Mercurial > repos > alenail > pieplot_macs

comparison pieplot_macs/pieplots_macs.py @ 16:8dae9fdd2afe draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author alenail
date Fri, 15 Apr 2016 11:51:20 -0400
parents 4ec317901ac3
children
comparison
equal deleted inserted replaced
15:4ec317901ac3 16:8dae9fdd2afe
104 # df = pd.DataFrame(data=fracs, index=indexDataFrame) 104 # df = pd.DataFrame(data=fracs, index=indexDataFrame)
105 # dfFileName = outfile.replace("pdf","csv") 105 # dfFileName = outfile.replace("pdf","csv")
106 # df.to_csv(dfFileName, sep=',') 106 # df.to_csv(dfFileName, sep=',')
107 #plt.title('MACS peaks in %s'%(name)) 107 #plt.title('MACS peaks in %s'%(name))
108 plt.figtext(.5, .1, 'Total: %i'%totalpks, ha='center') 108 plt.figtext(.5, .1, 'Total: %i'%totalpks, ha='center')
109 fig.savefig(outfile) 109 fig.savefig(outfile, format='pdf')
110 110
111 def main(): 111 def main():
112 usage = "usage: %prog --genefile MACSoutfile_genes.txt --peakfile MACSoutfile_peaks.bed --outfile MACSdirectory/piechart.pdf" 112 usage = "usage: %prog --genefile MACSoutfile_genes.txt --peakfile MACSoutfile_peaks.bed --outfile MACSdirectory/piechart.pdf"
113 parser = ArgumentParser(usage) 113 parser = ArgumentParser(usage)
114 parser.add_argument("--genefile", dest="genefile", help="Path to file MACS_mfold10,30_pval1e-5_genes.txt") 114 parser.add_argument("--genefile", dest="genefile", help="Path to file MACS_mfold10,30_pval1e-5_genes.txt")
115 parser.add_argument("--peakfile", dest="peakfile", help="Path to file MACS_mfold10,30_pval1e-5_peaks.bed") 115 parser.add_argument("--peakfile", dest="peakfile", help="Path to file MACS_mfold10,30_pval1e-5_peaks.bed")
116 parser.add_argument("--outfile", dest="outfile", default="MACS_piechart.pdf", help="Path to pdf file where you want to store the piechart") 116 parser.add_argument("--outfile", dest="outfile", default="MACS_piechart.pdf", help="Path to pdf file where you want to store the piechart")
117 parser.add_argument('--MACS',action='store_true',default=False,help='Set this value if you have MACS peaks') 117 parser.add_argument('--MACS', action='store_true', default=False, help='Set this value if you have MACS peaks')
118 118
119 args=parser.parse_args() 119 args=parser.parse_args()
120 120
121 map_peaks(args.genefile, args.peakfile, args.outfile, args.MACS) 121 map_peaks(args.genefile, args.peakfile, args.outfile, args.MACS)
122 122