Making 1kb center histone data.

extend_histone_1kb.py

+#!/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()

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)