add community script

scripts/merge_community

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+from framed import load_cbmodel, save_cbmodel, Environment
+from framed.community.model import Community
+from carveme import config, project_dir
+from carveme.reconstruction.utils import load_media_db
+
+
+def main(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None, mediadb=None, outputfile=None):
+
+    if not flavor:
+        flavor = config.get('sbml', 'default_flavor')
+
+    if outputfile:
+        model_id = os.path.splitext(os.path.basename(outputfile))[0]
+    else:
+        model_id = 'community'
+        outputfile = 'community.xml'
+
+    models = [load_cbmodel(inputfile, flavor=flavor) for inputfile in inputfiles]
+
+    community = Community(model_id, models,
+                          extracellular_compartment_id='e',
+                          merge_extracellular_compartments=(not split_pool),
+                          create_biomass=(not no_biomass))
+
+    merged = community.generate_merged_model()
+
+    if init:
+        if not mediadb:
+            mediadb = project_dir + config.get('input', 'media_library')
+
+        try:
+            media_db = load_media_db(mediadb)
+        except IOError:
+            raise IOError('Failed to load media library:' + mediadb)
+
+        if split_pool:
+            exchange_format = "'R_EX_M_{}_e_pool'"
+        else:
+            exchange_format = "'R_EX_{}_e'"
+        init_env = Environment.from_compounds(media_db[init], exchange_format=exchange_format)
+        init_env.apply(merged, inplace=True)
+
+    save_cbmodel(merged, outputfile, flavor=flavor)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description="Merge single species models into a microbial community model")
+
+    parser.add_argument('input', metavar='INPUTFILES', nargs='+', help="SBML input files (single species)")
+
+    parser.add_argument('-o', '--output', dest='output', help="SBML output file (community)")
+
+    parser.add_argument('--split-pool', action='store_true', dest='split_pool',
+                        help='Keep individual extracellular compartments separated from common metabolite pool.')
+
+    parser.add_argument('--no-community-biomass', action='store_true', dest='no_biomass',
+                        help='Do not create a common community biomass equation.')
+
+    parser.add_argument('-i', '--init', dest='init',
+                        help="Initialize model with given medium")
+
+    parser.add_argument('--mediadb', help="Media database file")
+
+    sbml = parser.add_mutually_exclusive_group()
+    sbml.add_argument('--cobra', action='store_true', help="Output SBML in old cobra format")
+    sbml.add_argument('--fbc2', action='store_true', help="Output SBML in sbml-fbc2 format")
+
+    args = parser.parse_args()
+
+    if len(args.input) < 2:
+        print args.input
+        parser.error("Please provide two or more single species models as input files.")
+
+    if args.fbc2:
+        flavor = 'fbc2'
+    elif args.cobra:
+        flavor = 'cobra'
+    else:
+        flavor = None
+
+    main(inputfiles=args.input,
+         flavor=flavor,
+         split_pool=args.split_pool,
+         no_biomass=args.no_biomass,
+         init=args.init,
+         mediadb=args.mediadb,
+         outputfile=args.output)
+
+
+