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| MIT License | ||
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| Copyright (c) 2021 JiamanZhang | ||
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| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
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| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
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| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
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| # Lab_Annotate_enhancer_type | ||
| # -- codes to fit Annotate_enhancer_type models | ||
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| ## 1. System requirements | ||
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| - python 2.7 | ||
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| ## 2. Installation guide | ||
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| No installation needed. Directly run work.sh | ||
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| ## 3. Demo | ||
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| ### Input: | ||
| - chr20.H3K27ac.ROSE.test.txt | ||
| - chr20.PEI.Enhancer.data.test.txt | ||
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| ### Output: | ||
| - chr20.PEI.Enhancer.type.annotate.txt | ||
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| ## 4. Instructions for use | ||
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| Change the hard-coded paths in the code to your own paths where you place the input and output files |
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Lab_Annotate_Enhancer_type/codes/get.Enhancer.type.of.PEI.py
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| import sys | ||
| import os | ||
| def main(): | ||
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| inp = sys.argv[1] | ||
| f1 = open(inp,'r') | ||
| Ehancer_dict = {} | ||
| for line1 in f1: | ||
| info1 = line1.strip().split('\t') | ||
| if info1[0] == 'REGION_ID': | ||
| continue | ||
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| chrname = info1[1].replace('chr','') | ||
| start = int(info1[2]) | ||
| end = int(info1[3]) | ||
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| tname = info1[-1] | ||
| try: | ||
| Ehancer_dict[chrname].append([chrname,start,end,tname]) | ||
| except KeyError as reason: | ||
| Ehancer_dict[chrname] = [] | ||
| Ehancer_dict[chrname].append([chrname,start,end,tname]) | ||
| f1.close() | ||
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| oup = sys.argv[3] | ||
| out = open(oup,'w') | ||
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| inp = sys.argv[2] | ||
| f1 = open(inp,'r') | ||
| for line1 in f1: | ||
| info1 = line1.strip().split('\t') | ||
| if info1[0] == 'chrname': | ||
| continue | ||
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| chrname = info1[0] | ||
| Estart = int(info1[1]) | ||
| Eend = Estart + 5000 | ||
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| RE='NA' | ||
| SE='NA' | ||
| for a_list in Ehancer_dict[chrname]: | ||
| start = a_list[1] | ||
| end = a_list[2] | ||
| tname = a_list[3] | ||
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| ovlap = min(Eend,end) - max(start,Estart) | ||
| if ovlap <= 0: | ||
| continue | ||
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| if tname == '0': | ||
| if ovlap >= 1: | ||
| RE='RE' | ||
| REinfo = '_'.join([str(i) for i in a_list]) | ||
| elif tname == '1': | ||
| if ovlap >=2500: | ||
| SE='SE' | ||
| SEinfo = '_'.join([str(i) for i in a_list]) | ||
| else: | ||
| print 'wrong' | ||
| sys.exit(0) | ||
|
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| if SE =='SE': | ||
| Ehancer_name = 'SE' | ||
| posinfo = SEinfo | ||
| elif RE == 'RE': | ||
| Ehancer_name = 'RE' | ||
| posinfo = REinfo | ||
| else: | ||
| Ehancer_name = 'inactive' | ||
| posinfo = 'NA' | ||
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| info_list = info1+[posinfo,Ehancer_name] | ||
| out.write('{0}\n'.format('\t'.join(map(str,info_list)))) | ||
| f1.close() | ||
| out.close() | ||
|
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| if __name__ == '__main__': | ||
| main() |
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| python get.Enhancer.type.of.PEI.py chr20.H3K27ac.ROSE.test.txt chr20.PEI.Enhancer.data.test.txt chr20.PEI.Enhancer.type.annotate.txt |
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Lab_Annotate_Enhancer_type/demos/Annotate.Enhancer.type/input/chr20.H3K27ac.ROSE.test.txt
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...nnotate_Enhancer_type/demos/Annotate.Enhancer.type/input/chr20.PEI.Enhancer.data.test.txt
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| chrname Enhancer_start Promoter_start gene_ID | ||
| 20 9865000 10030000 ENSGALG00000006267 | ||
| 20 9920000 10030000 ENSGALG00000006267 | ||
| 20 9985000 10105000 ENSGALG00000006522 | ||
| 20 9990000 10220000 ENSGALG00000041732 | ||
| 20 10000000 10240000 ENSGALG00000006630 | ||
| 20 10015000 10035000 ENSGALG00000006211 | ||
| 20 10015000 10105000 ENSGALG00000006522 | ||
| 20 10045000 10240000 ENSGALG00000006630 | ||
| 20 10050000 10065000 ENSGALG00000030291 | ||
| 20 10050000 10220000 ENSGALG00000041732 | ||
| 20 10050000 10065000 ENSGALG00000043015 | ||
| 20 10075000 10220000 ENSGALG00000041732 | ||
| 20 10120000 10220000 ENSGALG00000041732 | ||
| 20 10125000 10145000 ENSGALG00000006604 | ||
| 20 10130000 10110000 ENSGALG00000006568 | ||
| 20 10145000 10220000 ENSGALG00000041732 | ||
| 20 10150000 10240000 ENSGALG00000006630 | ||
| 20 10160000 10240000 ENSGALG00000006630 | ||
| 20 10165000 10075000 ENSGALG00000006460 | ||
| 20 10165000 10075000 ENSGALG00000021017 | ||
| 20 10175000 10250000 ENSGALG00000041461 | ||
| 20 10195000 10155000 ENSGALG00000006612 | ||
| 20 10205000 10095000 ENSGALG00000006479 | ||
| 20 10205000 10220000 ENSGALG00000041732 | ||
| 20 10210000 10075000 ENSGALG00000006460 | ||
| 20 10210000 10110000 ENSGALG00000006568 | ||
| 20 10210000 10075000 ENSGALG00000021017 | ||
| 20 10215000 10030000 ENSGALG00000006267 | ||
| 20 10215000 10340000 ENSGALG00000006738 | ||
| 20 10220000 10075000 ENSGALG00000006460 | ||
| 20 10220000 10145000 ENSGALG00000006604 | ||
| 20 10220000 10240000 ENSGALG00000006630 | ||
| 20 10220000 10525000 ENSGALG00000006854 | ||
| 20 10220000 10525000 ENSGALG00000006876 | ||
| 20 10220000 10310000 ENSGALG00000020982 | ||
| 20 10220000 10075000 ENSGALG00000021017 | ||
| 20 10240000 10045000 ENSGALG00000006273 | ||
| 20 10240000 10220000 ENSGALG00000041732 | ||
| 20 10245000 10510000 ENSGALG00000006835 | ||
| 20 10260000 10350000 ENSGALG00000006756 | ||
| 20 10260000 10350000 ENSGALG00000047290 | ||
| 20 10265000 10035000 ENSGALG00000006211 | ||
| 20 10275000 10365000 ENSGALG00000006775 | ||
| 20 10275000 10500000 ENSGALG00000051275 | ||
| 20 10280000 10420000 ENSGALG00000006792 | ||
| 20 10285000 10365000 ENSGALG00000006775 | ||
| 20 10285000 10310000 ENSGALG00000020982 | ||
| 20 10290000 10340000 ENSGALG00000006738 | ||
| 20 10290000 10420000 ENSGALG00000006792 | ||
| 20 10300000 10365000 ENSGALG00000006775 | ||
| 20 10305000 10320000 ENSGALG00000006693 | ||
| 20 10310000 10285000 ENSGALG00000006662 | ||
| 20 10310000 10220000 ENSGALG00000041732 | ||
| 20 10315000 10300000 ENSGALG00000006666 | ||
| 20 10315000 10470000 ENSGALG00000006817 | ||
| 20 10325000 10310000 ENSGALG00000020982 | ||
| 20 10345000 10220000 ENSGALG00000041732 | ||
| 20 10350000 10260000 ENSGALG00000006657 | ||
| 20 10350000 10300000 ENSGALG00000006666 | ||
| 20 10365000 10300000 ENSGALG00000006666 | ||
| 20 10365000 10500000 ENSGALG00000051275 | ||
| 20 10385000 10300000 ENSGALG00000006666 | ||
| 20 10385000 10340000 ENSGALG00000006738 | ||
| 20 10385000 10365000 ENSGALG00000006775 | ||
| 20 10400000 10485000 ENSGALG00000054868 | ||
| 20 10405000 10365000 ENSGALG00000006775 | ||
| 20 10415000 10510000 ENSGALG00000006835 | ||
| 20 10420000 10480000 ENSGALG00000031164 | ||
| 20 10425000 10395000 ENSGALG00000006791 | ||
| 20 10445000 10395000 ENSGALG00000006791 | ||
| 20 10450000 10285000 ENSGALG00000006662 | ||
| 20 10460000 10300000 ENSGALG00000006666 | ||
| 20 10460000 10395000 ENSGALG00000006791 | ||
| 20 10475000 10420000 ENSGALG00000006792 | ||
| 20 10480000 10420000 ENSGALG00000006792 | ||
| 20 10480000 10565000 ENSGALG00000041370 | ||
| 20 10485000 10400000 ENSGALG00000006788 | ||
| 20 10490000 10535000 ENSGALG00000023547 | ||
| 20 10490000 10535000 ENSGALG00000036686 | ||
| 20 10495000 10470000 ENSGALG00000006817 | ||
| 20 10495000 10515000 ENSGALG00000006836 | ||
| 20 10495000 10515000 ENSGALG00000006842 | ||
| 20 10495000 10515000 ENSGALG00000006848 | ||
| 20 10500000 10365000 ENSGALG00000006775 | ||
| 20 10515000 10535000 ENSGALG00000023547 | ||
| 20 10515000 10535000 ENSGALG00000036686 | ||
| 20 10520000 10535000 ENSGALG00000023547 | ||
| 20 10520000 10535000 ENSGALG00000036686 | ||
| 20 10525000 10220000 ENSGALG00000041732 | ||
| 20 10535000 10520000 ENSGALG00000052682 | ||
| 20 10540000 10525000 ENSGALG00000006854 | ||
| 20 10540000 10525000 ENSGALG00000006876 | ||
| 20 10545000 10565000 ENSGALG00000041370 | ||
| 20 10550000 10520000 ENSGALG00000052682 | ||
| 20 10555000 10525000 ENSGALG00000006854 | ||
| 20 10555000 10525000 ENSGALG00000006876 | ||
| 20 10560000 10535000 ENSGALG00000023547 | ||
| 20 10560000 10535000 ENSGALG00000036686 | ||
| 20 10565000 10480000 ENSGALG00000031164 | ||
| 20 10580000 10515000 ENSGALG00000006836 | ||
| 20 10580000 10515000 ENSGALG00000006842 | ||
| 20 10580000 10515000 ENSGALG00000006848 | ||
| 20 10580000 10535000 ENSGALG00000023547 | ||
| 20 10580000 10535000 ENSGALG00000036686 | ||
| 20 10600000 10565000 ENSGALG00000041370 | ||
| 20 10600000 10575000 ENSGALG00000042199 | ||
| 20 10625000 10865000 ENSGALG00000007439 | ||
| 20 10635000 10760000 ENSGALG00000006974 | ||
| 20 10635000 10680000 ENSGALG00000007211 | ||
| 20 10635000 10535000 ENSGALG00000023547 | ||
| 20 10635000 10535000 ENSGALG00000036686 | ||
| 20 10650000 10680000 ENSGALG00000007211 | ||
| 20 10655000 10680000 ENSGALG00000007211 | ||
| 20 10655000 10890000 ENSGALG00000007447 | ||
| 20 10655000 10890000 ENSGALG00000007462 | ||
| 20 10665000 10680000 ENSGALG00000007211 | ||
| 20 10685000 10730000 ENSGALG00000020939 | ||
| 20 10700000 10620000 ENSGALG00000007009 | ||
| 20 10700000 10620000 ENSGALG00000007015 | ||
| 20 10705000 10575000 ENSGALG00000042199 | ||
| 20 10710000 10620000 ENSGALG00000007009 | ||
| 20 10710000 10620000 ENSGALG00000007015 | ||
| 20 10725000 10620000 ENSGALG00000007009 | ||
| 20 10725000 10620000 ENSGALG00000007015 | ||
| 20 10740000 10865000 ENSGALG00000007439 | ||
| 20 10760000 10865000 ENSGALG00000007439 | ||
| 20 10765000 10865000 ENSGALG00000007439 | ||
| 20 10765000 10855000 ENSGALG00000049068 | ||
| 20 10770000 10885000 ENSGALG00000051266 | ||
| 20 10775000 10760000 ENSGALG00000006974 | ||
| 20 10775000 10865000 ENSGALG00000007439 | ||
| 20 10775000 10885000 ENSGALG00000051266 | ||
| 20 10780000 10815000 ENSGALG00000040880 | ||
| 20 10785000 10815000 ENSGALG00000040880 | ||
| 20 10785000 10885000 ENSGALG00000051266 | ||
| 20 10795000 10855000 ENSGALG00000049068 | ||
| 20 10845000 10750000 ENSGALG00000049958 | ||
| 20 10850000 10760000 ENSGALG00000006974 | ||
| 20 10850000 10815000 ENSGALG00000040880 | ||
| 20 10865000 10760000 ENSGALG00000006974 | ||
| 20 10870000 10750000 ENSGALG00000049958 | ||
| 20 10890000 11045000 ENSGALG00000030859 | ||
| 20 10950000 11045000 ENSGALG00000030859 | ||
| 20 11035000 10910000 ENSGALG00000007477 | ||
| 20 11045000 10890000 ENSGALG00000007447 | ||
| 20 11045000 10890000 ENSGALG00000007462 | ||
| 20 11070000 11045000 ENSGALG00000030859 | ||
| 20 11085000 11155000 ENSGALG00000007543 | ||
| 20 11085000 11230000 ENSGALG00000007554 | ||
| 20 11090000 11155000 ENSGALG00000007543 | ||
| 20 11090000 11230000 ENSGALG00000007554 | ||
| 20 11110000 11155000 ENSGALG00000007543 | ||
| 20 11125000 11225000 ENSGALG00000007575 | ||
| 20 11130000 11155000 ENSGALG00000007543 | ||
| 20 11140000 11045000 ENSGALG00000030859 | ||
| 20 11155000 11085000 ENSGALG00000007541 | ||
| 20 11155000 11210000 ENSGALG00000007549 | ||
| 20 11160000 11085000 ENSGALG00000007541 | ||
| 20 11175000 11045000 ENSGALG00000030859 | ||
| 20 11180000 11085000 ENSGALG00000007541 | ||
| 20 11185000 11085000 ENSGALG00000007541 | ||
| 20 11210000 11155000 ENSGALG00000007543 | ||
| 20 11230000 11085000 ENSGALG00000007541 | ||
| 20 11280000 11560000 ENSGALG00000007636 | ||
| 20 11300000 11495000 ENSGALG00000037780 | ||
| 20 11330000 11300000 ENSGALG00000027484 | ||
| 20 11345000 11300000 ENSGALG00000027484 | ||
| 20 11345000 11495000 ENSGALG00000037780 | ||
| 20 11350000 11300000 ENSGALG00000027484 | ||
| 20 11360000 11300000 ENSGALG00000027484 | ||
| 20 11360000 11495000 ENSGALG00000037780 | ||
| 20 11370000 11560000 ENSGALG00000007636 | ||
| 20 11375000 11495000 ENSGALG00000037780 | ||
| 20 11380000 11495000 ENSGALG00000037780 | ||
| 20 11385000 11495000 ENSGALG00000037780 | ||
| 20 11390000 11300000 ENSGALG00000027484 | ||
| 20 11390000 11495000 ENSGALG00000037780 | ||
| 20 11430000 11560000 ENSGALG00000007636 | ||
| 20 11435000 11300000 ENSGALG00000027484 | ||
| 20 11440000 11560000 ENSGALG00000007636 | ||
| 20 11440000 11300000 ENSGALG00000027484 | ||
| 20 11450000 11560000 ENSGALG00000007636 | ||
| 20 11490000 11300000 ENSGALG00000027484 | ||
| 20 11495000 11300000 ENSGALG00000027484 | ||
| 20 11510000 11560000 ENSGALG00000007636 | ||
| 20 11550000 11300000 ENSGALG00000027484 | ||
| 20 11565000 11300000 ENSGALG00000027484 | ||
| 20 11605000 11625000 ENSGALG00000026081 | ||
| 20 11665000 11680000 ENSGALG00000007668 | ||
| 20 11735000 11645000 ENSGALG00000007653 | ||
| 20 11735000 11680000 ENSGALG00000007668 | ||
| 20 11785000 11945000 ENSGALG00000007690 | ||
| 20 12005000 11990000 ENSGALG00000007709 | ||
| 20 12035000 12065000 ENSGALG00000027260 | ||
| 20 12105000 12285000 ENSGALG00000007786 | ||
| 20 12240000 12065000 ENSGALG00000027260 | ||
| 20 12285000 12105000 ENSGALG00000030821 | ||
| 20 12295000 12380000 ENSGALG00000007796 | ||
| 20 12350000 12335000 ENSGALG00000007792 | ||
| 20 12355000 12335000 ENSGALG00000007792 | ||
| 20 12365000 12520000 ENSGALG00000040546 | ||
| 20 12385000 12530000 ENSGALG00000040886 | ||
| 20 12405000 12520000 ENSGALG00000040546 | ||
| 20 12420000 12520000 ENSGALG00000040546 | ||
| 20 12425000 12520000 ENSGALG00000040546 | ||
| 20 12435000 12520000 ENSGALG00000040546 | ||
| 20 12545000 12760000 ENSGALG00000007809 | ||
| 20 12715000 12555000 ENSGALG00000032352 | ||
| 20 12725000 12760000 ENSGALG00000007809 | ||
| 20 12750000 12555000 ENSGALG00000032352 | ||
| 20 12820000 12760000 ENSGALG00000007809 | ||
| 20 12955000 12530000 ENSGALG00000040886 | ||
| 20 12970000 12555000 ENSGALG00000032352 | ||
| 20 12980000 12760000 ENSGALG00000007809 | ||
| 20 12980000 12520000 ENSGALG00000040546 | ||
| 20 13000000 13085000 ENSGALG00000041365 | ||
| 20 13055000 13085000 ENSGALG00000041365 | ||
| 20 13070000 12990000 ENSGALG00000038858 | ||
| 20 13070000 13085000 ENSGALG00000041365 | ||
| 20 13200000 13170000 ENSGALG00000007963 | ||
| 20 13245000 13170000 ENSGALG00000007963 | ||
| 20 13265000 13360000 ENSGALG00000007980 | ||
| 20 13275000 13400000 ENSGALG00000007989 | ||
| 20 13290000 13360000 ENSGALG00000007980 | ||
| 20 13305000 13360000 ENSGALG00000007980 | ||
| 20 13580000 13735000 ENSGALG00000008015 | ||
| 20 13590000 13710000 ENSGALG00000008014 | ||
| 20 13590000 13710000 ENSGALG00000026906 | ||
| 20 13595000 13710000 ENSGALG00000008014 | ||
| 20 13595000 13710000 ENSGALG00000026906 | ||
| 20 13605000 13710000 ENSGALG00000008014 | ||
| 20 13605000 13710000 ENSGALG00000026906 | ||
| 20 13660000 13575000 ENSGALG00000008010 | ||
| 20 13725000 13575000 ENSGALG00000008010 | ||
| 20 13735000 13800000 ENSGALG00000008021 | ||
| 20 13760000 13795000 ENSGALG00000008018 | ||
| 20 13760000 13795000 ENSGALG00000008026 | ||
| 20 13765000 13795000 ENSGALG00000008018 | ||
| 20 13765000 13795000 ENSGALG00000008026 | ||
| 20 13800000 13735000 ENSGALG00000008015 | ||
| 20 13870000 13735000 ENSGALG00000008015 |
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