Added additional tests for 'csview' command.

MoseleyBioinformaticsLab · Oct 23, 2017 · 8c4809a · 8c4809a
1 parent b352b97
commit 8c4809a
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Showing 2 changed files with 21 additions and 23 deletions.
diff --git a/nmrstarlib/cli.py b/nmrstarlib/cli.py
@@ -22,7 +22,7 @@
     --bmrb_url=<url>                URL to BMRB REST interface [default: http://rest.bmrb.wisc.edu/bmrb/NMR-STAR3/].
     --aa=<aa>                       Comma-separated amino acid three-letter codes (e.g. --aa=ALA,SER).
     --at=<at>                       Comma-separated BMRB atom codes (e.g. --at=CA,CB).
-    --aa_at=<aa:at>                 Comma-separated amino acid three-letter codes and corresponding atoms (e.g. --aa_at=ALA:CA,CB;SER:CA,CB).
+    --aa_at=<aa:at>                 Comma-separated amino acid three-letter codes and corresponding atoms (e.g. --aa_at=ALA-CA,CB:LYS-CB,CG,CD).
     --csview_outfile=<path>         Where to save chemical shifts table.
     --csview_format=<format>        Format to which save chemical shift table [default: svg].
     --plsplit=<%>                   How to split peak list into chunks by percent [default: 100].
@@ -61,10 +61,10 @@ def cli(cmdargs):
     elif cmdargs["csview"]:
         amino_acids = cmdargs["--aa"].split(",") if cmdargs["--aa"] else None
         atoms = cmdargs["--at"].split(",") if cmdargs["--at"] else None
-
         amino_acids_and_atoms = cmdargs["--aa_at"]
+
         if amino_acids_and_atoms:
-            amino_acids_and_atoms_list = [pair.split(':') for pair in amino_acids_and_atoms.split(';')]
+            amino_acids_and_atoms_list = [pair.split('-') for pair in amino_acids_and_atoms.split(':')]
             amino_acids_and_atoms = {aa: at.split(",") for aa, at in amino_acids_and_atoms_list}
         else:
             amino_acids_and_atoms = None

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -95,25 +95,23 @@ def test_convert_command(from_path, to_path, from_format, to_format):
     assert starfiles_ids_set.issubset({"15000", "18569"})
 
 
-@pytest.mark.parametrize("from_path,amino_acids,atoms,nmrstar_version", [
-    ("tests/example_data/NMRSTAR3/bmr18569.str", None, None, "3"),
-    ("tests/example_data/NMRSTAR3/bmr18569.str", "SER,MET", None, "3"),
-    ("tests/example_data/NMRSTAR3/bmr18569.str", None, "CA,CB", "3"),
-    ("tests/example_data/NMRSTAR3/bmr18569.str", "SER,MET", "CA,CB", "3"),
-    ("tests/example_data/NMRSTAR2/bmr18569.str", None, None, "2"),
-    ("tests/example_data/NMRSTAR2/bmr18569.str", "SER,MET", None, "2"),
-    ("tests/example_data/NMRSTAR2/bmr18569.str", None, "CA,CB", "2"),
-    ("tests/example_data/NMRSTAR2/bmr18569.str", "SER,MET", "CA,CB", "2")
+@pytest.mark.parametrize("from_path,amino_acids,atoms,amino_acids_and_atoms,nmrstar_version", [
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "", "", "", "3"),
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "SER,MET", "", "", "3"),
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "", "CA,CB", "", "3"),
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "SER,MET", "CA,CB", "", "3"),
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "", "", "ALA-CA,CB:LYS-CB,CG,CD", "3"),
+    ("tests/example_data/NMRSTAR2/bmr18569.str", "", "", "", "2"),
+    ("tests/example_data/NMRSTAR2/bmr18569.str", "SER,MET", "", "", "2"),
+    ("tests/example_data/NMRSTAR2/bmr18569.str", "", "CA,CB", "", "2"),
+    ("tests/example_data/NMRSTAR2/bmr18569.str", "SER,MET", "CA,CB", "", "2"),
+    ("tests/example_data/NMRSTAR3/bmr18569.str", "", "", "ALA-CA,CB:LYS-CB,CG,CD", "2"),
 ])
-def test_csview_command(from_path, amino_acids, atoms, nmrstar_version):
+def test_csview_command(from_path, amino_acids, atoms, amino_acids_and_atoms, nmrstar_version):
 
-    if amino_acids == None and atoms == None:
-        command = "python -m nmrstarlib csview {} --nmrstar_version={}".format(from_path, nmrstar_version)
-    elif amino_acids == None and atoms != None:
-        command = "python -m nmrstarlib csview {} --at={} --nmrstar_version={}".format(from_path, atoms, nmrstar_version)
-    elif atoms == None and amino_acids != None:
-        command = "python -m nmrstarlib csview {} --aa={} --nmrstar_version={}".format(from_path, amino_acids, nmrstar_version)
-    else:
-        command = "python -m nmrstarlib csview {} --aa={} --at={} --nmrstar_version={}".format(from_path, amino_acids, atoms, nmrstar_version)
-
-    assert os.system(command) == 0
+    command = "python -m nmrstarlib csview {} --aa={} --at={} --aa_at={} --nmrstar_version={}".format(from_path,
+                                                                                           amino_acids,
+                                                                                           atoms,
+                                                                                           amino_acids_and_atoms,
+                                                                                           nmrstar_version)
+    assert os.system(command) == 0