skip logo generation if there are no conserved positions only for the appropriate logo

scripts/parseHHR.py

@@ -241,32 +241,29 @@ 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'):
-                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",
-                    yaxis_label="",
-                    #show_yaxis=False,
-                    color_scheme=weblogo.std_color_schemes["chemistry"],
-                    annotate=[ i+1 for i,b in enumerate(hhm.conserved) if b ],
-                    rotate_numbers=True,
-                    stack_aspect_ratio=3,
-                    stack_width=weblogo.std_sizes["large"],
-                    stacks_per_line=hhm.conserved.count_bits(),
-                    show_fineprint=False )
-            ldata = weblogo.LogoData.from_seqs( weblogo.read_seq_data(io.StringIO(fas_str)) )
-            lformat = weblogo.LogoFormat(ldata,loptions)
-            with open( os.path.join(args.outDir, "{}.conserved.pdf".format(hhmNameDict[queryName])), 'wb' ) as ofh:
-                ofh.write( weblogo.pdf_formatter(ldata,lformat) )
+        if hhm.conserved.count_bits() > 0:
+            with open( "{}/{}.fas".format( args.fasDir, queryName ), 'r' ) as fas:
+                fas_str = ""
+                for rec in SeqIO.parse(fas,'fasta'):
+                    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",
+                        yaxis_label="",
+                        #show_yaxis=False,
+                        color_scheme=weblogo.std_color_schemes["chemistry"],
+                        annotate=[ i+1 for i,b in enumerate(hhm.conserved) if b ],
+                        rotate_numbers=True,
+                        stack_aspect_ratio=3,
+                        stack_width=weblogo.std_sizes["large"],
+                        stacks_per_line=hhm.conserved.count_bits(),
+                        show_fineprint=False )
+                ldata = weblogo.LogoData.from_seqs( weblogo.read_seq_data(io.StringIO(fas_str)) )
+                lformat = weblogo.LogoFormat(ldata,loptions)
+                with open( os.path.join(args.outDir, "{}.conserved.pdf".format(hhmNameDict[queryName])), 'wb' ) as ofh:
+                    ofh.write( weblogo.pdf_formatter(ldata,lformat) )
 
         with open( "{}/{}.fas".format( args.fasDir, queryName ), 'r' ) as fas:
             loptions = weblogo.LogoOptions(