Feat medium

rptools/rpfba/Args.py

@@ -1,8 +1,16 @@
-from argparse  import ArgumentParser
+from argparse import ArgumentParser
+from typing import (
+    List,
+)
 from rptools._version import __version__
+from rptools.rpfba.medium import (
+    __MEDIUM_DEFAULT_ID,
+    __MEDIUM_PATH,
+    read_medium_ids
+)
 
-
-def add_arguments(parser):
+def add_arguments(
+    parser: ArgumentParser):
     parser.add_argument(
         'pathway_file',
         type=str,
@@ -60,4 +68,25 @@ def add_arguments(parser):
         default=True,
         help='ignore metabolites that are only consumed or produced (default: True)'
     )
+
+    parser_medium = parser.add_argument_group('Medium', 'Medium modifications')
+    parser_medium.add_argument('--medium_compartment_id',
+        type=str,
+        default='MNXC2',
+        help='Model compartiment id corresponding to the extra-cellular compartment'
+    )
+    parser_medium.add_argument(
+        '--medium_file',
+        type=str,
+        help='Provide a csv file with an header as <coumpond_id>,<upper_bound>. \
+                This file provides information about metabolites (Metanetx Id) to add or remove (giving upper bound value)'
+    )
+    parser_medium.add_argument(
+        '--medium_id',
+        type=str,
+        default=__MEDIUM_DEFAULT_ID,
+        choices=[__MEDIUM_DEFAULT_ID] + read_medium_ids(__MEDIUM_PATH),
+        help='Use a base medium composition. Data can be add with the option --medium_file'
+    )
+
     return parser

rptools/rpfba/__init__.py

@@ -4,6 +4,8 @@
 @author: Joan Hérisson
 """
 
-from rptools.rpfba.rpFBA import runFBA
+from rptools.rpfba.rpFBA import (
+    runFBA
+)
 
 __all__ = ['runFBA']

rptools/rpfba/__main__.py

@@ -1,3 +1,5 @@
+import pandas as pd
+
 from os import (
   path as os_path,
   makedirs as os_makedirs
@@ -17,10 +19,17 @@
 from copy import deepcopy
 from rptools import build_args_parser
 from rptools.rpfba.Args import add_arguments
-from rptools.rpfba import runFBA
+from rptools.rpfba.medium import (
+    __MEDIUM_PATH,
+    load_compounds,
+)
+from rptools.rpfba import (
+    runFBA
+)
 from rptools.rplibs.rpPathway import rpPathway
 
 def entry_point():
+    # Args.
     parser = build_args_parser(
         prog = 'rpfba',
         description='Process to Flux Balance Analysis',
@@ -36,6 +45,14 @@ def entry_point():
       logger=logger
     )
 
+    # Load compounds.
+    df_medium_base, df_medium_user = load_compounds(
+        medium_id=args.medium_id,
+        file_base=__MEDIUM_PATH,
+        file_user=args.medium_file,
+        logger=logger
+    )
+
     results = runFBA(
       pathway=pathway,
       gem_sbml_path=args.model_file,
@@ -46,6 +63,9 @@ def entry_point():
       fraction_coeff=args.fraction_of,
       merge=args.merge,
       ignore_orphan_species=args.ignore_orphan_species,
+      medium_compartment_id=args.medium_compartment_id,
+      df_medium_base=df_medium_base,
+      df_medium_user=df_medium_user,
       logger=logger
     )