Update documentation references to ATAC

jpiper · Jun 7, 2015 · dc0eb01 · dc0eb01
1 parent f64991d
commit dc0eb01
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/pyDNase/scripts/dnase_average_profile.py b/pyDNase/scripts/dnase_average_profile.py
@@ -25,7 +25,7 @@
 import matplotlib.pyplot as plt
 from matplotlib import rcParams
 
-parser = argparse.ArgumentParser(description='Plots average profile of DNase activity surrounding a list of regions in a BED file')
+parser = argparse.ArgumentParser(description='Plots average profile of DNase (or Tn5 for ATAC-seq) activity surrounding a list of regions in a BED file')
 parser.add_argument("-w", "--window_size", help="Size of flanking area around centre of the regions to plot (default: 100)",default=100,type=int)
 parser.add_argument("-bf", "--bias-file", help="Location of the sorted, index",default = None,type=str)
 parser.add_argument("-i",action="store_true", help="Ignores any strand information in BED file and plots data relative to reference strand",default=False)
@@ -107,5 +107,8 @@
 if args.bias_file:
     plt.gca().set_ylabel('Average DNase Activity\n (Observed/Expected)',size="32", multialignment='center')
 else:
-    plt.gca().set_ylabel('Average DNase Activity',size="26", multialignment='center')
+    if args.A:
+        plt.gca().set_ylabel('Average Tn5 integrations',size="26", multialignment='center')
+    else:
+        plt.gca().set_ylabel('Average DNase activity',size="26", multialignment='center')
 plt.savefig(args.output,bbox_inches='tight')
diff --git a/pyDNase/scripts/wellington_footprints.py b/pyDNase/scripts/wellington_footprints.py
@@ -23,7 +23,7 @@
 
 __version__ = "0.2.0"
 
-parser = argparse.ArgumentParser(description='Footprint the DHSs in a DNase-seq experiment using the Wellington Algorithm.')
+parser = argparse.ArgumentParser(description='Footprint the DHSs in a DNase-seq or ATAC-seq experiment using the Wellington Algorithm.')
 parser.add_argument("-b","--bonferroni",action="store_true", help="Performs a bonferroni correction (default: False)",default=False)
 parser.add_argument("-sh", "--shoulder-sizes", help="Range of shoulder sizes to try in format \"from,to,step\" (default: 35,36,1)",default="35,36,1",type=str)
 parser.add_argument("-fp", "--footprint-sizes", help="Range of footprint sizes to try in format \"from,to,step\" (default: 11,26,2)",default="11,26,2",type=str)