Clarified documentation regarding exact stoichiometry parameter.

README.md

@@ -32,7 +32,7 @@ Command-line options can be viewed using "--help" flag, as shown below:
     -v         Print merging statistics
     -up        Update metabolite ID mapping table
     -s         Save ID mapping table as CSV
-    -e         Uses exact stoichiometry for merging
+    -e         Uses exact stoichiometry when merging reactions
     --version  Show the version and exit.
     --help     Show this message and exit.
 
@@ -44,19 +44,23 @@ To print merging statistics, append the "-v" flag:
 
     mergem -i model1.xml -i model2.xml -obj 1 -v 
 
-#### Importing mergem
+#### Python usage
 
 To use mergem modules within a python script, simply import the package within the script:
 
     import mergem
 
 Provide the list of models to be merged as a list to the merge function:
 
-    merge_results = mergem.merge([model1, model2,..], objective)
+    merge_results = mergem.merge(input_models, set_objective='merge', exact_sto=False)
+
+* `input_models` is a list of COBRApy model objects or strings specifying file names.
+* `set_objective` specifies if the objective functions are merged ('merge') or copied from a single model (specifying the index of the model: '1', 2', '3', etc.).
+* `exact_sto` is set to true for using exact stoichiometry when merging reactions.
+
 
-where objective can be 'merge' or model index ('1', '2', '3', etc).
 The merge function returns a dictionary of results including the merged model,
-the metabolite and reaction jaccard distances of each model with respect to first model, and the 
+the metabolite and reaction Jaccard distances of each model with respect to the first model, and the 
 metabolite and reaction model sources. 
 
 ------

docs/source/usage.rst

@@ -19,7 +19,7 @@ Printing help text displays all the options.
 ::
 
     > mergem --help
-    Usage: mergem [OPTIONS] [INPUT_FILENAMES]...
+    Usage: mergem [INPUT_FILENAMES] [OPTIONS]
 
     mergem takes genome-scale metabolic models as input, merges them into a
     single model and saves merged model as .xml. Users can optionally select the
@@ -32,7 +32,7 @@ Printing help text displays all the options.
     -v         Print merging statistics
     -up        Update ID mapping table
     -s         Save ID mapping table as CSV
-    -e         Uses exact stoichiometry for merging
+    -e         Uses exact stoichiometry when merging reactions
     --version  Show the version and exit.
     --help     Show this message and exit.
 
@@ -75,7 +75,7 @@ Save the ID mapping table as a CSV file by using the :code:`-s` argument:
     mergem model1.xml model2.xml -obj 1 -s
 
 
-To use the exact stoichiometry of the metabolites for merging, use the :code:`-e` argument:
+By default, reactions are merged when they have both a similar set of reactants and a similar set of products, without comparing their stoichiometry. To merge reactions only when they have the same exact stoichiometry in their reactants and products, use the :code:`-e` argument:
 
 ::
 
@@ -84,7 +84,7 @@ To use the exact stoichiometry of the metabolites for merging, use the :code:`-e
 
 .. _python-import:
 
-Python import
+Python
 =======================
 
 Merge models
@@ -101,10 +101,11 @@ Provide the list of models to be merged:
 
 ::
 
-    merge_results = mergem.merge([model1, model2, ..], objective)
+    merge_results = mergem.merge(input_models, set_objective='merge', exact_sto=False)
 
-where the models can be COBRApy model objects, or filenames and objective can be 'merge' or
-model number ('1', 2', '3', etc.).
+* :code:`input_models` is a list of COBRApy model objects or strings specifying file names.
+* :code:`set_objective` specifies if the objective functions are merged ('merge') or copied from a single model (specifying the index of the model: '1', 2', '3', etc.).
+* :code:`exact_sto` is set to true for using exact stoichiometry when merging reactions.
 
 
 Other mergem functions

mergem/cli.py

@@ -24,7 +24,7 @@
 @click.option('-v', help='Print merging statistics', is_flag=True)
 @click.option('-up', help='Update ID mapping table', is_flag=True)
 @click.option('-s', help='Save ID mapping table as CSV', is_flag=True)
-@click.option('-e', help='Uses exact stoichiometry for merging', is_flag=True)
+@click.option('-e', help='Uses exact stoichiometry when merging reactions', is_flag=True)
 @click.version_option(_version + "\nLobo Lab (https://lobolab.umbc.edu)")
 def main(input_filenames, obj, o=None, v=False, up=False, s=False, e=False):
     """