skip logo generation if there are no conserved positions

scripts/parseHHR.py

@@ -241,11 +241,16 @@ def main( argv = None ):
         #queryConsensus = [ qc for i,qc in enumerate(hhm.consensus) ] # if hhm.conserved[i] ]
         #queryCovered = BitVector(size=len(hhm.master_seq))
 
+        # skip if no conserved positions
+        if hhm.conserved.count_bits() <= 0:
+            continue
+
         # output sequence logo restricted to conserved positions
         with open( "{}/{}.fas".format( args.fasDir, queryName ), 'r' ) as fas:
             fas_str = ""
             for rec in SeqIO.parse(fas,'fasta'):
-                fas_str += ">{}\n{}\n".format(rec.id,''.join([ c for i,c in enumerate(rec.seq) if hhm.conserved[i] ]))
+                seq = ''.join([ c for i,c in enumerate(rec.seq) if hhm.conserved[i] ])
+                fas_str += ">{}\n{}\n".format(rec.id,seq)
             loptions = weblogo.LogoOptions(
                     logo_title="{} ({})".format(hhmNameDict[queryName],queryName),
                     unit_name="bits",