Added two new options

README.md

@@ -67,6 +67,14 @@ Output base pairing probability matrix to a file with user specified name (overw
 ```
 Outputs base pairing probability matrices to files with user specified prefix. (default False)
 ```
+--unpaired FILE_NAME
+```
+Output unpaired probability for each nuc and average unpaired probability (AUP) to a file with user specified name. (default False)
+```
+--access_u or -U 
+```
+Print the accessible U%. (default False)
+```
 --part or -p
 ```
 Partition function calculation only. (default False)

linearpartition

@@ -29,6 +29,8 @@ def setgflags():
     flags.DEFINE_boolean('fasta', False, "input is in fasta format") # FASTA format
     flags.DEFINE_integer('dangles', 2, "the way to treat `dangling end' energies for bases adjacent to helices in free ends and multi-loops (only supporting `0' or `2', default=`2')", short_name="d")
     flags.DEFINE_string('evaly', "", "batch eval all sequences against structure for p(y|x)", short_name='y') # p(y|x)
+    flags.DEFINE_string('unpaired', '', "output unpaired probability for each nuc and average unpaired probability (AUP)") # AUP
+    flags.DEFINE_boolean('access_u', False, "Output the percentage of unpaired U", short_name='U') # accessible U%
     argv = FLAGS(sys.argv)
 
 def main():
@@ -52,8 +54,11 @@ def main():
     is_fasta = '1' if FLAGS.fasta else '0'
     dangles = str(FLAGS.dangles)    
     evaly = FLAGS.evaly
+    unpaired_file = str(FLAGS.unpaired)
+    access_u = '1' if FLAGS.U else '0'
 
-    if FLAGS.p and (FLAGS.o or FLAGS.prefix):
+
+    if FLAGS.p and (FLAGS.o or FLAGS.prefix or FLAGS.unpaired):
         print("\nWARNING: -p mode has no output for base pairing probability matrix!\n");
 
     if FLAGS.o and FLAGS.r:
@@ -85,8 +90,14 @@ def main():
     if FLAGS.evaly:
         use_vienna = True # eval p(y|x) only in Vienna mode
 
+    if FLAGS.unpaired:
+        if os.path.exists(unpaired_file):
+            print("WARNING: unpaired output file already exists. Choose another name.\n")
+            print("Exit!\n")
+            exit()
+
     path = os.path.dirname(os.path.abspath(__file__))
-    cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq, shape_file_path, is_fasta, dangles, evaly]
+    cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq, shape_file_path, is_fasta, dangles, evaly, unpaired_file, access_u]
     subprocess.call(cmd, stdin=sys.stdin)
 
 if __name__ == '__main__':