Merge pull request #79 from ypriverol/master

Added new enzymes for OpenMS

sdrf_pipelines/openms/openms.py

@@ -42,6 +42,17 @@ def __init__(self) -> None:
                           'TMT129N': 6, 'TMT129C': 7, 'TMT130N': 8, 'TMT130C': 9, 'TMT131': 10}
         self.tmt6plex = {'TMT126': 1, 'TMT127': 2, 'TMT128': 3,
                          'TMT129': 4, 'TMT130': 5, 'TMT131': 6}
+        # Hardcode enzymes from OpenMS
+        self.enzymes = {"Glutamyl endopeptidase":"glutamyl endopeptidase",
+                        "Trypsin/p":"Trypsin/P",
+                        "Lys-c":"Lys-C","Lys-n":"Lys-N","Arg-c":"Arg-C","Arg-c/p":"Arg-C/P",
+                        "Asp-n":"Asp-N","Asp-n/b":"Asp-N/B","Asp-n_ambic":"Asp-N_ambic",
+                        "Chymotrypsin/p":"Chymotrypsin/P","Cnbr":"CNBr",
+                        "V8-de":"V8-DE", "V8-e":"V8-E",
+                        "Elastase-trypsin-chymotrypsin":"elastase-trypsin-chymotrypsin",
+                        "Pepsina":"PepsinA",
+                        "Unspecific cleavage":"unspecific cleavage", "No cleavage":"no cleavage"}
+
         # TODO What about iTRAQ?
 
         # TODO How does this work? In OpenMS there are no such modifications. You can have different "isotope mods"
@@ -241,9 +252,13 @@ def openms_convert(self, sdrf_file: str = None, keep_raw: bool = False, one_tabl
                 source_name2n_reps[source_name] = int(f2c.file2technical_rep[raw])
 
             enzyme = re.search("NT=(.+?)(;|$)", row['comment[cleavage agent details]']).group(1)
+
             enzyme = enzyme.capitalize()
-            if "Trypsin/p" in enzyme:  # workaround
-                enzyme = "Trypsin/P"
+            # This is to check if the openMS map of enzymes
+            if enzyme in self.enzymes:
+              enzyme = self.enzymes[enzyme]
+
+
             f2c.file2enzyme[raw] = enzyme
 
             if 'comment[fraction identifier]' in row:

setup.py

@@ -6,7 +6,7 @@
 
 setup(
   name="sdrf-pipelines",
-  version="0.0.13",
+  version="0.0.14",
   author="BigBio Team",
   author_email="ypriverol@gmail.com",
   description="Translate, convert SDRF to configuration pipelines",