Merge branch 'master' into update_environment

HelikarLab · Nov 27, 2023 · e14c3e7 · e14c3e7
2 parents f12ebfc + 4147597
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diff --git a/README.md b/README.md
@@ -66,3 +66,8 @@ Please [follow this link](https://helikarlab.github.io/COMO/como_flowcharts.html
 
 Resources for packages used in COMO and other useful links, please
 see [here](https://helikarlab.github.io/COMO/como_resources.html)
+
+## Citation
+If you use this work, please cite it with the following
+
+Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya, COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery, Briefings in Bioinformatics, Volume 24, Issue 6, November 2023, bbad387, https://doi.org/10.1093/bib/bbad387
diff --git a/main/COMO.ipynb b/main/COMO.ipynb
@@ -705,9 +705,6 @@
     "general_model_file = \"GeneralModelUpdatedV2.mat\"\n",
     "recon_algorithms = ['IMAT']\n",
     "solver = \"GUROBI\"\n",
-    "boundary_reactions_filename = \"default_boundary_rxns.csv\"\n",
-    "force_reactions_filename = \"default_force_rxns.csv\"\n",
-    "exclude_reactions_filename = \"\"\n",
     "\n",
     "import os\n",
     "import json\n",

diff --git a/...a/boundary_rxns/default_boundary_rxns.csv → ...ta/boundary_rxns/naiveB_boundary_rxns.csv b/...a/boundary_rxns/default_boundary_rxns.csv → ...ta/boundary_rxns/naiveB_boundary_rxns.csv
diff --git a/main/data/boundary_rxns/smB_boundary_rxns.csv b/main/data/boundary_rxns/smB_boundary_rxns.csv
@@ -0,0 +1,70 @@
+Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
+Exchange,glc_D,Extracellular,-100,1000
+Exchange,fe2,Extracellular,-1000,1000
+Exchange,gal,Extracellular,0,1000
+Exchange,zn2,Extracellular,-1000,1000
+Exchange,ca2,Extracellular,-1000,1000
+Exchange,na1,Extracellular,-1000,1000
+Exchange,cl,Extracellular,-1000,1000
+Exchange,k,Extracellular,-1000,1000
+Exchange,h,Extracellular,-1000,1000
+Exchange,h2o,Extracellular,-1000,1000
+Exchange,o2,Extracellular,-1000,1000
+Exchange,pi,Extracellular,-1000,1000
+Exchange,ppi,Extracellular,-1000,1000
+Exchange,co2,Extracellular,-1000,1000
+Exchange,nh4,Extracellular,-1000,1000
+Exchange,no2,Extracellular,-1000,1000
+Exchange,co,Extracellular,-1000,1000
+Exchange,asn_L,Extracellular,-1,1000
+Exchange,asp_L,Extracellular,-1,1000
+Exchange,glu_L,Extracellular,-1,1000
+Exchange,ile_L,Extracellular,-1,1000
+Exchange,leu_L,Extracellular,-1,1000
+Exchange,lys_L,Extracellular,-1,1000
+Exchange,met_L,Extracellular,-1,1000
+Exchange,pro_L,Extracellular,-1,1000
+Exchange,ser_L,Extracellular,-1,1000
+Exchange,val_L,Extracellular,-1,1000
+Exchange,gly,Extracellular,-1,1000
+Exchange,cys_L,Extracellular,-1,1000
+Exchange,ala_L,Extracellular,-1,1000
+Exchange,his_L,Extracellular,-1,1000
+Exchange,thr_L,Extracellular,-1,1000
+Exchange,gln_L,Extracellular,-1,1000
+Exchange,phe_L,Extracellular,-1,1000
+Exchange,tyr_L,Extracellular,-1,1000
+Exchange,arg_L,Extracellular,-1,1000
+Exchange,trp_L,Extracellular,-1,1000
+Exchange,eicostet,Extracellular,-1,1000
+Exchange,hdca,Extracellular,-1,1000
+Exchange,hdcea,Extracellular,-1,1000
+Exchange,lnlc,Extracellular,-1,1000
+Exchange,lnlnca,Extracellular,-1,1000
+Exchange,lnlncg,Extracellular,-1,1000
+Exchange,ocdca,Extracellular,-1,1000
+Exchange,ocdcea,Extracellular,-1,1000
+Exchange,thmmp,Extracellular,0,1000
+Exchange,thmtp,Extracellular,0,1000
+Exchange,ncam,Extracellular,0,1000
+Exchange,pnto_R,Extracellular,0,1000
+Exchange,pydxn,Extracellular,0,1000
+Exchange,pydx,Extracellular,0,1000
+Exchange,pydam,Extracellular,0,1000
+Exchange,btn,Extracellular,0,1000
+Exchange,fol,Extracellular,-10,1000
+Exchange,aqcobal,Extracellular,0,1000
+Exchange,vitd3,Extracellular,-1,1000
+Exchange,ascb_L,Extracellular,0,1000
+Exchange,retinol,Extracellular,-10,1000
+Exchange,retinal,Extracellular,-10,1000
+Exchange,ala_B,Extracellular,-1,1000
+Exchange,ala_D,Extracellular,-1,1000
+Exchange,h2co3,Extracellular,-1000,1000
+Exchange,h2o2,Extracellular,-1000,1000
+Exchange,hco3,Extracellular,-1000,1000
+Exchange,orn,Extracellular,-1,1000
+Exchange,orn_D,Extracellular,-1,1000
+Exchange,so4,Extracellular,-1000,1000
+Exchange,ribflv,Extracellular,-1,1000
+Exchange,Lcystin,Extracellular,-1,1000
diff --git a/main/data/exclude_rxns/naiveB_exclude_rxns.csv b/main/data/exclude_rxns/naiveB_exclude_rxns.csv
@@ -0,0 +1 @@
+Abbreviation
diff --git a/main/data/exclude_rxns/smB_exclude_rxns.csv b/main/data/exclude_rxns/smB_exclude_rxns.csv
@@ -0,0 +1 @@
+Abbreviation
diff --git a/main/src/create_context_specific_model.py b/main/src/create_context_specific_model.py
@@ -775,7 +775,7 @@ def main(argv):
                 )
                 sys.exit()
 
-            exclude_rxns = df.iloc[:, 0].tolist()
+            exclude_rxns = df["Abbreviation"].tolist()
 
         except FileNotFoundError:
             print(

diff --git a/main/src/rnaseq_preprocess.py b/main/src/rnaseq_preprocess.py
@@ -429,15 +429,16 @@ async def main(argv):
         sys.exit()
 
     # handle species alternative ids
-    if type(args.taxon_id) == str:
+    if isinstance(args.taxon_id, str):
         if args.taxon_id.upper() == "HUMAN" or args.taxon_id.upper() == "HOMO SAPIENS":
             taxon_id = TaxonID.HOMO_SAPIENS
         elif args.taxon_id.upper() == "MOUSE" or args.taxon_id.upper() == "MUS MUSCULUS":
             taxon_id = TaxonID.MUS_MUSCULUS
         else:
             print("--taxon-id must be either an integer, or accepted string ('mouse', 'human')")
             sys.exit(1)
-    elif type(args.taxon_id) == int:
+
+    elif isinstance(args.taxon_id, int):
         taxon_id = args.taxon_id
     else:
         print("--taxon-id must be either an integer, or accepted string ('mouse', 'human')")