bit scores

Src/arnhack.py

@@ -235,8 +235,8 @@ class Arnhack(object):
         tmp_fasta.close()
 
         try:
-            call(['cmalign', '--mapali', ali_path, tmp_cm.name, tmp_fasta.name], 
-                 stdout=open(rdat_name, 'w'))
+            call(['cmalign', '-o', rdat_name, '--verbose',  '--mapali', ali_path, tmp_cm.name, tmp_fasta.name], )
+            #stdout=open(rdat_name, 'w'))
         except:
             print "Error with cmalign, from Infernal"
             sys.exit(1)

Src/final_graphs_shape_dist.py

@@ -130,7 +130,6 @@ def check_ali_quality():
         print i, j, title[zz]
         a = arnhack.Arnhack(x)
         a.add_msa(msa_path[zz], infernal_align=True)
-        raw_input()
         continue
         ss = a.get_ss_msa_on_wt()
         g = a.SSE_graph()
@@ -150,10 +149,10 @@ def check_ali_quality():
         #ax[i,j].set_xticks(range(len(a.wt_shape)), list(a.get_ss_msa_on_wt()))
         #ax[i,j].set_xticks(range(len(a.wt_shape)))
         #ax[i,j].set_xticklabels(list(a.get_ss_msa_on_wt()))
-    ax[0,0].set_ylabel('Nb. of pairs of nts.', fontsize=14)
+    #ax[0,0].set_ylabel('Nb. of pairs of nts.', fontsize=14)
     #print dir(ax[0,0].yaxis)
     #ax[0,0].xaxis.set_offset_position(-10)
-    ax[1, 1].set_xlabel(r'Secondary structure elements distances $\gamma$', fontsize=14)
+    #ax[1, 1].set_xlabel(r'Secondary structure elements distances $\gamma$', fontsize=14)
 
     #plt.ylabel('SHAPE reactivity', fontsize=14)
     #plt.xlabel('Sequence position', fontsize=14)

TeX/NAR/main_NAR.tex

@@ -399,13 +399,13 @@ To evaluate the efficiency of our method, data with the desired properties was a
 	\centering
 \colorbox{red}{
 	\begin{tabular}{lc}
-	\multicolumn{1}{l|}{RNA} & Total relative entropy \\\hline
-	5S & \phantom{0}70.210 \\
-	c-di-GMP ribo. & \phantom{0}56.898 \\
-	cobalamin ribo. & 112.690 \\
-	adenine ribo. & \phantom{0}60.180 \\
-	tRNA & \phantom{0}56.303  \\
-	glycine ribo. & \phantom{0}58.410 \\
+	\multicolumn{1}{l|}{RNA} & Bit Score \\\hline
+	5S & \phantom{0}48.65 \\
+	c-di-GMP ribo. & \phantom{0}44.23 \\
+	cobalamin ribo. & 118.96 \\
+	adenine ribo. & \phantom{0}62.68 \\
+	tRNA & \phantom{0}43.91  \\
+	glycine ribo. & \phantom{0}52.85 \\
 	\end{tabular}
 }
 	\caption{{\color{red}Each sequence total relative entropy when aligned to its RFAM sequence, obtained from \texttt{infernal}}}