Added tests for both NMR-STAR2 and NMR-STAR3 formats.

MoseleyBioinformaticsLab · Jan 11, 2017 · 9eed933 · 9eed933
1 parent f2f1502
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Showing 24 changed files with 25,938 additions and 80 deletions.
diff --git a/tests/example_data/NMRSTAR2/bmr15000.str b/tests/example_data/NMRSTAR2/bmr15000.str
diff --git a/tests/example_data/NMRSTAR2/bmr18569.str b/tests/example_data/NMRSTAR2/bmr18569.str
diff --git a/...mple_data/chem_shifts_by_residue_SER.json → .../NMRSTAR2/chem_shifts_by_residue_SER.json b/...mple_data/chem_shifts_by_residue_SER.json → .../NMRSTAR2/chem_shifts_by_residue_SER.json
diff --git a/...ata/chem_shifts_by_residue_SER_CA_CB.json → ...AR2/chem_shifts_by_residue_SER_CA_CB.json b/...ata/chem_shifts_by_residue_SER_CA_CB.json → ...AR2/chem_shifts_by_residue_SER_CA_CB.json
diff --git a/tests/example_data/NMRSTAR2/chem_shifts_by_residue_all.json b/tests/example_data/NMRSTAR2/chem_shifts_by_residue_all.json
diff --git a/tests/example_data/NMRSTAR2/starfiles_archive.tar.bz2 b/tests/example_data/NMRSTAR2/starfiles_archive.tar.bz2
diff --git a/tests/example_data/NMRSTAR2/starfiles_archive.tar.gz b/tests/example_data/NMRSTAR2/starfiles_archive.tar.gz
diff --git a/tests/example_data/NMRSTAR2/starfiles_archive.zip b/tests/example_data/NMRSTAR2/starfiles_archive.zip
diff --git a/tests/example_data/NMRSTAR2/starfiles_directory/bmr15000.str b/tests/example_data/NMRSTAR2/starfiles_directory/bmr15000.str
diff --git a/tests/example_data/NMRSTAR2/starfiles_directory/bmr18569.str b/tests/example_data/NMRSTAR2/starfiles_directory/bmr18569.str
diff --git a/tests/example_data/bmr15000.str → tests/example_data/NMRSTAR3/bmr15000.str b/tests/example_data/bmr15000.str → tests/example_data/NMRSTAR3/bmr15000.str
diff --git a/tests/example_data/bmr18569.str → tests/example_data/NMRSTAR3/bmr18569.str b/tests/example_data/bmr18569.str → tests/example_data/NMRSTAR3/bmr18569.str
diff --git a/tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER.json b/tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER.json
@@ -0,0 +1,81 @@
+[
+    {
+        "2": {
+            "AA3Code": "SER",
+            "Seq_ID": "2",
+            "H": "8.225",
+            "HA": "4.420",
+            "HB2": "3.805",
+            "HB3": "3.857",
+            "CA": "58.593",
+            "CB": "64.057",
+            "N": "117.197"
+        },
+        "8": {
+            "AA3Code": "SER",
+            "Seq_ID": "8",
+            "H": "8.558",
+            "HA": "5.308",
+            "HB2": "3.599",
+            "HB3": "3.738",
+            "CA": "57.456",
+            "CB": "64.863",
+            "N": "117.870"
+        },
+        "9": {
+            "AA3Code": "SER",
+            "Seq_ID": "9",
+            "H": "9.230",
+            "HA": "5.059",
+            "HB2": "3.820",
+            "HB3": "3.981",
+            "CA": "57.852",
+            "CB": "67.332",
+            "N": "120.237"
+        },
+        "34": {
+            "AA3Code": "SER",
+            "Seq_ID": "34",
+            "H": "8.830",
+            "HA": "5.156",
+            "HB2": "3.212",
+            "HB3": "3.600",
+            "CA": "59.113",
+            "CB": "66.248",
+            "N": "115.301"
+        },
+        "46": {
+            "AA3Code": "SER",
+            "Seq_ID": "46",
+            "H": "7.552",
+            "HA": "5.091",
+            "HB2": "3.564",
+            "HB3": "4.136",
+            "CA": "55.939",
+            "CB": "66.829",
+            "N": "109.443"
+        },
+        "95": {
+            "AA3Code": "SER",
+            "Seq_ID": "95",
+            "H": "7.621",
+            "HA": "4.841",
+            "HB2": "4.101",
+            "HB3": "4.284",
+            "CA": "57.013",
+            "CB": "66.501",
+            "N": "110.313"
+        },
+        "108": {
+            "AA3Code": "SER",
+            "Seq_ID": "108",
+            "H": "7.623",
+            "HA": "4.033",
+            "HB2": "3.779",
+            "HB3": "3.849",
+            "CA": "61.617",
+            "CB": "62.493",
+            "N": "114.205"
+        }
+    }
+]
diff --git a/tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_CA_CB.json b/tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_CA_CB.json
@@ -0,0 +1,46 @@
+[
+    {
+        "2": {
+            "AA3Code": "SER",
+            "Seq_ID": "2",
+            "CA": "58.593",
+            "CB": "64.057"
+        },
+        "8": {
+            "AA3Code": "SER",
+            "Seq_ID": "8",
+            "CA": "57.456",
+            "CB": "64.863"
+        },
+        "9": {
+            "AA3Code": "SER",
+            "Seq_ID": "9",
+            "CA": "57.852",
+            "CB": "67.332"
+        },
+        "34": {
+            "AA3Code": "SER",
+            "Seq_ID": "34",
+            "CA": "59.113",
+            "CB": "66.248"
+        },
+        "46": {
+            "AA3Code": "SER",
+            "Seq_ID": "46",
+            "CA": "55.939",
+            "CB": "66.829"
+        },
+        "95": {
+            "AA3Code": "SER",
+            "Seq_ID": "95",
+            "CA": "57.013",
+            "CB": "66.501"
+        },
+        "108": {
+            "AA3Code": "SER",
+            "Seq_ID": "108",
+            "CA": "61.617",
+            "CB": "62.493"
+        }
+    }
+]
diff --git a/...mple_data/chem_shifts_by_residue_all.json → .../NMRSTAR3/chem_shifts_by_residue_all.json b/...mple_data/chem_shifts_by_residue_all.json → .../NMRSTAR3/chem_shifts_by_residue_all.json
diff --git a/tests/example_data/starfiles_archive.tar.bz2 → ...e_data/NMRSTAR3/starfiles_archive.tar.bz2 b/tests/example_data/starfiles_archive.tar.bz2 → ...e_data/NMRSTAR3/starfiles_archive.tar.bz2
diff --git a/tests/example_data/starfiles_archive.tar.gz → ...le_data/NMRSTAR3/starfiles_archive.tar.gz b/tests/example_data/starfiles_archive.tar.gz → ...le_data/NMRSTAR3/starfiles_archive.tar.gz
diff --git a/tests/example_data/starfiles_archive.zip → ...ample_data/NMRSTAR3/starfiles_archive.zip b/tests/example_data/starfiles_archive.zip → ...ample_data/NMRSTAR3/starfiles_archive.zip
diff --git a/...ple_data/starfiles_directory/bmr15000.str → ...NMRSTAR3/starfiles_directory/bmr15000.str b/...ple_data/starfiles_directory/bmr15000.str → ...NMRSTAR3/starfiles_directory/bmr15000.str
diff --git a/...ple_data/starfiles_directory/bmr18569.str → ...NMRSTAR3/starfiles_directory/bmr18569.str b/...ple_data/starfiles_directory/bmr18569.str → ...NMRSTAR3/starfiles_directory/bmr18569.str
diff --git a/tests/test_api_methods.py b/tests/test_api_methods.py
@@ -4,33 +4,51 @@
 
 
 def test_chem_shift_by_residue_all():
-    starfile_generator = nmrstarlib.read_files("tests/example_data/bmr18569.str")
-    starfile = next(starfile_generator)
-    test_chem_shifts = starfile.chem_shifts_by_residue()
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
+                                               "tests/example_data/NMRSTAR2/bmr18569.str")
+    starfile1 = next(starfile_generator)
+    starfile2 = next(starfile_generator)
+    test_chem_shifts1 = starfile1.chem_shifts_by_residue(nmrstar_version="3")
+    test_chem_shifts2 = starfile2.chem_shifts_by_residue(nmrstar_version="2")
 
-    with open("tests/example_data/chem_shifts_by_residue_all.json", "r") as infile:
-        model_chem_shifts = json.load(infile, object_pairs_hook=OrderedDict)
+    with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_all.json", "r") as infile:
+        model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict)
+    with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_all.json", "r") as infile:
+        model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)
 
-    assert repr(test_chem_shifts) == repr(model_chem_shifts)
+    assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
+    assert repr(test_chem_shifts2) == repr(model_chem_shifts2)
 
 
 def test_chem_shift_by_residue_specific_amino_acid():
-    starfile_generator = nmrstarlib.read_files("tests/example_data/bmr18569.str")
-    starfile = next(starfile_generator)
-    test_chem_shifts = starfile.chem_shifts_by_residue(aminoacids=("SER"))
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
+                                               "tests/example_data/NMRSTAR2/bmr18569.str")
+    starfile1 = next(starfile_generator)
+    starfile2 = next(starfile_generator)
+    test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=("SER",), nmrstar_version="3")
+    test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=("SER",), nmrstar_version="2")
 
-    with open("tests/example_data/chem_shifts_by_residue_SER.json", "r") as infile:
-        model_chem_shifts = json.load(infile, object_pairs_hook=OrderedDict)
+    with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER.json", "r") as infile:
+        model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict)
+    with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER.json", "r") as infile:
+        model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)
 
-    assert repr(test_chem_shifts) == repr(model_chem_shifts)
+    assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
+    assert repr(test_chem_shifts2) == repr(model_chem_shifts2)
 
 
 def test_chem_shift_by_residue_specific_amino_acid_specific_atoms():
-    starfile_generator = nmrstarlib.read_files("tests/example_data/bmr18569.str")
-    starfile = next(starfile_generator)
-    test_chem_shifts = starfile.chem_shifts_by_residue(aminoacids=("SER"), atoms=("CA", "CB"))
-
-    with open("tests/example_data/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile:
-        model_chem_shifts = json.load(infile, object_pairs_hook=OrderedDict)
-
-    assert repr(test_chem_shifts) == repr(model_chem_shifts)
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
+                                               "tests/example_data/NMRSTAR2/bmr18569.str")
+    starfile1 = next(starfile_generator)
+    starfile2 = next(starfile_generator)
+    test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=("SER",), atoms=("CA", "CB"), nmrstar_version="3")
+    test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=("SER",), atoms=("CA", "CB"), nmrstar_version="2")
+
+    with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile:
+        model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict)
+    with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile:
+        model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)
+
+    assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
+    assert repr(test_chem_shifts2) == repr(model_chem_shifts2)
diff --git a/tests/test_converter.py b/tests/test_converter.py
@@ -4,50 +4,77 @@
 
 
 def teardown_module(module):
-    shutil.rmtree("tests/example_data/tmp")
+    shutil.rmtree("tests/example_data/NMRSTAR3/tmp")
+    shutil.rmtree("tests/example_data/NMRSTAR2/tmp")
 
 
 def test_from_nmrstar_to_json_single_file():
-    converter = Converter(from_path="tests/example_data/bmr18569.str",
-                          to_path="tests/example_data/tmp/bmr18569.json",
+    converter = Converter(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
+                          to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
                           from_format="nmrstar",
                           to_format="json")
     converter.convert()
-    starfile_generator = nmrstarlib.read_files("tests/example_data/tmp/bmr18569.json")
-    starfile = next(starfile_generator)
-    assert starfile.bmrbid == "18569"
+    converter = Converter(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
+                          to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
+                          from_format="nmrstar",
+                          to_format="json")
+    converter.convert()
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/bmr18569.json",
+                                               "tests/example_data/NMRSTAR2/tmp/bmr18569.json")
+    starfile1 = next(starfile_generator)
+    starfile2 = next(starfile_generator)
+    assert starfile1.bmrbid == "18569" and starfile2.bmrbid == "18569"
 
 
 def test_from_json_to_nmrstar_single_file():
-    converter = Converter(from_path="tests/example_data/tmp/bmr18569.json",
-                          to_path="tests/example_data/tmp/bmr18569.str",
+    converter = Converter(from_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
+                          to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.str",
                           from_format="json",
                           to_format="nmrstar")
     converter.convert()
-    starfile_generator = nmrstarlib.read_files("tests/example_data/tmp/bmr18569.str")
-    starfile = next(starfile_generator)
-    assert starfile.bmrbid == "18569"
+    converter = Converter(from_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
+                          to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.str",
+                          from_format="json",
+                          to_format="nmrstar")
+    converter.convert()
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/bmr18569.str",
+                                               "tests/example_data/NMRSTAR2/tmp/bmr18569.str")
+    starfile1 = next(starfile_generator)
+    starfile2 = next(starfile_generator)
+    assert starfile1.bmrbid == "18569" and starfile2.bmrbid == "18569"
 
 
 def test_from_nmrstar_to_json_directory():
-    converter = Converter(from_path="tests/example_data/starfiles_directory",
-                          to_path="tests/example_data/tmp/starfiles_directory_json",
+    converter = Converter(from_path="tests/example_data/NMRSTAR3/starfiles_directory",
+                          to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
                           from_format="nmrstar",
                           to_format="json")
     converter.convert()
-    starfile_generator = nmrstarlib.read_files("tests/example_data/tmp/starfiles_directory_json")
-    starfile1 = next(starfile_generator)
-    starfile2 = next(starfile_generator)
-    assert starfile1.bmrbid in ("15000", "18569") and starfile2.bmrbid in ("15000", "18569")
+    converter = Converter(from_path="tests/example_data/NMRSTAR2/starfiles_directory",
+                          to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
+                          from_format="nmrstar",
+                          to_format="json")
+    converter.convert()
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
+                                               "tests/example_data/NMRSTAR2/tmp/starfiles_directory_json")
+    starfiles_list = list(starfile_generator)
+    starfiles_ids_set = set(sf.bmrbid for sf in starfiles_list)
+    assert starfiles_ids_set == {"15000", "18569"}
 
 
 def test_from_json_to_nmrstar_directory():
-    converter = Converter(from_path="tests/example_data/tmp/starfiles_directory_json",
-                          to_path="tests/example_data/tmp/starfiles_directory_nmrstar",
+    converter = Converter(from_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
+                          to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_nmrstar",
                           from_format="json",
                           to_format="nmrstar")
     converter.convert()
-    starfile_generator = nmrstarlib.read_files("tests/example_data/tmp/starfiles_directory_nmrstar")
-    starfile1 = next(starfile_generator)
-    starfile2 = next(starfile_generator)
-    assert starfile1.bmrbid in ("15000", "18569") and starfile2.bmrbid in ("15000", "18569")
+    converter = Converter(from_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
+                          to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_nmrstar",
+                          from_format="json",
+                          to_format="nmrstar")
+    converter.convert()
+    starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/starfiles_directory_nmrstar",
+                                               "tests/example_data/NMRSTAR2/tmp/starfiles_directory_nmrstar")
+    starfiles_list = list(starfile_generator)
+    starfiles_ids_set = set(sf.bmrbid for sf in starfiles_list)
+    assert starfiles_ids_set == {"15000", "18569"}
diff --git a/tests/test_csviewer.py b/tests/test_csviewer.py
@@ -3,31 +3,59 @@
 
 
 def teardown_module(module):
-    shutil.rmtree("tests/example_data/tmp")
+    shutil.rmtree("tests/example_data/NMRSTAR3/tmp")
+    shutil.rmtree("tests/example_data/NMRSTAR2/tmp")
 
 
 def test_csviewer_all():
-    csviewer = CSViewer(from_path="tests/example_data/bmr18569.str",
-                        aminoacids=(),
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
+                        amino_acids=(),
                         atoms=(),
-                        filename="tests/example_data/tmp/18569",
-                        csview_format="png")
+                        filename="tests/example_data/NMRSTAR3/tmp/18569",
+                        csview_format="png",
+                        nmrstar_version="3")
+    csviewer.csview(view=False)
+
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
+                        amino_acids=(),
+                        atoms=(),
+                        filename="tests/example_data/NMRSTAR2/tmp/18569",
+                        csview_format="png",
+                        nmrstar_version="2")
     csviewer.csview(view=False)
 
 
 def test_csviewer_specific_amino_acid():
-    csviewer = CSViewer(from_path="tests/example_data/bmr18569.str",
-                        aminoacids=("SER",),
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
+                        amino_acids=("SER",),
                         atoms=(),
-                        filename="tests/example_data/tmp/18569_SER",
-                        csview_format="png")
+                        filename="tests/example_data/NMRSTAR3/tmp/18569_SER",
+                        csview_format="png",
+                        nmrstar_version="3")
+    csviewer.csview(view=False)
+
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
+                        amino_acids=("SER",),
+                        atoms=(),
+                        filename="tests/example_data/NMRSTAR2/tmp/18569_SER",
+                        csview_format="png",
+                        nmrstar_version="2")
     csviewer.csview(view=False)
 
 
 def test_csviewer_specific_amino_acid_specific_atom():
-    csviewer = CSViewer(from_path="tests/example_data/bmr18569.str",
-                        aminoacids=("SER",),
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
+                        amino_acids=("SER",),
+                        atoms=("CA", "CB"),
+                        filename="tests/example_data/NMRSTAR3/tmp/18569_SER_CA_CB",
+                        csview_format="png",
+                        nmrstar_version="3")
+    csviewer.csview(view=False)
+
+    csviewer = CSViewer(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
+                        amino_acids=("SER",),
                         atoms=("CA", "CB"),
-                        filename="tests/example_data/tmp/18569_SER_CA_CB",
-                        csview_format="png")
+                        filename="tests/example_data/NMRSTAR2/tmp/18569_SER_CA_CB",
+                        csview_format="png",
+                        nmrstar_version="2")
     csviewer.csview(view=False)