v2.2

Author: PhilippSpahn

Scripts/Bowtie2.py

@@ -10,7 +10,7 @@
 # =======================================================================
 # Imports
 import os
-
+import multiprocessing
 
 def BuildIndex(LibFastA,IndexDir,bw2Dir):
     os.chdir(IndexDir)
@@ -31,9 +31,9 @@ def RunBowtie2(ReadsCut_filename,DataDir,AlnDir,bw2Dir,IndexDir,L_bw,N_bw,i_bw):
     cp_cmdline = 'cp ' + ReadsCutFilename + ' ' + IndexDir   
     os.system(cp_cmdline)
     os.chdir(IndexDir)
-    bw2_cmdline1 = bw2Dir+'bowtie2 --local -L '+str(L_bw)+' -N '+str(N_bw)+' -i '+str(i_bw) 
-    bw2_cmdline2 = ' -q -x Library -U ' + ReadsCutFilename + ' -S ' + bw2output
-    bw2_cmdline = bw2_cmdline1 + bw2_cmdline2
+    num_cores = multiprocessing.cpu_count()
+    bw2_cmdline = bw2Dir+'bowtie2 --local -L '+str(L_bw)+' -N '+str(N_bw)+' -i '+str(i_bw) +\
+        ' -q -x Library -U ' + ReadsCutFilename + ' -S ' + bw2output + ' -p '+str(num_cores)
     os.system(bw2_cmdline)
     rm_cmdline = 'rm ' + ReadsCutFilename
     os.system(rm_cmdline)

Scripts/PlotCounts.py

@@ -98,7 +98,7 @@ def GOI_Scatterplot(sample,GOI='None'):
     os.chdir(PlotDir)   
     plt.figure(figsize=(6,5))
     plt.scatter(control_rest,sample_rest,s=dotsize,facecolor='black',lw=0,alpha=0.35)
-    plt.scatter(control_sig,sample_sig,s=dotsize,facecolor='green',lw=0,alpha=0.35,label='Significant')
+    plt.scatter(control_sig,sample_sig,s=dotsize,facecolor='green',lw=0,alpha=0.35,label='FDR<'+str(alpha))
     if GOI != 'None':
         plt.scatter(control_goi,sample_goi,s=1.5*dotsize,facecolor='red',lw=0,alpha=1.00,label=GOI)
     if len(K_nonT)>0: