working reformat

mfql_dessert.py

@@ -2,29 +2,39 @@ import os
 from chem_parser import txt2dict
 from gooey import Gooey, GooeyParser
 
-@Gooey(program_name="MFQL Dessert")
+@Gooey( program_name="MFQL Dessert")
 def getArgs():
     parser = GooeyParser(description='MFQL generator v0.0.1')
-    parser.add_argument('compound', metavar='Compound', help='Human reabable name for reference')
+    parser.add_argument('compound', metavar='Compound', help='Compound name')
+    parser.add_argument('mfql_dir', metavar='Directory where to store the results' , help='output dir for MFQL files'
+    ,default='.' , widget='DirChooser')
+
     ms1_group = parser.add_argument_group(
             "Chemical Formula", 
             "in normal (eg H2O) or ranged format (eg C[1..20]H[4..80]O[0..1])")
-    ms1_group.add_argument('formula_ms1', metavar='Chemical Formula for MS1' , help='Specify formula')
-    ms1_group.add_argument('adduct_ms1', metavar='Chemical Formula for MS1 Adduct', help='Specify adduct type (optional for ranged format)'
-                , nargs = '?', default='')
-    ms1_group.add_argument('ms_mode', metavar='Select the Mode to use', help='MS mode'
-                , choices=['+', '-'])
-    ms2_group = parser.add_argument_group(
-            "Fragment Formula", 
-            "Add fragments if applicable")
-    ms2_group.add_argument('formula_ms2', metavar='Chemical Formula for fragments,', help='Specify fragment formula seperated by comma'
-                , nargs = '?', default='')
+
+    ms1_group.add_argument('formula_ms1', metavar='Chemical Formula for MS1', help='Specify formula (eg h2o or C[1..20]H[4..80]O[0..1])')
+    ms1_group.add_argument('ms_mode', metavar='Select the Mode to use'
+            , choices=['+', '-'])
+    ms1_optgroup = parser.add_argument_group(
+            "MS1 Adduct (optional)", 
+            "Specify adduct type, this is optional for ranged formulas")
+    
+    ms1_optgroup.add_argument('adduct_ms1', metavar='Chemical Formula for MS1 Adduct' , help = 'for example H'
+            , nargs = '?', default='')
+
+    ms2_optgroup = parser.add_argument_group(
+            "Fragments (optional)", 
+            "Specify the chemical formulas of fragments, if applicable.")
+    
+    ms2_optgroup.add_argument('formula_ms2', metavar='Chemical Formulas fragments' , help = 'seperated by comma if there are multiple'
+            , nargs = '?', default='')
+
     
-    parser.add_argument('mfql_dir', metavar='Directory where to store the results', help='output dir for MFQL files'
-            ,default='./mfql_dir/' , widget='DirChooser')
     args = parser.parse_args()
     return args
 
+
 def addDicts(cc, af, ms):
     #adjust for the adduct
     # only H, NH4 and HCOO are defined
@@ -103,8 +113,6 @@ def res2dbe(res):
 
 def main():
     args = getArgs()
-    print(args.formula_ms2)
-    return
     ms = args.ms_mode
     cc = txt2dict(args.formula_ms1)
     af = txt2dict(args.adduct_ms1) #get chemical composition of adduct
@@ -133,4 +141,6 @@ def main():
         f.write(line6 + '\n')
 
 if __name__ == "__main__":
-    main()
+    # main()
+    args = getArgs()
+    print(vars(args))
\ No newline at end of file