Merge branch 'python-master' of github.com:josiahseaman/DDV into pyth…

…on-master # Conflicts: # DDV/MultipleAlignmentLayout.py
josiahseaman · May 23, 2018 · f103805 · f103805
2 parents ad5adfb + 45ce258
commit f103805
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/DDV/MultipleAlignmentLayout.py b/DDV/MultipleAlignmentLayout.py
@@ -103,9 +103,10 @@ def process_all_alignments(self, input_fasta_folder, output_folder, output_file_
 
 
     def draw_nucleotides(self):
-        for contig in self.contigs:
-            assert contig.consensus_width, \
-                "Error while reading: %s\n No consensus_width was set." % contig.name
+        bad_contigs = [c for c in self.contigs if not c.consensus_width]
+        for contig in bad_contigs:
+            print("Error while reading FASTA. Skipping: %s" % contig.name)
+            self.contigs.remove(contig)
         if self.sort_contigs:
             self.contigs.sort(key=lambda x: -x.height)
             self.layout_based_on_repeat_size(self.contigs[0].consensus_width,