.08630108833313 52.30722379684448 4 | pyBW app. 5 | 7.756523847579956 10.499606847763062 15.744327783584595 20.96443510055542 26.217120885849 31.45544147491455 36.698444843292236 41.80828809738159 47.10597634315491 52.326035022735596 6 | pyBG exact 7 | 0.027201175689697266 0.05348777770996094 0.07884573936462402 0.10374045372009277 0.12896728515625 0.15563654899597168 0.17684292793273926 0.20189714431762695 0.22810721397399902 0.25127625465393066 8 | pyBG app. bin=100 9 | 0.009063959121704102 0.018269062042236328 0.027796268463134766 0.03651714324951172 0.046035051345825195 0.053928375244140625 0.06332635879516602 0.07189273834228516 0.08064818382263184 0.08952450752258301 10 | pyBG app. bin=50 11 | 0.011410713195800781 0.022313833236694336 0.03429150581359863 0.046201229095458984 0.05634641647338867 0.06826305389404297 0.07881498336791992 0.0910787582397461 0.10011601448059082 0.11110711097717285 12 | pyBG app. bin=25 13 | 0.014336824417114258 0.02811288833618164 0.04140973091125488 0.05629849433898926 0.06952929496765137 0.08417057991027832 0.09598970413208008 0.11089348793029785 0.12305283546447754 0.13608241081237793 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF847JMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v2_graphs/ENCFF847JMY/interval_error.png -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF847JMY/interval_run_time.png: -------------------------------------------------------------------------------- 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0.00439906120300293 8 | pyBG app. bin=int_size/5 9 | 0.0012629032135009766 0.0011212825775146484 0.0010259151458740234 0.0009922981262207031 0.0009658336639404297 0.0008709430694580078 0.0008063316345214844 0.0007519721984863281 0.0007843971252441406 10 | pyBG app. bin=int_size/10 11 | 0.0015366077423095703 0.0013470649719238281 0.0012323856353759766 0.0012314319610595703 0.0012111663818359375 0.001155853271484375 0.0010349750518798828 0.0009751319885253906 0.0009248256683349609 12 | pyBG app. bin=int_size/20 13 | 0.0019235610961914062 0.0017688274383544922 0.001554250717163086 0.0015211105346679688 0.001451730728149414 0.0013985633850097656 0.0013325214385986328 0.0014376640319824219 0.0012521743774414062 14 | -------------------------------------------------------------------------------- /graphs/v2_graphs/ENCFF847JMY/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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900000 1000000 2 | pyBW exact 3 | 5.654881954193115 11.280436038970947 16.927783012390137 22.533876180648804 28.162071466445923 33.79266953468323 39.388039350509644 44.989710569381714 50.6418936252594 56.226160526275635 4 | pyBW app. 5 | 5.693177700042725 11.366830825805664 17.016271352767944 22.683306217193604 28.32013726234436 33.989392042160034 39.57805681228638 45.23899221420288 50.87777662277222 56.56852459907532 6 | pyBG exact 7 | 0.022959232330322266 0.04478287696838379 0.06688547134399414 0.08826732635498047 0.10892963409423828 0.129927396774292 0.14997553825378418 0.16995787620544434 0.1917736530303955 0.2127087116241455 8 | pyBG app. bin=100 9 | 0.009079456329345703 0.018509387969970703 0.028809547424316406 0.037760019302368164 0.04709219932556152 0.05576658248901367 0.06550025939941406 0.07451653480529785 0.0815134048461914 0.09181833267211914 10 | pyBG app. bin=50 11 | 0.011605024337768555 0.023351430892944336 0.0345921516418457 0.04569673538208008 0.05625033378601074 0.06886005401611328 0.08018636703491211 0.0907745361328125 0.10329890251159668 0.11311626434326172 12 | pyBG app. bin=25 13 | 0.014428138732910156 0.028493404388427734 0.04241037368774414 0.057225942611694336 0.07019209861755371 0.08426809310913086 0.09749531745910645 0.1106407642364502 0.12390494346618652 0.1368579864501953 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF000KYT/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF000KYT/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF000KYT/interval_run_time.png: -------------------------------------------------------------------------------- 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0.015914440155029297 0.023795127868652344 0.061763763427734375 0.10191845893859863 8 | pyBG app. bin=int_size/5 9 | 0.0015006065368652344 0.0007426738739013672 0.0009737014770507812 0.0007488727569580078 0.0007412433624267578 0.0007445812225341797 0.0006632804870605469 0.0005669593811035156 0.0003476142883300781 0.00030493736267089844 10 | pyBG app. bin=int_size/10 11 | 0.0022687911987304688 0.0015666484832763672 0.0009071826934814453 0.0014123916625976562 0.0009338855743408203 0.0009391307830810547 0.000827789306640625 0.0007703304290771484 0.0005614757537841797 0.00043272972106933594 12 | pyBG app. bin=int_size/20 13 | 0.0034682750701904297 0.002499818801879883 0.0014183521270751953 0.0013380050659179688 0.0013628005981445312 0.001308441162109375 0.0012319087982177734 0.0010979175567626953 0.0009381771087646484 0.000789642333984375 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF000KYT/interval_runtime_table.png: 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50.78951859474182 57.09746193885803 60.43101167678833 6 | pyBG exact 7 | 0.03554844856262207 0.06947898864746094 0.10412216186523438 0.1375889778137207 0.1697368621826172 0.20531177520751953 0.24089527130126953 0.27755212783813477 0.29738545417785645 0.32973146438598633 8 | pyBG app. bin=100 9 | 0.006853342056274414 0.01317143440246582 0.019583702087402344 0.025755882263183594 0.03217720985412598 0.038712263107299805 0.04464364051818848 0.051389217376708984 0.05832314491271973 0.06419897079467773 10 | pyBG app. bin=50 11 | 0.009019613265991211 0.016652345657348633 0.024847984313964844 0.03302431106567383 0.041390180587768555 0.049144744873046875 0.05776262283325195 0.06572484970092773 0.07430362701416016 0.0823373794555664 12 | pyBG app. bin=25 13 | 0.013296842575073242 0.02416539192199707 0.036989450454711914 0.04808664321899414 0.06179547309875488 0.07421660423278809 0.08438372611999512 0.0968625545501709 0.10813570022583008 0.1198117733001709 14 | 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10000 50000 100000 2 | pyBW exact 3 | 0.5793001651763916 0.586292028427124 0.5919339656829834 0.5985889434814453 0.5969841480255127 0.6232478618621826 0.6635510921478271 0.7313132286071777 1.2605295181274414 1.9317727088928223 4 | pyBW app. 5 | 0.5803477764129639 0.5846207141876221 0.5923473834991455 0.5919206142425537 0.5999078750610352 1.5938646793365479 1.6598598957061768 1.6580326557159424 1.5807538032531738 1.5008149147033691 6 | pyBG exact 7 | 0.0015985965728759766 0.0022122859954833984 0.002780914306640625 0.0030536651611328125 0.0035202503204345703 0.005862712860107422 0.008322000503540039 0.015491485595703125 0.05742168426513672 0.11007404327392578 8 | pyBG app. bin=int_size/5 9 | 0.0008058547973632812 0.0008504390716552734 0.000774383544921875 0.0007188320159912109 0.0007231235504150391 0.0006549358367919922 0.0005855560302734375 0.0004398822784423828 0.00033402442932128906 0.0002989768981933594 10 | pyBG app. bin=int_size/10 11 | 0.002101421356201172 0.0011377334594726562 0.0011332035064697266 0.0011706352233886719 0.0011470317840576172 0.0010156631469726562 0.0009284019470214844 0.0007481575012207031 0.0004863739013671875 0.0004684925079345703 12 | pyBG app. bin=int_size/20 13 | 0.002298593521118164 0.0021152496337890625 0.0013594627380371094 0.00177764892578125 0.001708984375 0.001386880874633789 0.0016286373138427734 0.0009765625 0.0005941390991210938 0.0005137920379638672 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF000LAB/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF000LAB/interval_runtime_table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF000LAB/pyBG_app._bin=int_size10_table.png: 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/graphs/v3_graphs/ENCFF000LAB/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 6.279058933258057 12.062033653259277 18.147300004959106 24.306592226028442 30.208177089691162 34.85798478126526 42.39837336540222 47.44673156738281 53.78402376174927 59.07096481323242 4 | pyBW app. 5 | 6.056436777114868 12.123692512512207 18.174171209335327 24.12892508506775 30.316993951797485 35.34707689285278 40.71613168716431 48.48203706741333 53.18345236778259 59.71691131591797 6 | pyBG exact 7 | 0.02601170539855957 0.05218005180358887 0.08306455612182617 0.10362362861633301 0.13940930366516113 0.1540677547454834 0.19342875480651855 0.20923161506652832 0.24289655685424805 0.26642465591430664 8 | pyBG app. bin=100 9 | 0.006929159164428711 0.013463497161865234 0.02025127410888672 0.029172658920288086 0.03472447395324707 0.04001617431640625 0.0479891300201416 0.05391120910644531 0.0607759952545166 0.06890439987182617 10 | pyBG app. bin=50 11 | 0.010583162307739258 0.02144145965576172 0.03144407272338867 0.041686296463012695 0.05287981033325195 0.06231069564819336 0.07282471656799316 0.08284187316894531 0.0940093994140625 0.10173296928405762 12 | pyBG app. bin=25 13 | 0.012566566467285156 0.02597784996032715 0.0381011962890625 0.050798654556274414 0.06317543983459473 0.07634377479553223 0.09346556663513184 0.10283374786376953 0.1124577522277832 0.1261427402496338 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF050CCI/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF050CCI/interval_error.png -------------------------------------------------------------------------------- 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0.0018210411071777344 0.002109527587890625 0.002427339553833008 0.0027081966400146484 0.0029675960540771484 0.004331827163696289 0.006433963775634766 0.01064157485961914 0.04351925849914551 0.08418679237365723 8 | pyBG app. bin=int_size/5 9 | 0.0007131099700927734 0.0007047653198242188 0.0006706714630126953 0.0006535053253173828 0.0006389617919921875 0.0005755424499511719 0.0004968643188476562 0.00041294097900390625 0.00029850006103515625 0.0002818107604980469 10 | pyBG app. bin=int_size/10 11 | 0.0011713504791259766 0.0010466575622558594 0.001073598861694336 0.0010399818420410156 0.0010094642639160156 0.0009129047393798828 0.0007717609405517578 0.0006313323974609375 0.00039768218994140625 0.0003535747528076172 12 | pyBG app. bin=int_size/20 13 | 0.0015544891357421875 0.0013680458068847656 0.0012197494506835938 0.0013425350189208984 0.0011866092681884766 0.00116729736328125 0.0010595321655273438 0.0009000301361083984 0.0005548000335693359 0.0004868507385253906 14 | 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| pyBW app. 5 | 6.4273600578308105 12.8555588722229 19.281309843063354 25.691550254821777 32.13766646385193 38.56461191177368 45.06330060958862 51.38920879364014 57.917476177215576 64.24775004386902 6 | pyBG exact 7 | 0.022150039672851562 0.04388284683227539 0.06567597389221191 0.08768200874328613 0.1085977554321289 0.1296989917755127 0.15191411972045898 0.17333269119262695 0.19467949867248535 0.21623969078063965 8 | pyBG app. bin=100 9 | 0.005800485610961914 0.011546850204467773 0.01715707778930664 0.022859811782836914 0.028565645217895508 0.03505873680114746 0.040007591247558594 0.045845746994018555 0.05152153968811035 0.0572199821472168 10 | pyBG app. bin=50 11 | 0.008874177932739258 0.0177309513092041 0.026432037353515625 0.03526186943054199 0.04399681091308594 0.05277657508850098 0.06178689002990723 0.07027006149291992 0.07932877540588379 0.08770012855529785 12 | pyBG app. bin=25 13 | 0.010849475860595703 0.021704673767089844 0.03243517875671387 0.04323101043701172 0.05435800552368164 0.06496644020080566 0.07568860054016113 0.08729314804077148 0.09695243835449219 0.10792112350463867 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF321FZQ/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF321FZQ/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF321FZQ/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF321FZQ/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF321FZQ/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2500 5000 10000 50000 100000 2 | pyBW exact 3 | 0.6353926658630371 0.6552703380584717 0.689927339553833 0.7052640914916992 0.7322788238525391 0.8652782440185547 1.0892012119293213 1.5342223644256592 4.996546745300293 9.282490253448486 4 | pyBW app. 5 | 0.6412379741668701 0.6602094173431396 1.3449716567993164 1.3501789569854736 1.3516762256622314 1.3247413635253906 1.3330466747283936 1.21425199508667 1.2208349704742432 1.2103915214538574 6 | pyBG exact 7 | 0.0023279190063476562 0.0028290748596191406 0.003590822219848633 0.004218578338623047 0.004843711853027344 0.008465051651000977 0.014429569244384766 0.026382923126220703 0.12049722671508789 0.23619437217712402 8 | pyBG app. bin=int_size/5 9 | 0.0007290840148925781 0.0006349086761474609 0.0006585121154785156 0.0006248950958251953 0.0006127357482910156 0.0005464553833007812 0.0004951953887939453 0.00042176246643066406 0.00029754638671875 0.00028586387634277344 10 | pyBG app. bin=int_size/10 11 | 0.0011866092681884766 0.0010633468627929688 0.0009465217590332031 0.0010213851928710938 0.000985860824584961 0.0008423328399658203 0.0007200241088867188 0.0006191730499267578 0.00039887428283691406 0.00034737586975097656 12 | pyBG app. bin=int_size/20 13 | 0.0015118122100830078 0.0013644695281982422 0.0012521743774414062 0.001177072525024414 0.0011224746704101562 0.0010943412780761719 0.0009922981262207031 0.0008516311645507812 0.0005540847778320312 0.0004971027374267578 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF321FZQ/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF321FZQ/interval_runtime_table.png 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-------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF321FZQ/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 6.778792381286621 13.548947811126709 20.311233043670654 27.168550729751587 33.875070333480835 40.676509857177734 47.57030153274536 54.18317413330078 61.04581570625305 67.81108331680298 4 | pyBW app. 5 | 13.469681978225708 26.885284662246704 40.30745601654053 53.773985862731934 67.16142129898071 80.59117531776428 94.21429896354675 107.54163551330566 121.06244659423828 134.35767912864685 6 | pyBG exact 7 | 0.03310513496398926 0.06513428688049316 0.09688878059387207 0.12877416610717773 0.16071844100952148 0.19350028038024902 0.22463440895080566 0.25660014152526855 0.2888829708099365 0.3202197551727295 8 | pyBG app. bin=100 9 | 0.005999088287353516 0.011892318725585938 0.01806950569152832 0.023735523223876953 0.029581308364868164 0.0357213020324707 0.04165935516357422 0.047272682189941406 0.05330920219421387 0.05939650535583496 10 | pyBG app. bin=50 11 | 0.00956583023071289 0.018887758255004883 0.028288602828979492 0.037738800048828125 0.04716348648071289 0.056455373764038086 0.06582403182983398 0.0751194953918457 0.0853416919708252 0.09420537948608398 12 | pyBG app. bin=25 13 | 0.011722087860107422 0.0231478214263916 0.034728050231933594 0.046442508697509766 0.05767536163330078 0.06982421875 0.08079862594604492 0.09250903129577637 0.1037895679473877 0.11554455757141113 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF376VCU/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF376VCU/interval_error.png 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1.1701433658599854 1.1763293743133545 1.0987827777862549 1.115283727645874 6 | pyBG exact 7 | 0.0016477108001708984 0.0019383430480957031 0.002256155014038086 0.0024607181549072266 0.0026695728302001953 0.0037384033203125 0.005326747894287109 0.00833582878112793 0.03232908248901367 0.06220078468322754 8 | pyBG app. bin=int_size/5 9 | 0.0006554126739501953 0.0006601810455322266 0.0006108283996582031 0.0006041526794433594 0.0005888938903808594 0.0005278587341308594 0.00045871734619140625 0.00038552284240722656 0.00028634071350097656 0.0002779960632324219 10 | pyBG app. bin=int_size/10 11 | 0.0011401176452636719 0.0010867118835449219 0.0009996891021728516 0.0009100437164306641 0.0008945465087890625 0.0008029937744140625 0.0006883144378662109 0.0005652904510498047 0.0003757476806640625 0.0003364086151123047 12 | pyBG app. bin=int_size/20 13 | 0.0014584064483642578 0.0013260841369628906 0.0011065006256103516 0.0012640953063964844 0.0012183189392089844 0.0010862350463867188 0.0009372234344482422 0.0007798671722412109 0.0005240440368652344 0.0004673004150390625 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF376VCU/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF376VCU/interval_runtime_table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF376VCU/pyBG_app._bin=int_size10_table.png -------------------------------------------------------------------------------- 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60.297382831573486 4 | pyBW app. 5 | 6.049558877944946 12.079203605651855 18.12564969062805 24.182039499282837 30.198872804641724 36.27035212516785 42.34398603439331 48.354437589645386 54.51335835456848 60.40108275413513 6 | pyBG exact 7 | 0.020879745483398438 0.04171013832092285 0.0626840591430664 0.08328866958618164 0.1035008430480957 0.12376785278320312 0.14510607719421387 0.16556334495544434 0.1855168342590332 0.2063002586364746 8 | pyBG app. bin=100 9 | 0.0058100223541259766 0.011255979537963867 0.01680779457092285 0.02234816551208496 0.028067588806152344 0.03388571739196777 0.03965902328491211 0.04471540451049805 0.05025005340576172 0.05578494071960449 10 | pyBG app. bin=50 11 | 0.009356021881103516 0.018652677536010742 0.02782297134399414 0.03702282905578613 0.046268463134765625 0.05547523498535156 0.06470608711242676 0.07386374473571777 0.0834660530090332 0.09229207038879395 12 | pyBG app. bin=25 13 | 0.011754274368286133 0.02339005470275879 0.035048484802246094 0.04671287536621094 0.05831456184387207 0.07061433792114258 0.0816795825958252 0.09336352348327637 0.1048884391784668 0.11791014671325684 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF384CMP/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF384CMP/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF384CMP/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF384CMP/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF384CMP/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2500 5000 10000 50000 100000 2 | pyBW exact 3 | 0.571075439453125 0.5763473510742188 0.5822618007659912 0.5877752304077148 0.593641996383667 0.6252124309539795 0.671759843826294 0.7658026218414307 1.4571726322174072 2.317309617996216 4 | pyBW app. 5 | 0.5730547904968262 0.578488826751709 0.5837209224700928 0.5890953540802002 1.094545841217041 1.1005744934082031 1.1521966457366943 1.1552951335906982 1.072587251663208 1.0609040260314941 6 | pyBG exact 7 | 0.0014660358428955078 0.0018887519836425781 0.0021600723266601562 0.002355337142944336 0.0025217533111572266 0.0034170150756835938 0.004695892333984375 0.007205486297607422 0.026941776275634766 0.0514674186706543 8 | pyBG app. bin=int_size/5 9 | 0.0006473064422607422 0.0006597042083740234 0.0006160736083984375 0.0006082057952880859 0.0005922317504882812 0.0005195140838623047 0.00045752525329589844 0.00038433074951171875 0.00029015541076660156 0.0002777576446533203 10 | pyBG app. bin=int_size/10 11 | 0.0011339187622070312 0.0010824203491210938 0.0010001659393310547 0.0009121894836425781 0.0008978843688964844 0.0007996559143066406 0.000682830810546875 0.0005667209625244141 0.00037789344787597656 0.0003368854522705078 12 | pyBG app. bin=int_size/20 13 | 0.0015022754669189453 0.0013225078582763672 0.0011105537414550781 0.001252889633178711 0.0011608600616455078 0.0010449886322021484 0.0009393692016601562 0.0007801055908203125 0.0005292892456054688 0.0005385875701904297 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF384CMP/interval_runtime_table.png: -------------------------------------------------------------------------------- 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0.14007163047790527 0.15961551666259766 0.17927908897399902 0.1992192268371582 8 | pyBG app. bin=100 9 | 0.005667209625244141 0.011167049407958984 0.01670217514038086 0.0222470760345459 0.027827739715576172 0.033624887466430664 0.03945660591125488 0.04469943046569824 0.04998493194580078 0.055381059646606445 10 | pyBG app. bin=50 11 | 0.009361028671264648 0.018505096435546875 0.027945995330810547 0.03680419921875 0.04605293273925781 0.0550990104675293 0.06466484069824219 0.07346248626708984 0.08266282081604004 0.09190058708190918 12 | pyBG app. bin=25 13 | 0.011750936508178711 0.023336172103881836 0.034906625747680664 0.046416521072387695 0.05884885787963867 0.07078862190246582 0.08161520957946777 0.09280037879943848 0.10455751419067383 0.11661052703857422 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF631HEX/interval_error.png: -------------------------------------------------------------------------------- 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2.0551609992980957 4 | pyBW app. 5 | 1.2529563903808594 1.2553422451019287 1.2615222930908203 1.2621004581451416 1.2658109664916992 1.0842926502227783 1.087099313735962 1.1148526668548584 1.142266035079956 1.1496832370758057 6 | pyBG exact 7 | 0.0009963512420654297 0.0015690326690673828 0.0017960071563720703 0.0019207000732421875 0.002045154571533203 0.0025408267974853516 0.003246784210205078 0.004575014114379883 0.014570236206054688 0.027035951614379883 8 | pyBG app. bin=int_size/5 9 | 0.0007202625274658203 0.0007050037384033203 0.0006763935089111328 0.000659942626953125 0.0006434917449951172 0.0005681514739990234 0.0005021095275878906 0.00041031837463378906 0.0002987384796142578 0.00027823448181152344 10 | pyBG app. bin=int_size/10 11 | 0.0011703968048095703 0.0010552406311035156 0.001081228256225586 0.0010347366333007812 0.0010190010070800781 0.0009207725524902344 0.0007722377777099609 0.0006272792816162109 0.00039768218994140625 0.0003495216369628906 12 | pyBG app. bin=int_size/20 13 | 0.00151824951171875 0.0013670921325683594 0.0012309551239013672 0.0013365745544433594 0.0011897087097167969 0.0011742115020751953 0.0010654926300048828 0.0008831024169921875 0.0005548000335693359 0.0004868507385253906 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF631HEX/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF631HEX/interval_runtime_table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF631HEX/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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900000 1000000 2 | pyBW exact 3 | 12.580040693283081 25.209125757217407 37.79087972640991 50.338520526885986 62.932780504226685 75.55070424079895 88.14873886108398 100.75489902496338 113.3356614112854 125.89942264556885 4 | pyBW app. 5 | 12.580682039260864 25.17516279220581 37.7394380569458 50.337392807006836 62.96270489692688 75.5359423160553 88.19380927085876 100.71778845787048 113.36481475830078 125.93784832954407 6 | pyBG exact 7 | 0.016402482986450195 0.03306460380554199 0.049239158630371094 0.06543421745300293 0.08159136772155762 0.09695100784301758 0.11383557319641113 0.12971138954162598 0.1453263759613037 0.16307520866394043 8 | pyBG app. bin=100 9 | 0.005843639373779297 0.011561870574951172 0.01724386215209961 0.023023128509521484 0.02868485450744629 0.035382747650146484 0.04020977020263672 0.046196699142456055 0.05214643478393555 0.05769014358520508 10 | pyBG app. bin=50 11 | 0.008955955505371094 0.01776885986328125 0.026627540588378906 0.035494327545166016 0.04434347152709961 0.05312967300415039 0.06195425987243652 0.07072710990905762 0.07950115203857422 0.0885019302368164 12 | pyBG app. bin=25 13 | 0.010907411575317383 0.021732568740844727 0.032659053802490234 0.04342246055603027 0.054596662521362305 0.06499242782592773 0.07611751556396484 0.08762145042419434 0.09758353233337402 0.1082758903503418 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF643WMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF643WMY/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF643WMY/interval_run_time.png: -------------------------------------------------------------------------------- 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0.004869937896728516 0.007574558258056641 0.02851247787475586 0.054808855056762695 8 | pyBG app. bin=int_size/5 9 | 0.0006480216979980469 0.0006587505340576172 0.0006151199340820312 0.0006117820739746094 0.0005917549133300781 0.0005266666412353516 0.0004520416259765625 0.0003833770751953125 0.0002899169921875 0.00027632713317871094 10 | pyBG app. bin=int_size/10 11 | 0.0011243820190429688 0.0010836124420166016 0.0009920597076416016 0.0009016990661621094 0.0008883476257324219 0.0007927417755126953 0.0006773471832275391 0.0005590915679931641 0.0003745555877685547 0.0003402233123779297 12 | pyBG app. bin=int_size/20 13 | 0.001462697982788086 0.0013194084167480469 0.0011036396026611328 0.0012478828430175781 0.0011706352233886719 0.0010366439819335938 0.0009410381317138672 0.0007944107055664062 0.0005223751068115234 0.0004642009735107422 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF643WMY/interval_runtime_table.png: 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48.05230951309204 54.1609411239624 60.06488633155823 6 | pyBG exact 7 | 0.020334959030151367 0.04067111015319824 0.06090140342712402 0.08114194869995117 0.10074305534362793 0.12024378776550293 0.14102482795715332 0.1604905128479004 0.18002724647521973 0.20061516761779785 8 | pyBG app. bin=100 9 | 0.005719661712646484 0.011370420455932617 0.01684093475341797 0.022473812103271484 0.028111934661865234 0.033879995346069336 0.039764404296875 0.04472661018371582 0.05035972595214844 0.055884361267089844 10 | pyBG app. bin=50 11 | 0.009285688400268555 0.01847672462463379 0.027616262435913086 0.0367741584777832 0.04596376419067383 0.055124521255493164 0.06456208229064941 0.07369303703308105 0.08253979682922363 0.09179258346557617 12 | pyBG app. bin=25 13 | 0.011748075485229492 0.02344799041748047 0.03499627113342285 0.04661965370178223 0.058365821838378906 0.07003092765808105 0.08139967918395996 0.09306955337524414 0.10505867004394531 0.11686396598815918 14 | 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10000 50000 100000 2 | pyBW exact 3 | 0.6246099472045898 0.6259829998016357 0.6281213760375977 0.6310830116271973 0.6340129375457764 0.6462161540985107 0.6663029193878174 0.7043018341064453 0.9903514385223389 1.3379778861999512 4 | pyBW app. 5 | 0.6246316432952881 0.6262948513031006 1.469404697418213 1.4691615104675293 1.4701428413391113 1.4800758361816406 1.4809749126434326 1.4613862037658691 1.4692037105560303 1.4490633010864258 6 | pyBG exact 7 | 0.0016674995422363281 0.0026509761810302734 0.004145383834838867 0.0055696964263916016 0.006930351257324219 0.014796257019042969 0.02644181251525879 0.0464632511138916 0.15866446495056152 0.2522876262664795 8 | pyBG app. bin=int_size/5 9 | 0.002997159957885742 0.0016026496887207031 0.0005664825439453125 0.0005521774291992188 0.0005564689636230469 0.0005438327789306641 0.0005013942718505859 0.00048422813415527344 0.0004241466522216797 0.0004012584686279297 10 | pyBG app. bin=int_size/10 11 | 0.00424647331237793 0.002691984176635742 0.0014913082122802734 0.0006566047668457031 0.000659942626953125 0.0006616115570068359 0.0006206035614013672 0.0006077289581298828 0.0005784034729003906 0.0005605220794677734 12 | pyBG app. bin=int_size/20 13 | 0.005613803863525391 0.0042231082916259766 0.0029942989349365234 0.0010492801666259766 0.001062154769897461 0.0009877681732177734 0.0009865760803222656 0.0008940696716308594 0.0008215904235839844 0.0008244514465332031 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF726XVA/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF726XVA/interval_runtime_table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF726XVA/pyBG_app._bin=int_size10_table.png: 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/graphs/v3_graphs/ENCFF726XVA/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 6.284644603729248 12.544445276260376 18.83427667617798 25.140806674957275 31.420111894607544 37.71089196205139 44.094207525253296 50.15883255004883 56.5121853351593 62.83603000640869 4 | pyBW app. 5 | 14.80697226524353 29.324021100997925 43.97670578956604 58.71601057052612 73.33260536193848 88.0549168586731 102.80879616737366 117.32295322418213 131.99406909942627 146.8298578262329 6 | pyBG exact 7 | 0.040259599685668945 0.0814354419708252 0.12149953842163086 0.1611320972442627 0.20026278495788574 0.2399134635925293 0.2803483009338379 0.3209950923919678 0.360398530960083 0.40038228034973145 8 | pyBG app. bin=100 9 | 0.004749774932861328 0.009314537048339844 0.01383519172668457 0.018337011337280273 0.02290034294128418 0.028301715850830078 0.03210091590881348 0.03675198554992676 0.041132211685180664 0.0459139347076416 10 | pyBG app. bin=50 11 | 0.005709409713745117 0.011445760726928711 0.01689934730529785 0.02240276336669922 0.027998924255371094 0.03362107276916504 0.039101362228393555 0.04475903511047363 0.05024838447570801 0.05595660209655762 12 | pyBG app. bin=25 13 | 0.009394168853759766 0.01858234405517578 0.027914762496948242 0.03707575798034668 0.04672646522521973 0.055513620376586914 0.06501603126525879 0.07454609870910645 0.08323192596435547 0.09235930442810059 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF770CQD/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF770CQD/interval_error.png -------------------------------------------------------------------------------- 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0.0015306472778320312 0.0019271373748779297 0.002244234085083008 0.0024690628051757812 0.0026667118072509766 0.003747224807739258 0.005416154861450195 0.008528947830200195 0.03310894966125488 0.0639944076538086 8 | pyBG app. bin=int_size/5 9 | 0.0006859302520751953 0.0006661415100097656 0.0006136894226074219 0.0006060600280761719 0.0005936622619628906 0.0005214214324951172 0.0004432201385498047 0.00038361549377441406 0.00028777122497558594 0.0002753734588623047 10 | pyBG app. bin=int_size/10 11 | 0.001131296157836914 0.0009768009185791016 0.000995635986328125 0.0009083747863769531 0.0008909702301025391 0.0007948875427246094 0.0006830692291259766 0.0005524158477783203 0.0003764629364013672 0.0003330707550048828 12 | pyBG app. bin=int_size/20 13 | 0.0014736652374267578 0.0013289451599121094 0.0010988712310791016 0.0012493133544921875 0.0011775493621826172 0.0010251998901367188 0.0009479522705078125 0.0008332729339599609 0.0005228519439697266 0.0004646778106689453 14 | 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56.481964111328125 4 | pyBW app. 5 | 5.656538963317871 11.294918537139893 16.943374156951904 22.60336399078369 28.266626596450806 33.928849935531616 39.65944480895996 45.225255727767944 50.94544196128845 56.51733422279358 6 | pyBG exact 7 | 0.02077174186706543 0.04171395301818848 0.06259655952453613 0.0831596851348877 0.10331082344055176 0.12322473526000977 0.14418864250183105 0.16523385047912598 0.185089111328125 0.2056741714477539 8 | pyBG app. bin=100 9 | 0.005803346633911133 0.011366844177246094 0.017026662826538086 0.022515058517456055 0.028101444244384766 0.033983469009399414 0.03982853889465332 0.044881582260131836 0.050559282302856445 0.05621480941772461 10 | pyBG app. bin=50 11 | 0.009369850158691406 0.018709659576416016 0.02788996696472168 0.037183284759521484 0.046337127685546875 0.05565929412841797 0.06580257415771484 0.07413363456726074 0.08357763290405273 0.09276127815246582 12 | pyBG app. bin=25 13 | 0.012357950210571289 0.023633956909179688 0.035307884216308594 0.04702425003051758 0.058678627014160156 0.0705418586730957 0.08626151084899902 0.09365296363830566 0.1054232120513916 0.1171565055847168 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF847JMY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF847JMY/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF847JMY/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF847JMY/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF847JMY/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2500 5000 10000 50000 100000 2 | pyBW exact 3 | 0.6006636619567871 0.6032867431640625 0.6098928451538086 0.614006519317627 0.6188192367553711 0.6422786712646484 0.6747848987579346 0.7411973476409912 1.2660167217254639 1.9017479419708252 4 | pyBW app. 5 | 0.6029081344604492 0.6075012683868408 0.6136155128479004 0.617774486541748 0.6240749359130859 1.167543888092041 1.1720502376556396 1.0644137859344482 1.1371779441833496 1.141540765762329 6 | pyBG exact 7 | 0.0011076927185058594 0.0014638900756835938 0.0018317699432373047 0.0019981861114501953 0.0021708011627197266 0.0028378963470458984 0.0037841796875 0.0056149959564208984 0.019757986068725586 0.03714275360107422 8 | pyBG app. bin=int_size/5 9 | 0.0007336139678955078 0.0007483959197998047 0.0006682872772216797 0.0006690025329589844 0.0006136894226074219 0.0005443096160888672 0.0004725456237792969 0.00041365623474121094 0.0002970695495605469 0.0002799034118652344 10 | pyBG app. bin=int_size/10 11 | 0.0011746883392333984 0.0010600090026855469 0.0009639263153076172 0.0010309219360351562 0.0009350776672363281 0.000827789306640625 0.0007231235504150391 0.0005998611450195312 0.00039315223693847656 0.0003447532653808594 12 | pyBG app. bin=int_size/20 13 | 0.0015034675598144531 0.0013675689697265625 0.0011708736419677734 0.0011625289916992188 0.0011827945709228516 0.0010917186737060547 0.0010275840759277344 0.0008437633514404297 0.0005524158477783203 0.00048422813415527344 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF847JMY/interval_runtime_table.png: -------------------------------------------------------------------------------- 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0.11623716354370117 0.132765531539917 0.1483139991760254 0.16532373428344727 8 | pyBG app. bin=100 9 | 0.005798816680908203 0.011555671691894531 0.017220735549926758 0.022957324981689453 0.028910398483276367 0.035147905349731445 0.04008293151855469 0.04602503776550293 0.051436662673950195 0.0574951171875 10 | pyBG app. bin=50 11 | 0.008846759796142578 0.0176236629486084 0.026469945907592773 0.03523445129394531 0.04403352737426758 0.052823543548583984 0.06149458885192871 0.07012033462524414 0.07885456085205078 0.0877838134765625 12 | pyBG app. bin=25 13 | 0.010844707489013672 0.021660327911376953 0.03252911567687988 0.04325723648071289 0.05466604232788086 0.0648198127746582 0.0757906436920166 0.08725333213806152 0.09723973274230957 0.10792684555053711 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/interval_error.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF877IHY/interval_error.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/interval_run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF877IHY/interval_run_time.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/interval_runtime_results.txt: -------------------------------------------------------------------------------- 1 | 100 250 500 750 1000 2500 5000 10000 50000 100000 2 | pyBW exact 3 | 0.6268537044525146 0.6278090476989746 0.6296887397766113 0.6329269409179688 0.6342718601226807 0.6430292129516602 0.6554133892059326 0.6811361312866211 0.8759102821350098 1.1133439540863037 4 | pyBW app. 5 | 0.6280555725097656 0.6293683052062988 1.3786118030548096 1.3768141269683838 1.3779077529907227 1.4124224185943604 1.41341233253479 1.4418690204620361 1.4520659446716309 1.4272305965423584 6 | pyBG exact 7 | 0.0016429424285888672 0.002595186233520508 0.004108905792236328 0.005468130111694336 0.006813526153564453 0.014550209045410156 0.0264737606048584 0.047899723052978516 0.1788034439086914 0.293565034866333 8 | pyBG app. bin=int_size/5 9 | 0.0034055709838867188 0.0005710124969482422 0.0009107589721679688 0.0005917549133300781 0.0005805492401123047 0.0005209445953369141 0.0004897117614746094 0.00046181678771972656 0.0003979206085205078 0.0004048347473144531 10 | pyBG app. bin=int_size/10 11 | 0.004667520523071289 0.003092050552368164 0.0006251335144042969 0.0006492137908935547 0.0006461143493652344 0.0006306171417236328 0.0006072521209716797 0.0005848407745361328 0.0005247592926025391 0.0005238056182861328 12 | pyBG app. bin=int_size/20 13 | 0.0058879852294921875 0.004643678665161133 0.001031637191772461 0.0010259151458740234 0.0009970664978027344 0.0010440349578857422 0.0009267330169677734 0.0008947849273681641 0.0007600784301757812 0.0007681846618652344 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/interval_runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF877IHY/interval_runtime_table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/pyBG_app._bin=int_size10_table.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/pyBW_app._table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF877IHY/pyBW_app._table.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/run_time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/ENCFF877IHY/run_time.png -------------------------------------------------------------------------------- /graphs/v3_graphs/ENCFF877IHY/run_time_results.txt: -------------------------------------------------------------------------------- 1 | 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 2 | pyBW exact 3 | 6.306516885757446 12.601510763168335 18.890897035598755 25.168465614318848 31.43573307991028 37.72267174720764 44.108246088027954 50.37564277648926 56.76311540603638 62.97527027130127 4 | pyBW app. 5 | 13.918392658233643 27.505555629730225 41.23606085777283 54.97918224334717 68.70012426376343 82.4586193561554 96.252277135849 109.98207807540894 123.83403396606445 137.5205569267273 6 | pyBG exact 7 | 0.03953146934509277 0.07938551902770996 0.11873149871826172 0.15804386138916016 0.19751763343811035 0.23637914657592773 0.275407075881958 0.3146188259124756 0.3557741641998291 0.3941469192504883 8 | pyBG app. bin=100 9 | 0.004811525344848633 0.009353160858154297 0.013852357864379883 0.018378257751464844 0.022963285446166992 0.027860641479492188 0.032184600830078125 0.03681659698486328 0.04121136665344238 0.045685768127441406 10 | pyBG app. bin=50 11 | 0.005805015563964844 0.011665582656860352 0.017185688018798828 0.022919893264770508 0.028559207916259766 0.03429126739501953 0.04002785682678223 0.0456697940826416 0.051299333572387695 0.05713820457458496 12 | pyBG app. bin=25 13 | 0.011980056762695312 0.015946626663208008 0.02382659912109375 0.030863046646118164 0.03842496871948242 0.04633140563964844 0.05389833450317383 0.061504364013671875 0.06947183609008789 0.07664656639099121 14 | -------------------------------------------------------------------------------- /graphs/v3_graphs/runtime_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/graphs/v3_graphs/runtime_table.png -------------------------------------------------------------------------------- /pyBedGraph/__init__.py: -------------------------------------------------------------------------------- 1 | from .include_missing_bp import * 2 | from .ignore_missing_bp import * 3 | from .Chrom_Data import Chrom_Data 4 | from .Chrom_Data_Complete import Chrom_Data_Complete 5 | from .BedGraph import BedGraph 6 | 7 | ''' 8 | NUM_TESTS = 10000 9 | 10 | MIN_INTERVAL_SIZE = 100 11 | MAX_INTERVAL_SIZE = 1000 12 | INTERVAL_STEP = 300 13 | 14 | MIN_BIN_SIZE = 50 15 | MAX_BIN_SIZE = 500 16 | BIN_STEP = 100 17 | # List of arguments (required) 18 | # arg1 - bedgraph file 19 | # arg2 - name of chromosome 20 | # arg3 - 'b' for benchmark, 'r' to run 21 | 22 | # arg4 - file containing intervals to search for 23 | # or 24 | # arg4 - bigWig file to benchmark pyBigWig 25 | if len(sys.argv) != 3: 26 | print("List of required arguments:\n" 27 | "arg1 - bedgraph file\n" 28 | "arg2 - name of chromosome to search in\n" 29 | "arg4 - bigWig file to benchmark pyBigWig | file containing intervals to search for\n") 30 | exit(-1) 31 | 32 | genome = Genome(sys.argv[1], sys.argv[2]) 33 | 34 | bin_size = 512 35 | while True: 36 | 37 | action = input("Enter 'b' for benchmarking pyBigWig | 's' to search for intervals: ") 38 | 39 | if action == 'b': 40 | bigWig_file = input("Enter a file to benchmark pyBigWig: ") 41 | Benchmark(genome.chromosomes[sys.argv[2]], NUM_TESTS, bin_size, 500, sys.argv[4], 'exact') 42 | 43 | elif action == 's': 44 | interval_file = input("Enter a file that contains intervals to search for: ") 45 | stat = input("Enter the statistic to search for") 46 | with open(interval_file) as in_file: 47 | for line in in_file: 48 | interval = line.split("") 49 | 50 | if len(interval) != 2: 51 | print(f"{sys.argv[4]} has incorrect formatting. It must be in the format:\n" 52 | "start_of_interval1 end_of_interval1\n" 53 | "start_of_interval2 end_of_interval2\n" 54 | "...") 55 | break 56 | 57 | genome.stats() 58 | 59 | else: 60 | print(f"{action} is not a valid action") 61 | 62 | if input('enter y to run again: ') != 'y': 63 | break 64 | 65 | bin_size = int(input('enter maximum bin size: ')) 66 | ''' 67 | -------------------------------------------------------------------------------- /pyBedGraph/util.pyx: -------------------------------------------------------------------------------- 1 | def fill_value_array(unsigned int[:] start_list, unsigned int[:] end_list, 2 | double[:] value_map, double[:] value_list): 3 | assert tuple(start_list.shape) == tuple(end_list.shape) 4 | 5 | cdef size_t size = start_list.size, i, start, end 6 | 7 | for i in range(size): 8 | start = start_list[i] 9 | end = end_list[i] 10 | value_list[start:end] = value_map[i] 11 | 12 | def fill_index_array(unsigned int[:] start_list, unsigned int[:] end_list, 13 | double[:] value_map, int[:] index_list): 14 | assert tuple(start_list.shape) == tuple(end_list.shape) 15 | 16 | cdef size_t size = start_list.size, i, start, end 17 | 18 | for i in range(size): 19 | start = start_list[i] 20 | end = end_list[i] 21 | index_list[start:end]= i 22 | 23 | cpdef get_bin_value(double[:] value_map, int[:] index_list, 24 | unsigned int[:] interval_start, unsigned int[:] interval_end, 25 | int start, int end): 26 | 27 | cdef size_t i, value_index 28 | cdef unsigned int numb_value, temp_end, interval_size, numb_intervals = interval_start.size 29 | cdef double total 30 | 31 | total = 0 32 | numb_value = 0 33 | 34 | # get to an interval 35 | while start < index_list.size and index_list[start] == -1 and start < end: 36 | start += 1 37 | 38 | if start == end or start == index_list.size: 39 | return -1 40 | 41 | value_index = index_list[start] 42 | while start < end: 43 | temp_end = interval_end[value_index] 44 | if temp_end > end: 45 | temp_end = end 46 | interval_size = temp_end - start 47 | 48 | total += value_map[value_index] * interval_size 49 | numb_value += interval_size 50 | 51 | value_index += 1 52 | if value_index == numb_intervals: 53 | break 54 | start = interval_start[value_index] 55 | 56 | return total 57 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import setuptools 2 | from distutils.extension import Extension 3 | 4 | USE_CYTHON = False 5 | try: 6 | from Cython.Distutils import build_ext 7 | USE_CYTHON = True 8 | except ImportError: 9 | pass 10 | 11 | ext = '.pyx' if USE_CYTHON else '.c' 12 | 13 | extensions = [ 14 | Extension('pyBedGraph.ignore_missing_bp', ['pyBedGraph/ignore_missing_bp' + ext]), 15 | Extension('pyBedGraph.include_missing_bp', ['pyBedGraph/include_missing_bp' + ext]), 16 | Extension('pyBedGraph.util', ['pyBedGraph/util' + ext]), 17 | ] 18 | 19 | if USE_CYTHON: 20 | from Cython.Build import cythonize 21 | extensions = cythonize(extensions, language_level=3) 22 | 23 | NAME = 'pyBedGraph' 24 | VERSION = '0.5.43' 25 | 26 | setuptools.setup( 27 | 28 | name=NAME, 29 | 30 | version=VERSION, 31 | 32 | author="Henry Zhang", 33 | 34 | author_email="henrybzhang.99@gmail.com", 35 | 36 | description="A package for fast operations on 1-dimensional genomic signal tracks", 37 | 38 | long_description=open('README.md').read(), 39 | 40 | long_description_content_type="text/markdown", 41 | 42 | url="https://github.com/TheJacksonLaboratory/pyBedGraph", 43 | 44 | packages=setuptools.find_packages(), 45 | 46 | install_requires=['numpy>=1.16.4'], 47 | 48 | python_requires='>=3.6', 49 | 50 | ext_modules=extensions, 51 | 52 | data_files=[("", ["LICENSE"])], 53 | 54 | classifiers=[ 55 | "Programming Language :: Python :: 3", 56 | "License :: OSI Approved :: MIT License", 57 | "Operating System :: OS Independent", 58 | ], 59 | 60 | ) 61 | -------------------------------------------------------------------------------- /test/default.conf: -------------------------------------------------------------------------------- 1 | [loggers] 2 | keys=root 3 | 4 | [logger_root] 5 | level=DEBUG 6 | handlers=screen,root_file 7 | 8 | [handlers] 9 | keys=screen,root_file 10 | 11 | [handler_root_file] 12 | class=FileHandler 13 | level=DEBUG 14 | formatter=simple 15 | args=('main.log',) 16 | 17 | [handler_screen] 18 | class=StreamHandler 19 | level=INFO 20 | formatter=simple 21 | args=(sys.stdout,) 22 | 23 | [formatters] 24 | keys=simple 25 | 26 | [formatter_simple] 27 | format=%(levelname)s - %(asctime)s - %(name)s:%(filename)s:%(lineno)d - %(message)s 28 | datefmt=%H:%M:%S 29 | -------------------------------------------------------------------------------- /test/make_test_files.py: -------------------------------------------------------------------------------- 1 | import random 2 | 3 | NUMB_TEST_CASES = 5 4 | MAX_CHROM_SIZE = 30 # mouse chr1 5 | 6 | '''with open('test_files/sequential_test_same.bedgraph', 'w') as test: 7 | output = "" 8 | value = 0.1 9 | for i in range(NUMB_TEST_CASES): 10 | start = i * 100 + 1 11 | end = start + 99 12 | output += f"chr1\t{start}\t{end}\t{value}\n" 13 | 14 | test.write(output) 15 | 16 | with open('test_files/sequential_test_ascending.bedgraph', 'w') as test: 17 | output = "" 18 | value = 0.1 19 | for i in range(NUMB_TEST_CASES): 20 | start = i * 100 + 1 21 | end = start + 99 22 | output += f"chr1\t{start}\t{end}\t{round(value * i, 1)}\n" 23 | 24 | test.write(output) 25 | 26 | with open('test_files/skip_test_same.bedgraph', 'w') as test: 27 | output = "" 28 | value = 0.1 29 | for i in range(1, NUMB_TEST_CASES * 2, 200): 30 | start = i * 100 + 1 31 | end = start + 99 32 | output += f"chr1\t{start}\t{end}\t{value}\n" 33 | 34 | test.write(output)''' 35 | 36 | with open('test_files/random_test.bedGraph', 'w') as test: 37 | output = "" 38 | current_index = 0 39 | for i in range(NUMB_TEST_CASES): 40 | start = current_index 41 | end = start + random.randint(1, 5) 42 | current_index = end + random.randint(0, 5) 43 | value = random.random() 44 | value = round(value, 1) 45 | output += f"chr1\t{start}\t{end}\t{value}\n" 46 | 47 | if end > MAX_CHROM_SIZE: 48 | print(f"Cannot create a chromosome above size: {MAX_CHROM_SIZE}") 49 | exit(-1) 50 | 51 | test.write(output) 52 | 53 | with open('test_files/myChrom.sizes', 'w+') as test: 54 | test.write(f"chr1\t{MAX_CHROM_SIZE}") 55 | 56 | with open('test_files/test_intervals.txt', 'w+') as test: 57 | output = "" 58 | for i in range(NUMB_TEST_CASES): 59 | interval_size = random.randint(1, 5) 60 | start = random.randint(0, MAX_CHROM_SIZE - interval_size) 61 | end = start + interval_size 62 | output += f"chr1\t{start}\t{end}\n" 63 | 64 | test.write(output) 65 | -------------------------------------------------------------------------------- /test/run_tests.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | pip3 install pyBigWig 4 | 5 | echo "Running simple tests ..." 6 | python3 test.py 7 | 8 | if [ $? -ne 0 ]; then 9 | exit 1 10 | fi 11 | 12 | if [ -f "test_files/ENCFF376VCU.bigWig" ] && [ -f "test_files/ENCFF376VCU.bedGraph" ]; then 13 | echo "Running extensive tests ..." 14 | python3 extensive_test.py 15 | if [ $? -ne 0 ]; then 16 | exit 1 17 | fi 18 | 19 | fi 20 | -------------------------------------------------------------------------------- /test/test_files/custom_intervals.txt: -------------------------------------------------------------------------------- 1 | chr1 869360 870361 2 | -------------------------------------------------------------------------------- /test/test_files/mm10.chrom.sizes: -------------------------------------------------------------------------------- 1 | chr1 195471971 2 | chr2 182113224 3 | chrX 171031299 4 | chr3 160039680 5 | chr4 156508116 6 | chr5 151834684 7 | chr6 149736546 8 | chr7 145441459 9 | chr10 130694993 10 | chr8 129401213 11 | chr14 124902244 12 | chr9 124595110 13 | chr11 122082543 14 | chr13 120421639 15 | chr12 120129022 16 | chr15 104043685 17 | chr16 98207768 18 | chr17 94987271 19 | chrY 91744698 20 | chr18 90702639 21 | chr19 61431566 22 | chr5_JH584299_random 953012 23 | chrX_GL456233_random 336933 24 | chrY_JH584301_random 259875 25 | chr1_GL456211_random 241735 26 | chr4_GL456350_random 227966 27 | chr4_JH584293_random 207968 28 | chr1_GL456221_random 206961 29 | chr5_JH584297_random 205776 30 | chr5_JH584296_random 199368 31 | chr5_GL456354_random 195993 32 | chr4_JH584294_random 191905 33 | chr5_JH584298_random 184189 34 | chrY_JH584300_random 182347 35 | chr7_GL456219_random 175968 36 | chr1_GL456210_random 169725 37 | chrY_JH584303_random 158099 38 | chrY_JH584302_random 155838 39 | chr1_GL456212_random 153618 40 | chrUn_JH584304 114452 41 | chrUn_GL456379 72385 42 | chr4_GL456216_random 66673 43 | chrUn_GL456393 55711 44 | chrUn_GL456366 47073 45 | chrUn_GL456367 42057 46 | chrUn_GL456239 40056 47 | chr1_GL456213_random 39340 48 | chrUn_GL456383 38659 49 | chrUn_GL456385 35240 50 | chrUn_GL456360 31704 51 | chrUn_GL456378 31602 52 | chrUn_GL456389 28772 53 | chrUn_GL456372 28664 54 | chrUn_GL456370 26764 55 | chrUn_GL456381 25871 56 | chrUn_GL456387 24685 57 | chrUn_GL456390 24668 58 | chrUn_GL456394 24323 59 | chrUn_GL456392 23629 60 | chrUn_GL456382 23158 61 | chrUn_GL456359 22974 62 | chrUn_GL456396 21240 63 | chrUn_GL456368 20208 64 | chrM 16299 65 | chr4_JH584292_random 14945 66 | chr4_JH584295_random 1976 67 | -------------------------------------------------------------------------------- /test/test_files/myChrom.sizes: -------------------------------------------------------------------------------- 1 | chr1 30 -------------------------------------------------------------------------------- /test/test_files/random_test.bedGraph: -------------------------------------------------------------------------------- 1 | chr1 0 2 0.7 2 | chr1 2 5 0.9 3 | chr1 8 9 0.1 4 | chr1 13 14 0.9 5 | chr1 19 20 0.4 6 | chr1 29 30 1 7 | -------------------------------------------------------------------------------- /test/test_files/random_test.bigWig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheJacksonLaboratory/pyBedGraph/4c5db67f7b239c7653675dfc8385544abac49c1c/test/test_files/random_test.bigWig -------------------------------------------------------------------------------- /test/test_files/test_intervals.txt: -------------------------------------------------------------------------------- 1 | chr1 24 26 2 | chr1 12 15 3 | chr1 8 12 4 | chr1 9 10 5 | chr1 0 5 6 | chr1 0 30 7 | --------------------------------------------------------------------------------