Test get XX line between features (FT) and sequence (SQ)

gff3toembl/tests/EMBLContig_test.py

@@ -852,18 +852,19 @@ def create_uninitialized_sequence(self):
 
   def test_init(self):
     sequence = EMBLSequence('AAAACCCGGTNN')
-    expected_header = "SQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
+    expected_header = "XX\nSQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
     expected_body = '     aaaacccggt nn                                                            12\n'
     self.assertEqual(sequence.header, expected_header)
     self.assertEqual(sequence.body, expected_body)
     self.assertEqual(sequence.length, 12)
 
   def test_format(self):
     sequence = self.create_uninitialized_sequence()
-    sequence.header = "SQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
+    sequence.header = "XX\nSQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
     sequence.body = '     aaaacccggt nn                                                            12\n'
     calculated_string = sequence.format()
     expected_string = """\
+XX
 SQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;
      aaaacccggt nn                                                            12
 """
@@ -891,19 +892,19 @@ def test_format_header(self):
     sequence = self.create_uninitialized_sequence()
     neucleotide_counts = {'a': 4, 'c': 3, 'g': 2, 't': 1, 'other': 2}
     calculated_header = sequence.format_header(neucleotide_counts)
-    expected_header = "SQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
+    expected_header = "XX\nSQ   Sequence 12 BP; 4 A; 3 C; 2 G; 1 T; 2 other;"
 
     neucleotide_counts = {'a': 12, 'c': 0, 'g': 0, 't': 0, 'other': 0}
     calculated_header = sequence.format_header(neucleotide_counts)
-    expected_header = "SQ   Sequence 12 BP; 12 A; 0 C; 0 G; 0 T; 0 other;"
+    expected_header = "XX\nSQ   Sequence 12 BP; 12 A; 0 C; 0 G; 0 T; 0 other;"
 
     neucleotide_counts = {'a': 0, 'c': 0, 'g': 0, 't': 0, 'other': 12}
     calculated_header = sequence.format_header(neucleotide_counts)
-    expected_header = "SQ   Sequence 12 BP; 0 A; 0 C; 0 G; 0 T; 12 other;"
+    expected_header = "XX\nSQ   Sequence 12 BP; 0 A; 0 C; 0 G; 0 T; 12 other;"
 
     neucleotide_counts = {'a': 2, 'c': 2, 'g': 2, 't': 6, 'other': 0}
     calculated_header = sequence.format_header(neucleotide_counts)
-    expected_header = "SQ   Sequence 12 BP; 2 A; 2 C; 2 G; 6 T; 0 other;"
+    expected_header = "XX\nSQ   Sequence 12 BP; 2 A; 2 C; 2 G; 6 T; 0 other;"
 
   def test_split_line_of_sequence(self):
     sequence = self.create_uninitialized_sequence()

gff3toembl/tests/data/expected_duplicate_coords.embl

@@ -32,6 +32,7 @@ FT   rRNA            6029..6142
 FT                   /product="5S ribosomal RNA"
 FT                   /inference="COORDINATES:profile:RNAmmer:1.2"
 FT                   /locus_tag="6730_5#19_02228"
+XX
 SQ   Sequence 6181 BP; 1767 A; 1220 C; 1744 G; 1449 T; 1 other;
      gttgaagaaa tgaacattga aaactgaatg acaatatgtc aacgttaatt ccaataaagt        60
      aacttaaatg ttacaaacac tatttagtat tatgagctaa tcaaacatca taaattttta       120

gff3toembl/tests/data/expected_large_annotation.embl

@@ -1716,6 +1716,7 @@ FT   tRNA            complement(174883..174959)
 FT                   /product="tRNA-Ile(gat)"
 FT                   /inference="COORDINATES:profile:Aragorn:1.2.34"
 FT                   /locus_tag="8233_4#93_02312"
+XX
 SQ   Sequence 175120 BP; 55731 A; 31266 C; 25419 G; 62704 T; 0 other;
      tctgacaatc gctttcttta aaaagaaact attgtcgaga atttgcatta gcaatatcac        60
      tttgtcaaaa agatgtttga atgttaaata aacattcaaa actgaataca atatgtcacg       120
@@ -5768,6 +5769,7 @@ FT   tRNA            108243..108316
 FT                   /product="tRNA-Gly(tcc)"
 FT                   /inference="COORDINATES:profile:Aragorn:1.2.34"
 FT                   /locus_tag="8233_4#93_02421"
+XX
 SQ   Sequence 108420 BP; 39263 A; 15735 C; 20016 G; 33406 T; 0 other;
      ctatagcaag gaggtcacac ctgttcccat gccgaacaca gaagttaagc tccttagcgt        60
      cgatggtagt tggacttacg ttccgctaga gtagaacgtt gccaggctat atattattcc       120
@@ -8172,6 +8174,7 @@ FT                   /inference="ab initio prediction:Prodigal:2.60"
 FT                   /inference="similar to AA sequence:RefSeq:YP_005742519.1"
 FT                   /locus_tag="8233_4#93_02500"
 FT                   /transl_table=11
+XX
 SQ   Sequence 52142 BP; 18748 A; 7364 C; 8937 G; 17093 T; 0 other;
      cacctgttcc catgccgaac acagaagtta agctccttag cgtcgatggt agttggactt        60
      acgttccgct agagtagaac gttgccaggc aagatatatt tggagaatta gctcagctgg       120
@@ -9502,6 +9505,7 @@ FT                   /db_xref="CDD:PRK09737"
 FT                   /db_xref="PFAM:PF01420.13"
 FT                   /locus_tag="8233_4#93_02548"
 FT                   /transl_table=11
+XX
 SQ   Sequence 51716 BP; 16183 A; 10270 C; 6898 G; 18365 T; 0 other;
      tttttggaat taacgttgac atattgtcat tcagttttca atgttcattt ttcttaccga        60
      caagaattaa ttatacattt tatcaacatt taaatcaaca actttttgaa attaattttt       120
@@ -10864,6 +10868,7 @@ FT   tRNA            39165..39240
 FT                   /product="tRNA-Ala(tgc)"
 FT                   /inference="COORDINATES:profile:Aragorn:1.2.34"
 FT                   /locus_tag="8233_4#93_02595"
+XX
 SQ   Sequence 39433 BP; 14273 A; 5313 C; 7870 G; 11977 T; 0 other;
      gacgaatact aatcgatcga agacttaatc aaaataaatg ttttgcgaag caaaatcact        60
      tttacttact atctagtttt gaatgtataa tctacattcg tatgtctggt gactatagca       120
@@ -11760,6 +11765,7 @@ FT                   /inference="ab initio prediction:Prodigal:2.60"
 FT                   /inference="similar to AA sequence:RefSeq:YP_302592.1"
 FT                   /locus_tag="8233_4#93_02624"
 FT                   /transl_table=11
+XX
 SQ   Sequence 21936 BP; 8100 A; 2662 C; 3389 G; 7784 T; 1 other;
      gactatataa aaagaaccgc agatctcttc agatctacgg gttttcgcca tgccgtgtaa        60
      ttagcatcat gctagctagt taatacgaag tattatttta aacataaggt tagacactta       120
@@ -12199,6 +12205,7 @@ FT                   /inference="ab initio prediction:Prodigal:2.60"
 FT                   /inference="similar to AA sequence:RefSeq:YP_005759108.1"
 FT                   /locus_tag="8233_4#93_02631"
 FT                   /transl_table=11
+XX
 SQ   Sequence 4804 BP; 1694 A; 684 C; 780 G; 1645 T; 1 other;
      tgtaattatc atttgaggtt tgccaaattg tttaataaga cgtttaataa acgtatatgc        60
      tgagtgatta tctcgtttct tacgtaacga aatatctagt gtatggccat ctgcatcaat       120
@@ -12315,6 +12322,7 @@ FT                   /inference="ab initio prediction:Prodigal:2.60"
 FT                   /db_xref="TIGRFAM:TIGR01295"
 FT                   /locus_tag="8233_4#93_02633"
 FT                   /transl_table=11
+XX
 SQ   Sequence 969 BP; 336 A; 157 C; 116 G; 360 T; 0 other;
      gactatataa aaagaaccgc agatctcttc agatctacgg gttttcgcca tgccgtgtaa        60
      ttagcatcat gctagctagt taatacgaag tattatttta aacataaggt tagacactta       120
@@ -12360,6 +12368,7 @@ FT   tRNA            complement(370..446)
 FT                   /product="tRNA-Ile(gat)"
 FT                   /inference="COORDINATES:profile:Aragorn:1.2.34"
 FT                   /locus_tag="8233_4#93_02634"
+XX
 SQ   Sequence 656 BP; 184 A; 154 C; 100 G; 218 T; 0 other;
      aagcatatcg tcgttagtaa cgtccttcat cggcttctag tgccaaggca tccaccgtgc        60
      gcccttaata acttaatcta tgtttccacc atttttacaa gtcaaacgct cacatactgt       120
@@ -12395,6 +12404,7 @@ FT                   /organism="Organism"
 FT                   /mol_type="genomic DNA"
 FT                   /db_xref="taxon:1234"
 FT                   /note="ERS154949|SC|contig000012"
+XX
 SQ   Sequence 465 BP; 139 A; 103 C; 64 G; 159 T; 0 other;
      ccccaaagca tatcgtcgtt agtaacgtcc ttcatcggct tctagtgcca aggcatccac        60
      cgtgcgccct taataactta atctatgttt ccaccatttt tataaatcaa acgttaacac       120

gff3toembl/tests/data/expected_single_feature.embl

@@ -30,6 +30,7 @@ FT                   /db_xref="PFAM:PF01475.13"
 FT                   /locus_tag="8233_4#93_02128"
 FT                   /gene="perR"
 FT                   /transl_table=11
+XX
 SQ   Sequence 240 BP; 76 A; 54 C; 36 G; 74 T; 0 other;
      tctgacaatc gctttcttta aaaagaaact attgtcgaga atttgcatta gcaatatcac        60
      tttgtcaaaa agatgtttga atgttaaata aacattcaaa actgaataca atatgtcacg       120

gff3toembl/tests/data/expected_single_feature_new_locus_tag.embl

@@ -30,6 +30,7 @@ FT                   /db_xref="PFAM:PF01475.13"
 FT                   /locus_tag="new_locus_tag_02128"
 FT                   /gene="perR"
 FT                   /transl_table=11
+XX
 SQ   Sequence 240 BP; 76 A; 54 C; 36 G; 74 T; 0 other;
      tctgacaatc gctttcttta aaaagaaact attgtcgaga atttgcatta gcaatatcac        60
      tttgtcaaaa agatgtttga atgttaaata aacattcaaa actgaataca atatgtcacg       120

gff3toembl/tests/data/expected_single_feature_translation_table.embl

@@ -30,6 +30,7 @@ FT                   /db_xref="PFAM:PF01475.13"
 FT                   /locus_tag="8233_4#93_02128"
 FT                   /gene="perR"
 FT                   /transl_table=1
+XX
 SQ   Sequence 240 BP; 76 A; 54 C; 36 G; 74 T; 0 other;
      tctgacaatc gctttcttta aaaagaaact attgtcgaga atttgcatta gcaatatcac        60
      tttgtcaaaa agatgtttga atgttaaata aacattcaaa actgaataca atatgtcacg       120