From 7010f0eaf32d033581cc6be0d0538898178602a5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Thu, 23 Feb 2017 11:07:57 -0600
Subject: [PATCH] Making 1kb center histone data.
---
ES_D0_Histone_enhancers_1kb.bed | 30775 ++++++++++++++++++++++++
ES_D10_Histone_enhancers_1kb.bed | 33542 ++++++++++++++++++++++++++
ES_D2_Histone_enhancers_1kb.bed | 27600 ++++++++++++++++++++++
ES_D5_Histone_enhancers_1kb.bed | 28029 ++++++++++++++++++++++
ES_D7_Histone_enhancers_1kb.bed | 36233 +++++++++++++++++++++++++++++
extend_histone_1kb.py | 46 +
intervene_test/update_barplot.py | 2 +-
7 files changed, 156226 insertions(+), 1 deletion(-)
create mode 100644 ES_D0_Histone_enhancers_1kb.bed
create mode 100644 ES_D10_Histone_enhancers_1kb.bed
create mode 100644 ES_D2_Histone_enhancers_1kb.bed
create mode 100644 ES_D5_Histone_enhancers_1kb.bed
create mode 100644 ES_D7_Histone_enhancers_1kb.bed
create mode 100644 extend_histone_1kb.py
diff --git a/ES_D0_Histone_enhancers_1kb.bed b/ES_D0_Histone_enhancers_1kb.bed
new file mode 100644
index 0000000..449d965
--- /dev/null
+++ b/ES_D0_Histone_enhancers_1kb.bed
@@ -0,0 +1,30775 @@
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diff --git a/ES_D10_Histone_enhancers_1kb.bed b/ES_D10_Histone_enhancers_1kb.bed
new file mode 100644
index 0000000..69a24dc
--- /dev/null
+++ b/ES_D10_Histone_enhancers_1kb.bed
@@ -0,0 +1,33542 @@
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diff --git a/ES_D2_Histone_enhancers_1kb.bed b/ES_D2_Histone_enhancers_1kb.bed
new file mode 100644
index 0000000..0c1aa9d
--- /dev/null
+++ b/ES_D2_Histone_enhancers_1kb.bed
@@ -0,0 +1,27600 @@
+chr1 1614366 1615367 HE_54
+chr1 1778313 1779314 HE_65
+chr1 1780185 1781186 HE_66
+chr1 1790147 1791148 HE_69
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+chr1 1814365 1815366 HE_75
+chr1 2168905 2169906 HE_97
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+chrX 154119764 154120765 HE_218425
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+chrY 4352615 4353616 HE_218460
+chrY 6620111 6621112 HE_218465
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diff --git a/ES_D5_Histone_enhancers_1kb.bed b/ES_D5_Histone_enhancers_1kb.bed
new file mode 100644
index 0000000..d08340a
--- /dev/null
+++ b/ES_D5_Histone_enhancers_1kb.bed
@@ -0,0 +1,28029 @@
+chr1 846568 847569 HE_3
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+chr1 1059397 1060398 HE_16
+chr1 1067555 1068556 HE_19
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+chr1 1103588 1104589 HE_29
+chr1 1350900 1351901 HE_43
+chr1 1614366 1615367 HE_54
+chr1 1695114 1696115 HE_57
+chr1 1780185 1781186 HE_66
+chr1 1809041 1810042 HE_73
+chr1 1812493 1813494 HE_74
+chr1 1830461 1831462 HE_77
+chr1 1964017 1965018 HE_83
+chr1 2154093 2155094 HE_96
+chr1 2168905 2169906 HE_97
+chr1 2172869 2173870 HE_98
+chr1 2179857 2180858 HE_99
+chr1 2220879 2221880 HE_109
+chr1 2223749 2224750 HE_110
+chr1 2253550 2254551 HE_117
+chr1 2378024 2379025 HE_124
+chr1 2466335 2467336 HE_134
+chr1 2473278 2474279 HE_135
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+chr1 2885013 2886014 HE_155
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+chr1 2955955 2956956 HE_158
+chr1 2992284 2993285 HE_161
+chr1 3006217 3007218 HE_166
+chr1 3018205 3019206 HE_169
+chr1 3022225 3023226 HE_170
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+chr1 3042570 3043571 HE_172
+chr1 3058334 3059335 HE_175
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+chr1 3102784 3103785 HE_184
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+chr1 3165617 3166618 HE_195
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diff --git a/ES_D7_Histone_enhancers_1kb.bed b/ES_D7_Histone_enhancers_1kb.bed
new file mode 100644
index 0000000..fe115c9
--- /dev/null
+++ b/ES_D7_Histone_enhancers_1kb.bed
@@ -0,0 +1,36233 @@
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+chrX 37853170 37854171 HE_214518
+chrX 37872525 37873526 HE_214519
+chrX 38311461 38312462 HE_214556
+chrX 38327709 38328710 HE_214558
+chrX 38669545 38670546 HE_214580
+chrX 38845795 38846796 HE_214604
+chrX 38859062 38860063 HE_214608
+chrX 39226514 39227515 HE_214649
+chrX 39256725 39257726 HE_214654
+chrX 39473000 39474001 HE_214681
+chrX 39618498 39619499 HE_214696
+chrX 39623391 39624392 HE_214697
+chrX 39709708 39710709 HE_214716
+chrX 39862391 39863392 HE_214734
+chrX 40125718 40126719 HE_214753
+chrX 40131820 40132821 HE_214754
+chrX 40239289 40240290 HE_214765
+chrX 40326942 40327943 HE_214776
+chrX 40330980 40331981 HE_214778
+chrX 40403324 40404325 HE_214784
+chrX 40546124 40547125 HE_214786
+chrX 40855741 40856742 HE_214798
+chrX 40970124 40971125 HE_214814
+chrX 41242433 41243434 HE_214827
+chrX 41595949 41596950 HE_214852
+chrX 41974263 41975264 HE_214877
+chrX 42279330 42280331 HE_214885
+chrX 43085321 43086322 HE_214914
+chrX 43881101 43882102 HE_214956
+chrX 44757510 44758511 HE_214969
+chrX 46186817 46187818 HE_215034
+chrX 46777754 46778755 HE_215069
+chrX 46817881 46818882 HE_215074
+chrX 46828491 46829492 HE_215078
+chrX 46914819 46915820 HE_215084
+chrX 47894709 47895710 HE_215139
+chrX 49051398 49052399 HE_215165
+chrX 49109745 49110746 HE_215167
+chrX 49605280 49606281 HE_215179
+chrX 49626262 49627263 HE_215182
+chrX 49683421 49684422 HE_215184
+chrX 49878734 49879735 HE_215197
+chrX 50091943 50092944 HE_215201
+chrX 50358721 50359722 HE_215219
+chrX 51698049 51699050 HE_215280
+chrX 53722769 53723770 HE_215315
+chrX 54453553 54454554 HE_215332
+chrX 54473306 54474307 HE_215335
+chrX 55124851 55125852 HE_215356
+chrX 55135833 55136834 HE_215357
+chrX 55161553 55162554 HE_215360
+chrX 57182794 57183795 HE_215395
+chrX 62981400 62982401 HE_215426
+chrX 64801914 64802915 HE_215462
+chrX 67335006 67336007 HE_215502
+chrX 67453745 67454746 HE_215504
+chrX 68204568 68205569 HE_215540
+chrX 68209395 68210396 HE_215541
+chrX 68247136 68248137 HE_215545
+chrX 68279842 68280843 HE_215550
+chrX 68326808 68327809 HE_215563
+chrX 68499081 68500082 HE_215587
+chrX 68509675 68510676 HE_215589
+chrX 68823261 68824262 HE_215610
+chrX 69250833 69251834 HE_215627
+chrX 70301177 70302178 HE_215655
+chrX 70447430 70448431 HE_215664
+chrX 71165032 71166033 HE_215683
+chrX 71211074 71212075 HE_215690
+chrX 71215808 71216809 HE_215691
+chrX 71237900 71238901 HE_215695
+chrX 71301105 71302106 HE_215705
+chrX 71343344 71344345 HE_215713
+chrX 73651476 73652477 HE_215776
+chrX 74122666 74123667 HE_215797
+chrX 76234433 76235434 HE_215830
+chrX 76758074 76759075 HE_215842
+chrX 77828679 77829680 HE_215858
+chrX 78707721 78708722 HE_215866
+chrX 78857043 78858044 HE_215869
+chrX 79857247 79858248 HE_215884
+chrX 81589390 81590391 HE_215902
+chrX 87128279 87129280 HE_215988
+chrX 87609855 87610856 HE_215995
+chrX 87859750 87860751 HE_215997
+chrX 87892247 87893248 HE_215998
+chrX 88012712 88013713 HE_215999
+chrX 94012864 94013865 HE_216039
+chrX 94208944 94209945 HE_216045
+chrX 95056509 95057510 HE_216060
+chrX 95158384 95159385 HE_216063
+chrX 95661821 95662822 HE_216071
+chrX 97111736 97112737 HE_216137
+chrX 99449052 99450053 HE_216178
+chrX 99546659 99547660 HE_216184
+chrX 99671845 99672846 HE_216194
+chrX 99685438 99686439 HE_216196
+chrX 99842942 99843943 HE_216210
+chrX 100609380 100610381 HE_216234
+chrX 101428778 101429779 HE_216256
+chrX 102406636 102407637 HE_216286
+chrX 102412089 102413090 HE_216287
+chrX 102615649 102616650 HE_216300
+chrX 102948265 102949266 HE_216326
+chrX 102953483 102954484 HE_216329
+chrX 105958830 105959831 HE_216410
+chrX 106156518 106157519 HE_216416
+chrX 106947298 106948299 HE_216455
+chrX 106953984 106954985 HE_216457
+chrX 106969097 106970098 HE_216458
+chrX 106984849 106985850 HE_216461
+chrX 107276332 107277333 HE_216476
+chrX 107460041 107461042 HE_216487
+chrX 107468037 107469038 HE_216490
+chrX 107498316 107499317 HE_216495
+chrX 107542181 107543182 HE_216500
+chrX 107554206 107555207 HE_216506
+chrX 107564641 107565642 HE_216509
+chrX 107586810 107587811 HE_216512
+chrX 107639319 107640320 HE_216526
+chrX 107658754 107659755 HE_216531
+chrX 107659968 107660969 HE_216532
+chrX 107758883 107759884 HE_216538
+chrX 108832918 108833919 HE_216574
+chrX 109100114 109101115 HE_216592
+chrX 109114876 109115877 HE_216597
+chrX 109255644 109256645 HE_216612
+chrX 109289208 109290209 HE_216622
+chrX 109308108 109309109 HE_216623
+chrX 109309756 109310757 HE_216624
+chrX 109330435 109331436 HE_216626
+chrX 109353969 109354970 HE_216627
+chrX 109362708 109363709 HE_216630
+chrX 109388168 109389169 HE_216632
+chrX 109688581 109689582 HE_216656
+chrX 109908275 109909276 HE_216667
+chrX 110290426 110291427 HE_216686
+chrX 110527707 110528708 HE_216696
+chrX 110553624 110554625 HE_216697
+chrX 110606685 110607686 HE_216707
+chrX 110754888 110755889 HE_216719
+chrX 111074219 111075220 HE_216731
+chrX 111079702 111080703 HE_216732
+chrX 111982799 111983800 HE_216757
+chrX 112075662 112076663 HE_216768
+chrX 112102724 112103725 HE_216774
+chrX 113339515 113340516 HE_216819
+chrX 114482026 114483027 HE_216850
+chrX 115088990 115089991 HE_216886
+chrX 115126008 115127009 HE_216888
+chrX 117322278 117323279 HE_216933
+chrX 118125645 118126646 HE_216966
+chrX 119645779 119646780 HE_217042
+chrX 119805988 119806989 HE_217047
+chrX 119882670 119883671 HE_217049
+chrX 119886079 119887080 HE_217050
+chrX 120350673 120351674 HE_217066
+chrX 122226760 122227761 HE_217111
+chrX 122302109 122303110 HE_217112
+chrX 122905172 122906173 HE_217148
+chrX 122913814 122914815 HE_217150
+chrX 124064963 124065964 HE_217189
+chrX 124919918 124920919 HE_217214
+chrX 127733966 127734967 HE_217239
+chrX 128186009 128187010 HE_217275
+chrX 128228334 128229335 HE_217280
+chrX 128278714 128279715 HE_217296
+chrX 128318078 128319079 HE_217297
+chrX 128496277 128497278 HE_217309
+chrX 128537973 128538974 HE_217310
+chrX 128567075 128568076 HE_217311
+chrX 128919879 128920880 HE_217332
+chrX 129095316 129096317 HE_217343
+chrX 129189354 129190355 HE_217350
+chrX 129847686 129848687 HE_217381
+chrX 130391158 130392159 HE_217414
+chrX 131119343 131120344 HE_217439
+chrX 132074682 132075683 HE_217511
+chrX 132399082 132400083 HE_217526
+chrX 133015575 133016576 HE_217630
+chrX 133025971 133026972 HE_217633
+chrX 133141040 133142041 HE_217648
+chrX 133646011 133647012 HE_217663
+chrX 133703984 133704985 HE_217669
+chrX 133717554 133718555 HE_217670
+chrX 133803774 133804775 HE_217676
+chrX 133825791 133826792 HE_217677
+chrX 133850070 133851071 HE_217680
+chrX 133875582 133876583 HE_217684
+chrX 133880571 133881572 HE_217685
+chrX 133883900 133884901 HE_217686
+chrX 133959838 133960839 HE_217691
+chrX 133961126 133962127 HE_217692
+chrX 134006222 134007223 HE_217693
+chrX 134435853 134436854 HE_217711
+chrX 134439613 134440614 HE_217713
+chrX 134536999 134538000 HE_217721
+chrX 134711452 134712453 HE_217737
+chrX 135491190 135492191 HE_217754
+chrX 136015643 136016644 HE_217777
+chrX 137075826 137076827 HE_217857
+chrX 139428715 139429716 HE_217974
+chrX 139470752 139471753 HE_217979
+chrX 139754677 139755678 HE_217998
+chrX 140001026 140002027 HE_218004
+chrX 142182153 142183154 HE_218035
+chrX 142371932 142372933 HE_218039
+chrX 142372991 142373992 HE_218040
+chrX 142383703 142384704 HE_218042
+chrX 142386126 142387127 HE_218043
+chrX 142394549 142395550 HE_218044
+chrX 144920251 144921252 HE_218075
+chrX 145583382 145584383 HE_218094
+chrX 145835528 145836529 HE_218099
+chrX 146975670 146976671 HE_218114
+chrX 146997963 146998964 HE_218116
+chrX 147622034 147623035 HE_218139
+chrX 148592188 148593189 HE_218172
+chrX 148883126 148884127 HE_218186
+chrX 148893197 148894198 HE_218188
+chrX 149437664 149438665 HE_218220
+chrX 149716100 149717101 HE_218243
+chrX 150935709 150936710 HE_218305
+chrX 152127386 152128387 HE_218343
+chrX 152616904 152617905 HE_218350
+chrX 152888575 152889576 HE_218362
+chrX 153290391 153291392 HE_218389
+chrX 153311721 153312722 HE_218394
+chrX 153339668 153340669 HE_218399
+chrX 153357157 153358158 HE_218402
+chrX 153962432 153963433 HE_218419
+chrX 154146133 154147134 HE_218426
+chrX 154216358 154217359 HE_218429
+chrY 2872190 2873191 HE_218452
+chrY 6626019 6627020 HE_218466
+chrY 14485494 14486495 HE_218541
+chrY 14506853 14507854 HE_218546
+chrY 14590620 14591621 HE_218550
+chrY 14637743 14638744 HE_218552
+chrY 14733095 14734096 HE_218558
+chrY 14991175 14992176 HE_218574
+chrY 15010022 15011023 HE_218575
+chrY 15765402 15766403 HE_218607
+chrY 16171998 16172999 HE_218620
+chrY 16174565 16175566 HE_218621
+chrY 16184856 16185857 HE_218622
+chrY 17535945 17536946 HE_218648
+chrY 19220267 19221268 HE_218686
+chrY 21223788 21224789 HE_218712
+chrY 21393694 21394695 HE_218717
+chrY 21394698 21395699 HE_218718
diff --git a/extend_histone_1kb.py b/extend_histone_1kb.py
new file mode 100644
index 0000000..ca4055c
--- /dev/null
+++ b/extend_histone_1kb.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+
+# -*- coding: latin-1 -*-
+'''Midpoint extend by 500 on either side of histone enhancers'''
+
+EPILOG = '''
+For more details:
+ %(prog)s --help
+'''
+
+import numpy
+import pybedtools
+import pybedtools.featurefuncs
+import argparse
+import os
+from subprocess import Popen
+
+
+def get_args():
+ parser = argparse.ArgumentParser(
+ description=__doc__, epilog=EPILOG,
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ )
+ parser.add_argument('-e', '--enhancers',
+ help="The enhancers",
+ required = True)
+ parser.add_argument('-o', '--outfile',
+ help="The outfile",
+ required = True)
+ args = parser.parse_args()
+ return args
+
+
+def main():
+ args = get_args()
+ # Read in bedtools:
+ histone_bed = pybedtools.BedTool(args.enhancers)
+ chromsizes = pybedtools.helpers.chromsizes("hg19")
+ input_bed_mid = histone_bed.each(pybedtools.featurefuncs.midpoint)
+ input_extend = input_bed_mid.slop(b=500,g=chromsizes)
+ input_extend.saveas(args.outfile + '.bed')
+
+
+
+if __name__ == '__main__':
+ main()
diff --git a/intervene_test/update_barplot.py b/intervene_test/update_barplot.py
index a649ea9..39725d0 100644
--- a/intervene_test/update_barplot.py
+++ b/intervene_test/update_barplot.py
@@ -27,7 +27,7 @@ axis[1].spines['top'].set_visible(False)
axis[0].xaxis.tick_top()
axis[0].tick_params(labeltop='off')
axis[1].xaxis.tick_bottom()
-d = .02
+d = .015
kwargs = dict(transform=axis[0].transAxes, color='#1E8EC9', clip_on=False)
axis[0].plot((-d,+d),(-d,+d), **kwargs)
axis[0].plot((1-d,1+d),(-d,+d), **kwargs)
--
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