Commit aa4fd49d authored by Vladimir Reinharz's avatar Vladimir Reinharz
Browse files

bit scores

parent 2408c7f1
......@@ -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)
......
......@@ -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)
......
......@@ -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}}}
......
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