updated code to v7.20

Author: bgoli

src/CBRead.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBRead.py 604 2017-07-17 12:30:08Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBRead.py 648 2018-05-23 20:01:54Z bgoli $)
 
 """
 
@@ -91,6 +91,37 @@
     zfile.close()
     del zipfile, zfile
 
+def loadModel(sbmlfile):
+    """
+    Loads any SBML model in COBRA, FAME (SBML2FBA), SBML3FBCv1, SBML3FBCv2 format.
+    
+     - *sbmlfile* an SBML model file
+     
+    """
+    mod = res = None
+    print('Attempting to load SBML file: {}'.format(sbmlfile))
+    try:
+        res = CBXML.sbml_fileFindVersion(sbmlfile)[0]
+    except Exception as ex:
+        print(ex)
+        print('\nERROR: cannot determine SBML model type for file {}'.format(sbmlfile))
+        return None
+            
+    try:
+        if res == 'L3V1FBC2':
+            mod = readSBML3FBC(sbmlfile)
+        elif res == 'L3V1FBC1':
+            mod = readSBML3FBC(sbmlfile)
+        elif res == 'COBRA':
+            mod = readCOBRASBML(sbmlfile, delete_intermediate=True)
+        elif res == 'L2FBA':
+            mod = readSBML2FBA(sbmlfile)
+    except Exception as ex:
+        print(ex)
+        print('\nERROR: model load failed for SBML file: {}'.format(sbmlfile))
+        return None
+    return mod
+
 
 def readSBML3FBC(fname, work_dir=None, return_sbml_model=False, xoptions={'validate' : False}, scan_notes_gpr=True):
     """

src/CBWrite.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBWrite.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBWrite.py 648 2018-05-23 20:01:54Z bgoli $)
 
 """
 
@@ -67,6 +67,21 @@
 except ImportError:
     print('\nINFO: No xlwt module available, Excel spreadsheet creation disabled')
 
+
+def saveModel(model, filename, compress=False):
+    """
+    Saves the model to an SBML file using the lates SBML3 FBC version.
+    
+    - *model* the CBMPy model
+    - *filename* the filename to write
+    
+    """
+    
+    writeSBML3FBCV2(model, filename, directory=None, gpr_from_annot=False, add_groups=True,\
+                    add_cbmpy_annot=True, add_cobra_annot=False, validate=False, compress_bounds=True,\
+                    zip_model=compress, return_model_string=False)
+    
+
 def writeSBML3FBC(fba, fname, directory=None, gpr_from_annot=False,\
                        add_groups=True, add_cbmpy_annot=True, add_cobra_annot=False,\
                        xoptions={'fbc_version': 1, 'validate' : False, 'compress_bounds' : True}):

src/CBXML.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBXML.py 643 2018-03-08 23:17:53Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBXML.py 648 2018-05-23 20:01:54Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -3002,13 +3002,13 @@ def sbml_fileFindVersion(f):
 
     msg = ''
     if output == 'L3V1FBC1':
-        msg = 'SBML Level 3 FBC version 1 model detected, load with cbmpy.readSBML3FBC()'
+        msg = 'SBML Level 3 FBC version 1 model detected, loading with cbmpy.readSBML3FBC()'
     elif output == 'L3V1FBC2':
-        msg = 'SBML Level 3 FBC version 2 model detected, load with cbmpy.readSBML3FBC()'
+        msg = 'SBML Level 3 FBC version 2 model detected, loading with cbmpy.readSBML3FBC()'
     elif output == 'L2FBA':
-        msg = 'SBML Level 2 FAME model detected, load with cbmpy.readSBML2FBA()'
+        msg = 'SBML Level 2 FAME model detected, loading with cbmpy.readSBML2FBA()'
     elif output == 'COBRA':
-        msg = 'COBRA SBML L2 model detected, load with cbmpy.readCOBRASBML()'
+        msg = 'COBRA SBML L2 model detected, loading with cbmpy.readCOBRASBML()'
     else:
         msg = 'Unknown model type, contact the SBML community or developer for more details.'
     del D

src/__init__.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: __init__.py 640 2017-12-18 18:13:40Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: __init__.py 648 2018-05-23 20:01:54Z bgoli $)
 
 """
 #
@@ -58,8 +58,8 @@
 from .CBXML import _HAVE_SBML_
 if _HAVE_SBML_:
     from .CBXML import sbml_fileFindVersion, sbml_fileValidate
-    from .CBRead import readSBML3FBC, readSBML2FBA, readCOBRASBML
-    from .CBWrite import writeSBML3FBC, writeModelToExcel97, writeModelToCOMBINEarchive, writeCOBRASBML, writeSBML3FBCV2
+    from .CBRead import loadModel, readSBML3FBC, readSBML2FBA, readCOBRASBML
+    from .CBWrite import saveModel, writeSBML3FBC, writeModelToExcel97, writeModelToCOMBINEarchive, writeCOBRASBML, writeSBML3FBCV2
 else:
     print('\nWARNING: No SBML support, top-level SBML read/write functions disabled.\n')
 

src/nosetests/test_loadSBML.py

@@ -62,14 +62,18 @@ def setup_class(klass):
         """This method is run once for each class before any tests are run"""
         klass.m = {}
         for m in DATA:
+            cmod = None
             if m.startswith('L2CBR_'):
                 cmod = cbmpy.readCOBRASBML(m, work_dir=MDIR,\
                                            output_dir=self.CDIR, delete_intermediate=True)
             elif m.startswith('L2FBA_'):
                 cmod = cbmpy.readSBML2FBA(os.path.join(MDIR, m))
             elif m.startswith('L3FBCV1_') or m.startswith('L3FBCV2_'):
                 cmod = cbmpy.readSBML3FBC(os.path.join(MDIR, m))
-            klass.m[m] = cmod
+            else:
+                cmod = None
+            if cmod is not None:
+                klass.m[m] = cmod
         if 'HOME' in os.environ:
             klass.CDIR = os.environ['HOME']
         else: