Fix string concatenation style in Tests/

Some of these are recent regressions introduced by black
psf/black#26

Others are long standing pre-existing style issues.

Tests/run_tests.py

@@ -181,8 +181,10 @@ def _have_bug17666():
         return False
     import gzip
     # Would like to use byte literal here:
-    bgzf_eof = "\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00BC" + \
-               "\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00"
+    bgzf_eof = (
+        "\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00BC"
+        "\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00"
+    )
     if sys.version_info[0] >= 3:
         import codecs
         bgzf_eof = codecs.latin_1_encode(bgzf_eof)[0]

Tests/search_tests_common.py

@@ -127,8 +127,8 @@ def compare_search_obj(obj_a, obj_b):
     # compare objects recursively if it's not an HSPFragment
     if not isinstance(obj_a, SearchIO.HSPFragment):
         # check the number of hits contained
-        assert len(obj_a) == len(obj_b), "length: %i vs %i for " \
-            "%r vs %r" % (len(obj_a), len(obj_b), obj_a, obj_b)
+        assert len(obj_a) == len(obj_b), ("length: %i vs %i for %r vs %r"
+                                          % (len(obj_a), len(obj_b), obj_a, obj_b))
 
         for item_a, item_b in zip(obj_a, obj_b):
             assert compare_search_obj(item_a, item_b)

Tests/seq_tests_common.py

@@ -275,9 +275,8 @@ def compare_record(old, new):
             old_comment = old_comment.replace("\n", " ").replace("  ", " ")
             new_comment = new_comment.replace("\n", " ").replace("  ", " ")
             assert old_comment == new_comment, \
-                "Comment annotation changed by load/retrieve\n" \
-                "Was:%s\nNow:%s" \
-                % (repr(old_comment), repr(new_comment))
+                ("Comment annotation changed by load/retrieve\n"
+                 "Was:%s\nNow:%s" % (repr(old_comment), repr(new_comment)))
         elif key in ["taxonomy", "organism", "source"]:
             # If there is a taxon id recorded, these fields get overwritten
             # by data from the taxon/taxon_name tables.  There is no

Tests/test_AlignIO_FastaIO.py

@@ -58,24 +58,24 @@ def test_output001(self):
             self.assertEqual(len(alignments[2]), 2)
             self.assertEqual(alignments[2].get_alignment_length(), 38)
             self.assertEqual(
-                alignments[2][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDI" "YSPSEFFSKIE"
+                alignments[2][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE"
             )
             self.assertEqual(alignments[2][0].id, "gi|10955264|ref|NP_052605.1|")
             self.assertEqual(alignments[2][0].annotations["original_length"], 126)
             self.assertEqual(
-                alignments[2][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKK" "YPVAELLSVLQ"
+                alignments[2][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ"
             )
             self.assertEqual(alignments[2][1].id, "gi|152973462|ref|YP_001338513.1|")
             self.assertEqual(alignments[2][1].annotations["original_length"], 101)
             self.assertEqual(len(alignments[3]), 2)
             self.assertEqual(alignments[3].get_alignment_length(), 43)
             self.assertEqual(
-                alignments[3][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SL" "IMKKIDVEMEDYSTYC"
+                alignments[3][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEMEDYSTYC"
             )
             self.assertEqual(alignments[3][0].id, "gi|10955265|ref|NP_052606.1|")
             self.assertEqual(alignments[3][0].annotations["original_length"], 346)
             self.assertEqual(
-                alignments[3][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQ" "VEEALDMLISSHGEYC"
+                alignments[3][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLISSHGEYC"
             )
             self.assertEqual(alignments[3][1].id, "gi|152973545|ref|YP_001338596.1|")
             self.assertEqual(alignments[3][1].annotations["original_length"], 242)
@@ -110,13 +110,13 @@ def test_output002(self):
             self.assertEqual(alignments[1].get_alignment_length(), 53)
             self.assertEqual(
                 alignments[1][0].seq,
-                "EIRKRAAECGKTVSGFLRAAA-L" "GKKV----NSLTDDRVLKEVMRL" "GALQKKL",
+                "EIRKRAAECGKTVSGFLRAAA-LGKKV----NSLTDDRVLKEVMRLGALQKKL",
             )
             self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|")
             self.assertEqual(alignments[1][0].annotations["original_length"], 107)
             self.assertEqual(
                 alignments[1][1].seq,
-                "EIKPRGTSKGEAIAAFMQEAPFI" "GRTPVFLGDDLTDESGFAVVNRL" "GGMSVKI",
+                "EIKPRGTSKGEAIAAFMQEAPFIGRTPVFLGDDLTDESGFAVVNRLGGMSVKI",
             )
             self.assertEqual(alignments[1][1].id, "gi|15831859|ref|NP_310632.1|")
             self.assertEqual(alignments[1][1].annotations["original_length"], 266)
@@ -165,13 +165,13 @@ def test_output002(self):
             self.assertEqual(alignments[4].get_alignment_length(), 63)
             self.assertEqual(
                 alignments[4][0].seq,
-                "VDIKK-ETIESELHSKLPKSIDK" "IHEDIKKQLSCSLI--MKKID-V" "EMEDYSTYCFSALRAIE",
+                "VDIKK-ETIESELHSKLPKSIDKIHEDIKKQLSCSLI--MKKID-VEMEDYSTYCFSALRAIE",
             )
             self.assertEqual(alignments[4][0].id, "gi|10955265|ref|NP_052606.1|")
             self.assertEqual(alignments[4][0].annotations["original_length"], 346)
             self.assertEqual(
                 alignments[4][1].seq,
-                "IDPKKIEQIARQVHESMPKGIRE" "FGEDVEKKIRQTLQAQLTRLDLV" "SREEFDVQTQVLLRTRE",
+                "IDPKKIEQIARQVHESMPKGIREFGEDVEKKIRQTLQAQLTRLDLVSREEFDVQTQVLLRTRE",
             )
             self.assertEqual(alignments[4][1].id, "gi|38704138|ref|NP_311957.2|")
             self.assertEqual(alignments[4][1].annotations["original_length"], 111)
@@ -212,13 +212,13 @@ def test_output003(self):
             self.assertEqual(alignments[0].get_alignment_length(), 55)
             self.assertEqual(
                 alignments[0][0].seq,
-                "ISISNNKDQYEELQKEQGERDLK" "TVDQLVRIAAAGGGLRLSASTKT" "VDQLVRIAA",
+                "ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGGGLRLSASTKTVDQLVRIAA",
             )
             self.assertEqual(alignments[0][0].id, "gi|152973837|ref|YP_001338874.1|")
             self.assertEqual(alignments[0][0].annotations["original_length"], 183)
             self.assertEqual(
                 alignments[0][1].seq,
-                "VRLTAEEDQ--EIRKRAAECG-K" "TVSGFLRAAALGKKVNSLTDDR" "VLKEVMRLGA",
+                "VRLTAEEDQ--EIRKRAAECG-KTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGA",
             )
             self.assertEqual(alignments[0][1].id, "gi|10955263|ref|NP_052604.1|")
             self.assertEqual(alignments[0][1].annotations["original_length"], 107)
@@ -234,13 +234,13 @@ def test_output003(self):
             self.assertEqual(alignments[2].get_alignment_length(), 63)
             self.assertEqual(
                 alignments[2][0].seq,
-                "VFGSFEQPKGEHLSGQVSEQ--R" "DTAFADQNEQVIRHLKQEIEHLN" "TLLLSKDSHIDSLKQAM",
+                "VFGSFEQPKGEHLSGQVSEQ--RDTAFADQNEQVIRHLKQEIEHLNTLLLSKDSHIDSLKQAM",
             )
             self.assertEqual(alignments[2][0].id, "gi|152973841|ref|YP_001338878.1|")
             self.assertEqual(alignments[2][0].annotations["original_length"], 133)
             self.assertEqual(
                 alignments[2][1].seq,
-                "VYTSFN---GEKFSSYTLNKVTK" "TDEYNDLSELSASFFKKNFDKIN" "VNLLSKATSF-ALKKGI",
+                "VYTSFN---GEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSF-ALKKGI",
             )
             self.assertEqual(alignments[2][1].id, "gi|10955264|ref|NP_052605.1|")
             self.assertEqual(alignments[2][1].annotations["original_length"], 126)
@@ -383,24 +383,24 @@ def test_output007(self):
             self.assertEqual(len(alignments[2]), 2)
             self.assertEqual(alignments[2].get_alignment_length(), 45)
             self.assertEqual(
-                alignments[2][0].seq, "EIRKRAAECGKTVSGFLRAAA--" "---LGKKVNSLTDDRVLKEVMR"
+                alignments[2][0].seq, "EIRKRAAECGKTVSGFLRAAA-----LGKKVNSLTDDRVLKEVMR"
             )
             self.assertEqual(alignments[2][0].id, "gi|10955263|ref|NP_052604.1|")
             self.assertEqual(alignments[2][0].annotations["original_length"], 107)
             self.assertEqual(
-                alignments[2][1].seq, "ELVKLIADMGISVRALLRKNVEP" "YEELGLEEDKFTDDQLIDFMLQ"
+                alignments[2][1].seq, "ELVKLIADMGISVRALLRKNVEPYEELGLEEDKFTDDQLIDFMLQ"
             )
             self.assertEqual(alignments[2][1].id, "gi|152973480|ref|YP_001338531.1|")
             self.assertEqual(alignments[2][1].annotations["original_length"], 141)
             self.assertEqual(len(alignments[3]), 2)
             self.assertEqual(alignments[3].get_alignment_length(), 38)
             self.assertEqual(
-                alignments[3][0].seq, "MKKDKKYQIEAIKNKDKTLFIVY" "ATDIYSPSEFFSKIE"
+                alignments[3][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE"
             )
             self.assertEqual(alignments[3][0].id, "gi|10955264|ref|NP_052605.1|")
             self.assertEqual(alignments[3][0].annotations["original_length"], 126)
             self.assertEqual(
-                alignments[3][1].seq, "IKKDLGVSFLKLKNREKTLIVDA" "LKKKYPVAELLSVLQ"
+                alignments[3][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ"
             )
             self.assertEqual(alignments[3][1].id, "gi|152973462|ref|YP_001338513.1|")
             self.assertEqual(alignments[3][1].annotations["original_length"], 101)
@@ -415,32 +415,32 @@ def test_output007(self):
             self.assertEqual(len(alignments[5]), 2)
             self.assertEqual(alignments[5].get_alignment_length(), 40)
             self.assertEqual(
-                alignments[5][0].seq, "DKTLFIVYATDIYSPSE-FFSKI" "ESDLKKKKSKGD-VFFD"
+                alignments[5][0].seq, "DKTLFIVYATDIYSPSE-FFSKIESDLKKKKSKGD-VFFD"
             )
             self.assertEqual(alignments[5][0].id, "gi|10955264|ref|NP_052605.1|")
             self.assertEqual(alignments[5][0].annotations["original_length"], 126)
             self.assertEqual(
-                alignments[5][1].seq, "ESVVFILMAGFAMSVCYLFFSVL" "EKVINARKSKDESIYHD"
+                alignments[5][1].seq, "ESVVFILMAGFAMSVCYLFFSVLEKVINARKSKDESIYHD"
             )
             self.assertEqual(alignments[5][1].id, "gi|152973581|ref|YP_001338632.1|")
             self.assertEqual(alignments[5][1].annotations["original_length"], 84)
             self.assertEqual(len(alignments[6]), 2)
             self.assertEqual(alignments[6].get_alignment_length(), 30)
-            self.assertEqual(alignments[6][0].seq, "ASFFKKNFDKINVNLLSKATSFA" "LKKGIPI")
+            self.assertEqual(alignments[6][0].seq, "ASFFKKNFDKINVNLLSKATSFALKKGIPI")
             self.assertEqual(alignments[6][0].id, "gi|10955264|ref|NP_052605.1|")
             self.assertEqual(alignments[6][0].annotations["original_length"], 126)
-            self.assertEqual(alignments[6][1].seq, "ASFSKEEQDKVAVDKVAADVAWQ" "ERMNKPV")
+            self.assertEqual(alignments[6][1].seq, "ASFSKEEQDKVAVDKVAADVAWQERMNKPV")
             self.assertEqual(alignments[6][1].id, "gi|152973536|ref|YP_001338587.1|")
             self.assertEqual(alignments[6][1].annotations["original_length"], 84)
             self.assertEqual(len(alignments[7]), 2)
             self.assertEqual(alignments[7].get_alignment_length(), 43)
             self.assertEqual(
-                alignments[7][0].seq, "SELHSKLPKSIDKIHEDIKKQLS" "C-SLIMKKIDVEMEDYSTYC"
+                alignments[7][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEMEDYSTYC"
             )
             self.assertEqual(alignments[7][0].id, "gi|10955265|ref|NP_052606.1|")
             self.assertEqual(alignments[7][0].annotations["original_length"], 346)
             self.assertEqual(
-                alignments[7][1].seq, "SRINSDVARRIPGIHRDPKDRLS" "SLKQVEEALDMLISSHGEYC"
+                alignments[7][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLISSHGEYC"
             )
             self.assertEqual(alignments[7][1].id, "gi|152973545|ref|YP_001338596.1|")
             self.assertEqual(alignments[7][1].annotations["original_length"], 242)
@@ -807,10 +807,10 @@ def test_output008(self):
             self.assertEqual(alignments[9][1].annotations["original_length"], 4301)
             self.assertEqual(len(alignments[10]), 2)
             self.assertEqual(alignments[10].get_alignment_length(), 30)
-            self.assertEqual(alignments[10][0].seq, "IMMNKQFRNCMLTTICCGKNPL" "GDDEASAT")
+            self.assertEqual(alignments[10][0].seq, "IMMNKQFRNCMLTTICCGKNPLGDDEASAT")
             self.assertEqual(alignments[10][0].id, "sp|P08100|OPSD_HUMAN")
             self.assertEqual(alignments[10][0].annotations["original_length"], 348)
-            self.assertEqual(alignments[10][1].seq, "MLLAFQFRNCMLTTLCCGKNPL" "GDDEASTT")
+            self.assertEqual(alignments[10][1].seq, "MLLAFQFRNCMLTTLCCGKNPLGDDEASTT")
             self.assertEqual(alignments[10][1].id, "gi|283855845|gb|GQ290303.1|")
             self.assertEqual(alignments[10][1].annotations["original_length"], 4301)
             self.assertEqual(len(alignments[11]), 2)
@@ -819,7 +819,7 @@ def test_output008(self):
             self.assertEqual(alignments[11][0].id, "sp|P08100|OPSD_HUMAN")
             self.assertEqual(alignments[11][0].annotations["original_length"], 348)
             self.assertEqual(
-                alignments[11][1].seq, "SQQIRNATTMMMTMRVTSFSAFW" "VVADSCCW"
+                alignments[11][1].seq, "SQQIRNATTMMMTMRVTSFSAFWVVADSCCW"
             )
             self.assertEqual(alignments[11][1].id, "gi|283855822|gb|GQ290312.1|")
             self.assertEqual(alignments[11][1].annotations["original_length"], 983)

Tests/test_GenBank.py

@@ -6354,7 +6354,7 @@ def test_001_genbank_bad_origin_wrapping_location(self):
             with self.assertRaises(BiopythonParserWarning) as cm:
                 record = SeqIO.read(path, "genbank")
             self.assertIn(
-                "It appears that '6801..100' is a feature " "that spans the origin",
+                "It appears that '6801..100' is a feature that spans the origin",
                 str(cm.exception),
             )
 
@@ -6385,19 +6385,19 @@ def test_compound_complex_origin_wrap(self):
             self.assertIsInstance(record.features[3].location, CompoundLocation)
             self.assertEqual(
                 str(record.features[3].location),
-                "join{[<5399:5600](+), [5699:6100](+), " "[6800:7000](+), [0:100](+)}",
+                "join{[<5399:5600](+), [5699:6100](+), [6800:7000](+), [0:100](+)}",
             )
 
             self.assertIsInstance(record.features[4].location, CompoundLocation)
             self.assertEqual(
                 str(record.features[4].location),
-                "join{[5399:5600](+), [5699:6100](+), " "[<6800:7000](+), [0:100](+)}",
+                "join{[5399:5600](+), [5699:6100](+), [<6800:7000](+), [0:100](+)}",
             )
 
             self.assertIsInstance(record.features[5].location, CompoundLocation)
             self.assertEqual(
                 str(record.features[5].location),
-                "join{[5399:5600](+), [5699:6100](+), " "[0:100](-), [<6800:7000](-)}",
+                "join{[5399:5600](+), [5699:6100](+), [0:100](-), [<6800:7000](-)}",
             )
 
     def test_implicit_orign_wrap_extract_and_translate(self):
@@ -6410,11 +6410,11 @@ def test_implicit_orign_wrap_extract_and_translate(self):
         seq_features = seq_record.features
         self.assertEqual(
             str(seq_features[1].extract(seq_record).seq.lower()),
-            "atgccctataaaacccagggctgccttggaaaaggcgcaacccc" "aaccccctcgagccgcggcatataa",
+            "atgccctataaaacccagggctgccttggaaaaggcgcaaccccaaccccctcgagccgcggcatataa",
         )
         self.assertEqual(
             str(seq_features[2].extract(seq_record).seq.lower()),
-            "atgccgcggctcgagggggttggggttgcgccttttccaaggca" "gccctgggttttatag",
+            "atgccgcggctcgagggggttggggttgcgccttttccaaggcagccctgggttttatag",
         )
         self.assertEqual(
             str(seq_features[1].extract(seq_record).seq.translate()),
@@ -7231,7 +7231,7 @@ def test_genbank_interaction(self):
         self.assertEqual(l_r[0].id, "NC_000932.1")
         self.assertEqual(l_r[0].name, "NC_000932")
         self.assertEqual(
-            l_r[0].description, "Arabidopsis thaliana chloroplast, " "complete genome"
+            l_r[0].description, "Arabidopsis thaliana chloroplast, complete genome"
         )
         self.assertEqual(len(l_r[0].features), 0)
 
@@ -7242,7 +7242,7 @@ def test_genbank_interaction(self):
         self.assertEqual(l_r[0].id, "NC_000932.1")
         self.assertEqual(l_r[0].name, "NC_000932")
         self.assertEqual(
-            l_r[0].description, "Arabidopsis thaliana chloroplast, " "complete genome"
+            l_r[0].description, "Arabidopsis thaliana chloroplast, complete genome"
         )
         self.assertEqual(len(l_r[0].features), 259)
 

Tests/test_GenomeDiagram.py

@@ -643,12 +643,14 @@ def tearDown(self):
 
     def test_str(self):
         """Test diagram's info as string."""
-        expected = "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>" \
-                   "\n1 tracks" \
-                   "\nTrack 1: " \
-                   "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>" \
-                   "\n0 sets" \
-                   "\n"
+        expected = (
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>"
+            "\n1 tracks"
+            "\nTrack 1: "
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>"
+            "\n0 sets"
+            "\n"
+        )
         self.assertEqual(expected, str(self.gdd))
 
     def test_add_track(self):
@@ -679,23 +681,27 @@ def test_get_tracks(self):
     def test_move_track(self):
         """Move a track."""
         self.gdd.move_track(1, 2)
-        expected = "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>" \
-                   "\n1 tracks" \
-                   "\nTrack 2: " \
-                   "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>" \
-                   "\n0 sets" \
-                   "\n"
+        expected = (
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>"
+            "\n1 tracks"
+            "\nTrack 2: "
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>"
+            "\n0 sets"
+            "\n"
+        )
         self.assertEqual(expected, str(self.gdd))
 
     def test_renumber(self):
         """Test renumbering tracks."""
         self.gdd.renumber_tracks(0)
-        expected = "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>" \
-                   "\n1 tracks" \
-                   "\nTrack 0: " \
-                   "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>" \
-                   "\n0 sets" \
-                   "\n"
+        expected = (
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Diagram.Diagram'>: Test Diagram>"
+            "\n1 tracks"
+            "\nTrack 0: "
+            "\n<<class 'Bio.Graphics.GenomeDiagram._Track.Track'>: CDS Features>"
+            "\n0 sets"
+            "\n"
+        )
         self.assertEqual(expected, str(self.gdd))
 
     def test_write_arguments(self):

Tests/test_Nexus.py

@@ -465,8 +465,10 @@ def test_TreeTest1(self):
 
     def test_TreeTest2(self):
         """Handle text labels on internal nodes."""
-        ts1b = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)" \
-               "TT1:25.000000)Taxaceae:90.000000;"
+        ts1b = (
+            "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"
+            "TT1:25.000000)Taxaceae:90.000000;"
+        )
         tree = Trees.Tree(ts1b)
         self.assertEqual(self._get_flat_nodes(tree), [("Taxaceae", 90.0, None, None),
                                                       ("Cephalotaxus", 125.0, None, None),