# HG changeset patch
# User alenail
# Date 1460735480 14400
# Node ID 8dae9fdd2afef5df68dd0dcf1058878b5ce41321
# Parent  4ec317901ac343984d2f316046bf0322462ae96f
Uploaded

diff -r 4ec317901ac3 -r 8dae9fdd2afe pieplot_macs/pieplots_macs.py
--- a/pieplot_macs/pieplots_macs.py	Fri Apr 15 11:46:20 2016 -0400
+++ b/pieplot_macs/pieplots_macs.py	Fri Apr 15 11:51:20 2016 -0400
@@ -106,7 +106,7 @@
     # df.to_csv(dfFileName, sep=',')
     #plt.title('MACS peaks in %s'%(name))
     plt.figtext(.5, .1, 'Total: %i'%totalpks, ha='center')
-    fig.savefig(outfile)
+    fig.savefig(outfile, format='pdf')
 
 def main():
     usage = "usage: %prog --genefile MACSoutfile_genes.txt --peakfile MACSoutfile_peaks.bed --outfile MACSdirectory/piechart.pdf"
@@ -114,7 +114,7 @@
     parser.add_argument("--genefile", dest="genefile", help="Path to file MACS_mfold10,30_pval1e-5_genes.txt")
     parser.add_argument("--peakfile", dest="peakfile", help="Path to file MACS_mfold10,30_pval1e-5_peaks.bed")
     parser.add_argument("--outfile", dest="outfile", default="MACS_piechart.pdf", help="Path to pdf file where you want to store the piechart")
-    parser.add_argument('--MACS',action='store_true',default=False,help='Set this value if you have MACS peaks')
+    parser.add_argument('--MACS', action='store_true', default=False, help='Set this value if you have MACS peaks')
 
     args=parser.parse_args()