Deal with base count misplaced

src/opencloning/dna_functions.py

@@ -274,6 +274,15 @@ def custom_file_parser(
     out = list()
 
     with file_streamer as handle:
+        if sequence_file_format == 'genbank':
+            # Filter out lines starting with "BASE COUNT" (ignore leading whitespace)
+            # TODO: Remove if biopython handles this correctly
+            filtered_lines = list()
+            for line in handle:
+                if not line.lstrip().startswith('BASE COUNT'):
+                    filtered_lines.append(line)
+            handle = io.StringIO(''.join(filtered_lines))
+
         try:
             for parsed_seq in seqio_parse(handle, sequence_file_format):
                 circularize = circularize or (

tests/test_dna_functions.py

@@ -52,6 +52,10 @@ def test_permissive_parser_other(self):
             plasmid = custom_file_parser(f, 'genbank')[0]
             self.assertEqual(plasmid.circular, True)
 
+    def test_permissive_parser_base_count_misplaced(self):
+        with open(f'{test_files}/base_count_misplaced.gb', 'r') as f:
+            custom_file_parser(f, 'genbank')[0]
+
 
 class MinorFunctionsTest(unittest.TestCase):
     def test_correct_name(self):

tests/test_files/base_count_misplaced.gb

@@ -0,0 +1,27 @@
+LOCUS       name                     136 bp    DNA     linear   UNK 01-JAN-1980
+DEFINITION  description.
+ACCESSION   id
+VERSION     id
+KEYWORDS    .
+SOURCE      .
+  ORGANISM  .
+            .
+BASE COUNT     1284 a   1068 c   1078 g   1308 t
+FEATURES             Location/Qualifiers
+     protein_bind    1..34
+                     /label="loxP"
+     protein_bind    35..68
+                     /label="lox66"
+     protein_bind    complement(69..102)
+                     /label="lox66"
+     protein_bind    69..102
+                     /label="lox71"
+     protein_bind    complement(35..68)
+                     /label="lox71"
+     protein_bind    103..136
+                     /label="loxP_mutant"
+ORIGIN
+        1 ataacttcgt atattttatt ttatacgaag ttatataact tcgtatattt tattttatac
+       61 gaacggtata ccgttcgtat attttatttt atacgaagtt attaccgttc gtatatttta
+      121 ttttatacga acggta
+//