From 1b2619fa41b29c31e2491b62ad6586713d4f727e Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Fri, 29 Nov 2019 11:47:13 +0000 Subject: [PATCH] Fix string concatenation style in Tests/ Some of these are recent regressions introduced by black https://github.com/psf/black/issues/26 Others are long standing pre-existing style issues. --- Tests/run_tests.py | 6 +++-- Tests/search_tests_common.py | 4 +-- Tests/seq_tests_common.py | 5 ++-- Tests/test_AlignIO_FastaIO.py | 50 +++++++++++++++++------------------ Tests/test_GenBank.py | 16 +++++------ Tests/test_GenomeDiagram.py | 42 ++++++++++++++++------------- Tests/test_Nexus.py | 6 +++-- Tests/test_PDB_MMCIFParser.py | 11 ++++---- Tests/test_SeqIO_PdbIO.py | 14 +++++----- Tests/test_SeqRecord.py | 6 +++-- Tests/test_Uniprot.py | 2 +- Tests/test_cellosaurus.py | 10 ++++--- Tests/test_phenotype.py | 27 ++++++++++--------- Tests/test_seq.py | 12 ++++++--- 14 files changed, 117 insertions(+), 94 deletions(-) diff --git a/Tests/run_tests.py b/Tests/run_tests.py index 15503f65d5a..7588b7d322c 100644 --- a/Tests/run_tests.py +++ b/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] diff --git a/Tests/search_tests_common.py b/Tests/search_tests_common.py index 1d5187aaa02..893eb8cd298 100644 --- a/Tests/search_tests_common.py +++ b/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) diff --git a/Tests/seq_tests_common.py b/Tests/seq_tests_common.py index 053bb8a44aa..5cc6dfa65e4 100644 --- a/Tests/seq_tests_common.py +++ 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 diff --git a/Tests/test_AlignIO_FastaIO.py b/Tests/test_AlignIO_FastaIO.py index 1f6b7b3f712..bb141318203 100644 --- a/Tests/test_AlignIO_FastaIO.py +++ b/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) diff --git a/Tests/test_GenBank.py b/Tests/test_GenBank.py index 01451ad2292..38d7b493624 100644 --- a/Tests/test_GenBank.py +++ b/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) diff --git a/Tests/test_GenomeDiagram.py b/Tests/test_GenomeDiagram.py index b9b07351bd5..b2bdcf8f6a1 100755 --- a/Tests/test_GenomeDiagram.py +++ b/Tests/test_GenomeDiagram.py @@ -643,12 +643,14 @@ def tearDown(self): def test_str(self): """Test diagram's info as string.""" - expected = "\n<: Test Diagram>" \ - "\n1 tracks" \ - "\nTrack 1: " \ - "\n<: CDS Features>" \ - "\n0 sets" \ - "\n" + expected = ( + "\n<: Test Diagram>" + "\n1 tracks" + "\nTrack 1: " + "\n<: 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<: Test Diagram>" \ - "\n1 tracks" \ - "\nTrack 2: " \ - "\n<: CDS Features>" \ - "\n0 sets" \ - "\n" + expected = ( + "\n<: Test Diagram>" + "\n1 tracks" + "\nTrack 2: " + "\n<: 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<: Test Diagram>" \ - "\n1 tracks" \ - "\nTrack 0: " \ - "\n<: CDS Features>" \ - "\n0 sets" \ - "\n" + expected = ( + "\n<: Test Diagram>" + "\n1 tracks" + "\nTrack 0: " + "\n<: CDS Features>" + "\n0 sets" + "\n" + ) self.assertEqual(expected, str(self.gdd)) def test_write_arguments(self): diff --git a/Tests/test_Nexus.py b/Tests/test_Nexus.py index 79385e09f11..40486b52105 100755 --- a/Tests/test_Nexus.py +++ b/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), diff --git a/Tests/test_PDB_MMCIFParser.py b/Tests/test_PDB_MMCIFParser.py index 0ed5b95ff4f..87484db538e 100644 --- a/Tests/test_PDB_MMCIFParser.py +++ b/Tests/test_PDB_MMCIFParser.py @@ -235,11 +235,12 @@ def test_insertions(self): self.assertEqual(pp[0].get_id()[1], 16) self.assertEqual(pp[-1].get_id()[1], 244) # Check the sequence - refseq = "IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGR" \ - "SRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMY" \ - "NDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQW" \ - "KTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE" - + refseq = ( + "IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGR" + "SRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMY" + "NDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQW" + "KTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE" + ) s = pp.get_sequence() self.assertTrue(isinstance(s, Seq)) self.assertEqual(s.alphabet, generic_protein) diff --git a/Tests/test_SeqIO_PdbIO.py b/Tests/test_SeqIO_PdbIO.py index 81de98898cc..eaa7c9edced 100644 --- a/Tests/test_SeqIO_PdbIO.py +++ b/Tests/test_SeqIO_PdbIO.py @@ -117,12 +117,14 @@ def test_atom_parse(self): with warnings.catch_warnings(): warnings.simplefilter("ignore", PDBConstructionWarning) chains = list(SeqIO.parse("PDB/2XHE." + extension, parser)) - actual_seq = "DRLSRLRQMAAENQXXXXXXXXXXXXXXXXXXXXXXXPEPFMADFFNRVK"\ - "RIRDNIEDIEQAIEQVAQLHTESLVAVSKEDRDRLNEKLQDTMARISALG"\ - "NKIRADLKQIEKENKRAQQEGTFEDGTVSTDLRIRQSQHSSLSRKFVKVM"\ - "TRYNDVQAENKRRYGENVARQCRVVEPSLSDDAIQKVIEHGXXXXXXXXX"\ - "XXXXXXXXNEIRDRHKDIQQLERSLLELHEMFTDMSTLVASQGEMIDRIE"\ - "FSVEQSHNYV" + actual_seq = ( + "DRLSRLRQMAAENQXXXXXXXXXXXXXXXXXXXXXXXPEPFMADFFNRVK" + "RIRDNIEDIEQAIEQVAQLHTESLVAVSKEDRDRLNEKLQDTMARISALG" + "NKIRADLKQIEKENKRAQQEGTFEDGTVSTDLRIRQSQHSSLSRKFVKVM" + "TRYNDVQAENKRRYGENVARQCRVVEPSLSDDAIQKVIEHGXXXXXXXXX" + "XXXXXXXXNEIRDRHKDIQQLERSLLELHEMFTDMSTLVASQGEMIDRIE" + "FSVEQSHNYV" + ) self.assertEqual(str(chains[1].seq), actual_seq) def test_atom_read(self): diff --git a/Tests/test_SeqRecord.py b/Tests/test_SeqRecord.py index f9c5580ab17..ad93005b84a 100644 --- a/Tests/test_SeqRecord.py +++ b/Tests/test_SeqRecord.py @@ -143,8 +143,10 @@ def test_str(self): self.assertEqual(expected.lstrip(), str(self.record)) def test_repr(self): - expected = "SeqRecord(seq=Seq('ABCDEFGHIJKLMNOPQRSTUVWZYX', ProteinAlphabet()), " \ - "id='TestID', name='TestName', description='TestDescr', dbxrefs=['TestXRef'])" + expected = ( + "SeqRecord(seq=Seq('ABCDEFGHIJKLMNOPQRSTUVWZYX', ProteinAlphabet()), " + "id='TestID', name='TestName', description='TestDescr', dbxrefs=['TestXRef'])" + ) self.assertEqual(expected, repr(self.record)) def test_format(self): diff --git a/Tests/test_Uniprot.py b/Tests/test_Uniprot.py index fe16956aa9a..1481b8e9839 100644 --- a/Tests/test_Uniprot.py +++ b/Tests/test_Uniprot.py @@ -221,7 +221,7 @@ def test_uni003(self): "muscle system."]) self.assertEqual(seq_record.annotations["comment_induction"], ["Repressed in presence of fatty acids. Repressed " - "3-fold by ""lipid precursors, inositol and " + "3-fold by lipid precursors, inositol and " "choline, and also controlled by regulatory " "factors INO2, INO4 and OPI1."]) self.assertEqual(seq_record.annotations["comment_interaction_intactId"], diff --git a/Tests/test_cellosaurus.py b/Tests/test_cellosaurus.py index bc7b03b1aba..49610f69b72 100644 --- a/Tests/test_cellosaurus.py +++ b/Tests/test_cellosaurus.py @@ -125,10 +125,12 @@ def test__str__(self): """Test string function.""" handle = open("Cellosaurus/cell_lines_3.txt") record = cellosaurus.read(handle) - input = "ID: ZZ-R 127 AC: CVCL_5418 AS: SY: ZZ-R DR: [('CCLV', 'CCLV-RIE 0127')] " \ - "RX: ['PubMed=19656987;', 'PubMed=19941903;'] WW: [] CC: [] ST: [] DI: [] " \ - "OX: ['NCBI_TaxID=9925; ! Capra hircus'] HI: [] OI: [] SX: CA: " \ - "Spontaneously immortalized cell line" + input = ( + "ID: ZZ-R 127 AC: CVCL_5418 AS: SY: ZZ-R DR: [('CCLV', 'CCLV-RIE 0127')] " + "RX: ['PubMed=19656987;', 'PubMed=19941903;'] WW: [] CC: [] ST: [] DI: [] " + "OX: ['NCBI_TaxID=9925; ! Capra hircus'] HI: [] OI: [] SX: CA: " + "Spontaneously immortalized cell line" + ) self.assertEquals(record.__str__(), input) diff --git a/Tests/test_phenotype.py b/Tests/test_phenotype.py index b68a3cc6c18..53ce70e8e32 100644 --- a/Tests/test_phenotype.py +++ b/Tests/test_phenotype.py @@ -142,10 +142,10 @@ def test_PlateRecord(self): p2 = p.subtract_control() self.assertEqual(p2.id, p.id) self.assertEqual(p2["A02"], p["A02"] - p["A01"]) - self.assertEqual(repr(p), "PlateRecord('WellRecord['A01'], WellRecord" + + self.assertEqual(repr(p), "PlateRecord('WellRecord['A01'], WellRecord" "['A02'], WellRecord['A03'], ..., WellRecord['B12']')") - self.assertEqual(str(p), "Plate ID: PM01\nWell: 24\nRows: 2\nColumns: " + - "12\nPlateRecord('WellRecord['A01'], WellRecord['A02'], WellRecord" + + self.assertEqual(str(p), "Plate ID: PM01\nWell: 24\nRows: 2\nColumns: " + "12\nPlateRecord('WellRecord['A01'], WellRecord['A02'], WellRecord" "['A03'], ..., WellRecord['B12']')") with open(SMALL_JSON_PLATE_2) as handle: @@ -232,15 +232,18 @@ def test_WellRecord(self): self.assertEqual(w.get_times()[-1], 95.75) self.assertEqual(w.get_signals()[0], 37.0) self.assertEqual(w.get_signals()[-1], 217.0) - self.assertEqual(repr(w), - "WellRecord('(0.0, 37.0), (0.25, 29.0), (0.5, 32.0)," + - " (0.75, 30.0), (1.0, 29.0), ..., (95.75, 217.0)')") - self.assertEqual(str(w), - "Well ID: A10\nTime points: 384\nMinum signal 0.25 at " + - "time 29.00\nMaximum signal 16.75 at time " + - "313.00\nWellRecord('(0.0, 37.0), (0.25, 29.0), " + - "(0.5, 32.0), (0.75, 30.0), " + - "(1.0, 29.0), ..., (95.75, 217.0)')") + self.assertEqual( + repr(w), + "WellRecord('(0.0, 37.0), (0.25, 29.0), (0.5, 32.0)," + " (0.75, 30.0), (1.0, 29.0), ..., (95.75, 217.0)')" + ) + self.assertEqual( + str(w), + "Well ID: A10\nTime points: 384\nMinum signal 0.25 at time 29.00\n" + "Maximum signal 16.75 at time 313.00\n" + "WellRecord('(0.0, 37.0), (0.25, 29.0), (0.5, 32.0), (0.75, 30.0), " + "(1.0, 29.0), ..., (95.75, 217.0)')" + ) w.fit(None) self.assertEqual(w.area, None) diff --git a/Tests/test_seq.py b/Tests/test_seq.py index c653d73ec53..e54915e04c6 100644 --- a/Tests/test_seq.py +++ b/Tests/test_seq.py @@ -103,8 +103,10 @@ def test_repr(self): def test_truncated_repr(self): seq = "TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGA" - expected = "Seq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGC" + \ - "ATCATG...GGA', IUPACAmbiguousDNA())" + expected = ( + "Seq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATG...GGA', " + "IUPACAmbiguousDNA())" + ) self.assertEqual(expected, repr(Seq.Seq(seq, IUPAC.ambiguous_dna))) def test_length(self): @@ -634,8 +636,10 @@ def test_repr(self): def test_truncated_repr(self): seq = "TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGA" - expected = "MutableSeq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAA" + \ - "AGGATGCATCATG...GGA', IUPACAmbiguousDNA())" + expected = ( + "MutableSeq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATG...GGA', " + "IUPACAmbiguousDNA())" + ) self.assertEqual(expected, repr(MutableSeq(seq, IUPAC.ambiguous_dna))) def test_equal_comparison(self):