Merge pull request #58 from AuReMe/fix-issue-54

Do not allow abbreviation in command arguments (issue #54).

metage2metabo/__main__.py

@@ -211,7 +211,8 @@ def main():
             parent_parser_xml
         ],
         description=
-        "Run metabolic network reconstruction for each annotated genome of the input directory, using Pathway Tools"
+        "Run metabolic network reconstruction for each annotated genome of the input directory, using Pathway Tools",
+        allow_abbrev=False
     )
     indivscope_parser = subparsers.add_parser(
         "iscope",
@@ -220,7 +221,8 @@ def main():
             parent_parser_n, parent_parser_s, parent_parser_o, parent_parser_q, parent_parser_c
         ],
         description=
-        "Compute individual scopes (reachable metabolites from seeds) for each metabolic network of the input directory"
+        "Compute individual scopes (reachable metabolites from seeds) for each metabolic network of the input directory",
+        allow_abbrev=False
     )
     comscope_parser = subparsers.add_parser(
         "cscope",
@@ -229,7 +231,7 @@ def main():
             parent_parser_n, parent_parser_s, parent_parser_o, parent_parser_m,
             parent_parser_q, parent_parser_t_optional
         ],
-        description="Compute the community scope of all metabolic networks")
+        description="Compute the community scope of all metabolic networks", allow_abbrev=False)
     added_value_parser = subparsers.add_parser(
         "addedvalue",
         help="added value of microbiota's metabolism over individual's",
@@ -238,7 +240,8 @@ def main():
             parent_parser_q
         ],
         description=
-        "Compute metabolites that are reachable by the community/microbiota and not by individual organisms"
+        "Compute metabolites that are reachable by the community/microbiota and not by individual organisms",
+        allow_abbrev=False
     )
     mincom_parser = subparsers.add_parser(
         "mincom",
@@ -248,13 +251,15 @@ def main():
             parent_parser_q, parent_parser_t_required
         ],
         description=
-        "Select minimal-size community to make reachable a set of metabolites")
+        "Select minimal-size community to make reachable a set of metabolites",
+        allow_abbrev=False)
     seeds_parser = subparsers.add_parser(
         "seeds",
         help="creation of seeds SBML file",
         parents=[parent_parser_o, parent_parser_q],
         description=
-        "Create a SBML file starting for a simple text file with metabolic compounds identifiers"
+        "Create a SBML file starting for a simple text file with metabolic compounds identifiers",
+        allow_abbrev=False
     )
     seeds_parser.add_argument(
         "--metabolites",
@@ -270,7 +275,8 @@ def main():
             parent_parser_t_optional, parent_parser_cl, parent_parser_xml
         ],
         description=
-        "Run the whole workflow: metabolic network reconstruction, individual and community scope analysis and community selection"
+        "Run the whole workflow: metabolic network reconstruction, individual and community scope analysis and community selection",
+        allow_abbrev=False
     )
     metacom_parser = subparsers.add_parser(
         "metacom",
@@ -280,16 +286,16 @@ def main():
             parent_parser_t_optional, parent_parser_q, parent_parser_c
         ],
         description=
-        "Run the whole metabolism community analysis: individual and community scope analysis and community selection"
+        "Run the whole metabolism community analysis: individual and community scope analysis and community selection",
+        allow_abbrev=False
     )
     test_parser = subparsers.add_parser(
         "test",
         help="test on sample data from rumen experiments",
         parents=[
             parent_parser_q, parent_parser_c, parent_parser_o
         ],
-        description=
-        "Test the whole workflow on a data sample")
+        description="Test the whole workflow on a data sample", allow_abbrev=False)
 
     args = parser.parse_args()
 

metage2metabo/__main_analysis__.py

@@ -183,7 +183,8 @@ def main():
             parent_parser_s, parent_parser_n, parent_parser_t, parent_parser_m, parent_parser_o, parent_parser_q
         ],
         description=
-        "Run miscoto enumeration on sbml species with seeds and targets"
+        "Run miscoto enumeration on sbml species with seeds and targets",
+        allow_abbrev=False
     )
     graph_parser = subparsers.add_parser(
         "graph",
@@ -192,7 +193,8 @@ def main():
             parent_parser_j, parent_parser_o, parent_parser_t, parent_parser_taxon, parent_parser_q,
             parent_parser_level
         ],
-        description="Create the solution graph using the JSON from miscoto enumeration")
+        description="Create the solution graph using the JSON from miscoto enumeration",
+        allow_abbrev=False)
     powergraph_parser = subparsers.add_parser(
         "powergraph",
         help="powergraph creation and visualization",
@@ -201,7 +203,8 @@ def main():
             parent_parser_level, parent_parser_o
         ],
         description=
-        "Compress the GMl graph of solution and create a powergraph (bbl), a website format of the powergraph and a svg of the graph (if you use the --oog option)"
+        "Compress the GMl graph of solution and create a powergraph (bbl), a website format of the powergraph and a svg of the graph (if you use the --oog option)",
+        allow_abbrev=False
     )
     wkf_parser = subparsers.add_parser(
         "workflow",
@@ -211,7 +214,8 @@ def main():
             parent_parser_taxon, parent_parser_q, parent_parser_level
         ],
         description=
-        "Run the whole workflow: miscoto enumeration, graph on solution and powergraph creation"
+        "Run the whole workflow: miscoto enumeration, graph on solution and powergraph creation",
+        allow_abbrev=False
     )
 
     args = parser.parse_args()