Skip to content

Commit 1b71970

Browse files
JoshLoeckerJoshLoecker
authored
Merge pull request #198 from HelikarLab/hotfix
Modify column names
2 parents 90f6155 + c55dcf2 commit 1b71970

3 files changed

Lines changed: 151 additions & 157 deletions

File tree

‎main/como/create_context_specific_model.py‎

Lines changed: 11 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -562,31 +562,25 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions:
562562
f"'Minimum Reaction Rate', and 'Maximum Reaction Rate'. Found: {column}"
563563
)
564564

565-
reactions: list[str] = []
565+
reactions: list[str] = [""] * len(df)
566566
boundary_type: list[str] = df["reaction"].tolist()
567567
reaction_abbreviation: list[str] = df["abbreviation"].tolist()
568568
reaction_compartment: list[str] = df["compartment"].tolist()
569-
lower_bounds = df["minimum reaction rate"].tolist()
570-
upper_bounds = df["maximum reaction rate"].tolist()
569+
lower_bound = df["minimum reaction rate"].tolist()
570+
upper_bound = df["maximum reaction rate"].tolist()
571+
boundary_map = {"exchange": "EX", "demand": "DM", "sink": "SK"}
571572
for i in range(len(boundary_type)):
572-
current_type: str = boundary_type[i]
573-
temp_reaction: str = ""
574-
575-
match current_type.lower():
576-
case "exchange":
577-
temp_reaction += "EX_"
578-
case "demand":
579-
temp_reaction += "DM_"
580-
case "sink":
581-
temp_reaction += "SK_"
573+
boundary: str = boundary_type[i].lower()
574+
if boundary not in boundary_map:
575+
raise ValueError(f"Boundary reaction type must be 'Exchange', 'Demand', or 'Sink'. Found: {boundary[i]}")
582576

583577
shorthand_compartment = Compartments.get(reaction_compartment[i])
584-
temp_reaction += f"{reaction_abbreviation[i]}[{shorthand_compartment}]"
585-
reactions.append(temp_reaction)
578+
reactions[i] = f"{boundary_map.get(boundary)}_{reaction_abbreviation[i]}[{shorthand_compartment}]"
579+
586580
return _BoundaryReactions(
587581
reactions=reactions,
588-
lower_bounds=lower_bounds,
589-
upper_bounds=upper_bounds,
582+
lower_bounds=lower_bound,
583+
upper_bounds=upper_bound,
590584
)
591585

592586

‎main/data/boundary_rxns/naiveB_boundary_rxns.csv‎

Lines changed: 70 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,70 +1,70 @@
1-
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2-
Demand,Exchange,glc_D,Extracellular,-100,1000
3-
Demand,Exchange,fe2,Extracellular,-1000,1000
4-
Demand,Exchange,gal,Extracellular,0,1000
5-
Demand,Exchange,zn2,Extracellular,-1000,1000
6-
Demand,Exchange,ca2,Extracellular,-1000,1000
7-
Demand,Exchange,na1,Extracellular,-1000,1000
8-
Demand,Exchange,cl,Extracellular,-1000,1000
9-
Demand,Exchange,k,Extracellular,-1000,1000
10-
Demand,Exchange,h,Extracellular,-1000,1000
11-
Demand,Exchange,h2o,Extracellular,-1000,1000
12-
Demand,Exchange,o2,Extracellular,-1000,1000
13-
Demand,Exchange,pi,Extracellular,-1000,1000
14-
Demand,Exchange,ppi,Extracellular,-1000,1000
15-
Demand,Exchange,co2,Extracellular,-1000,1000
16-
Demand,Exchange,nh4,Extracellular,-1000,1000
17-
Demand,Exchange,no2,Extracellular,-1000,1000
18-
Demand,Exchange,co,Extracellular,-1000,1000
19-
Demand,Exchange,asn_L,Extracellular,-1,1000
20-
Demand,Exchange,asp_L,Extracellular,-1,1000
21-
Demand,Exchange,glu_L,Extracellular,-1,1000
22-
Demand,Exchange,ile_L,Extracellular,-1,1000
23-
Demand,Exchange,leu_L,Extracellular,-1,1000
24-
Demand,Exchange,lys_L,Extracellular,-1,1000
25-
Demand,Exchange,met_L,Extracellular,-1,1000
26-
Demand,Exchange,pro_L,Extracellular,-1,1000
27-
Demand,Exchange,ser_L,Extracellular,-1,1000
28-
Demand,Exchange,val_L,Extracellular,-1,1000
29-
Demand,Exchange,gly,Extracellular,-1,1000
30-
Demand,Exchange,cys_L,Extracellular,-1,1000
31-
Demand,Exchange,ala_L,Extracellular,-1,1000
32-
Demand,Exchange,his_L,Extracellular,-1,1000
33-
Demand,Exchange,thr_L,Extracellular,-1,1000
34-
Demand,Exchange,gln_L,Extracellular,-1,1000
35-
Demand,Exchange,phe_L,Extracellular,-1,1000
36-
Demand,Exchange,tyr_L,Extracellular,-1,1000
37-
Demand,Exchange,arg_L,Extracellular,-1,1000
38-
Demand,Exchange,trp_L,Extracellular,-1,1000
39-
Demand,Exchange,eicostet,Extracellular,-1,1000
40-
Demand,Exchange,hdca,Extracellular,-1,1000
41-
Demand,Exchange,hdcea,Extracellular,-1,1000
42-
Demand,Exchange,lnlc,Extracellular,-1,1000
43-
Demand,Exchange,lnlnca,Extracellular,-1,1000
44-
Demand,Exchange,lnlncg,Extracellular,-1,1000
45-
Demand,Exchange,ocdca,Extracellular,-1,1000
46-
Demand,Exchange,ocdcea,Extracellular,-1,1000
47-
Demand,Exchange,thmmp,Extracellular,0,1000
48-
Demand,Exchange,thmtp,Extracellular,0,1000
49-
Demand,Exchange,ncam,Extracellular,0,1000
50-
Demand,Exchange,pnto_R,Extracellular,0,1000
51-
Demand,Exchange,pydxn,Extracellular,0,1000
52-
Demand,Exchange,pydx,Extracellular,0,1000
53-
Demand,Exchange,pydam,Extracellular,0,1000
54-
Demand,Exchange,btn,Extracellular,0,1000
55-
Demand,Exchange,fol,Extracellular,-10,1000
56-
Demand,Exchange,aqcobal,Extracellular,0,1000
57-
Demand,Exchange,vitd3,Extracellular,-1,1000
58-
Demand,Exchange,ascb_L,Extracellular,0,1000
59-
Demand,Exchange,retinol,Extracellular,-10,1000
60-
Demand,Exchange,retinal,Extracellular,-10,1000
61-
Demand,Exchange,ala_B,Extracellular,-1,1000
62-
Demand,Exchange,ala_D,Extracellular,-1,1000
63-
Demand,Exchange,h2co3,Extracellular,-1000,1000
64-
Demand,Exchange,h2o2,Extracellular,-1000,1000
65-
Demand,Exchange,hco3,Extracellular,-1000,1000
66-
Demand,Exchange,orn,Extracellular,-1,1000
67-
Demand,Exchange,orn_D,Extracellular,-1,1000
68-
Demand,Exchange,so4,Extracellular,-1000,1000
69-
Demand,Exchange,ribflv,Extracellular,-1,1000
70-
Demand,Exchange,Lcystin,Extracellular,-1,1000
1+
Boundary,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2+
Exchange,glc_D,Extracellular,-100,1000
3+
Exchange,fe2,Extracellular,-1000,1000
4+
Exchange,gal,Extracellular,0,1000
5+
Exchange,zn2,Extracellular,-1000,1000
6+
Exchange,ca2,Extracellular,-1000,1000
7+
Exchange,na1,Extracellular,-1000,1000
8+
Exchange,cl,Extracellular,-1000,1000
9+
Exchange,k,Extracellular,-1000,1000
10+
Exchange,h,Extracellular,-1000,1000
11+
Exchange,h2o,Extracellular,-1000,1000
12+
Exchange,o2,Extracellular,-1000,1000
13+
Exchange,pi,Extracellular,-1000,1000
14+
Exchange,ppi,Extracellular,-1000,1000
15+
Exchange,co2,Extracellular,-1000,1000
16+
Exchange,nh4,Extracellular,-1000,1000
17+
Exchange,no2,Extracellular,-1000,1000
18+
Exchange,co,Extracellular,-1000,1000
19+
Exchange,asn_L,Extracellular,-1,1000
20+
Exchange,asp_L,Extracellular,-1,1000
21+
Exchange,glu_L,Extracellular,-1,1000
22+
Exchange,ile_L,Extracellular,-1,1000
23+
Exchange,leu_L,Extracellular,-1,1000
24+
Exchange,lys_L,Extracellular,-1,1000
25+
Exchange,met_L,Extracellular,-1,1000
26+
Exchange,pro_L,Extracellular,-1,1000
27+
Exchange,ser_L,Extracellular,-1,1000
28+
Exchange,val_L,Extracellular,-1,1000
29+
Exchange,gly,Extracellular,-1,1000
30+
Exchange,cys_L,Extracellular,-1,1000
31+
Exchange,ala_L,Extracellular,-1,1000
32+
Exchange,his_L,Extracellular,-1,1000
33+
Exchange,thr_L,Extracellular,-1,1000
34+
Exchange,gln_L,Extracellular,-1,1000
35+
Exchange,phe_L,Extracellular,-1,1000
36+
Exchange,tyr_L,Extracellular,-1,1000
37+
Exchange,arg_L,Extracellular,-1,1000
38+
Exchange,trp_L,Extracellular,-1,1000
39+
Exchange,eicostet,Extracellular,-1,1000
40+
Exchange,hdca,Extracellular,-1,1000
41+
Exchange,hdcea,Extracellular,-1,1000
42+
Exchange,lnlc,Extracellular,-1,1000
43+
Exchange,lnlnca,Extracellular,-1,1000
44+
Exchange,lnlncg,Extracellular,-1,1000
45+
Exchange,ocdca,Extracellular,-1,1000
46+
Exchange,ocdcea,Extracellular,-1,1000
47+
Exchange,thmmp,Extracellular,0,1000
48+
Exchange,thmtp,Extracellular,0,1000
49+
Exchange,ncam,Extracellular,0,1000
50+
Exchange,pnto_R,Extracellular,0,1000
51+
Exchange,pydxn,Extracellular,0,1000
52+
Exchange,pydx,Extracellular,0,1000
53+
Exchange,pydam,Extracellular,0,1000
54+
Exchange,btn,Extracellular,0,1000
55+
Exchange,fol,Extracellular,-10,1000
56+
Exchange,aqcobal,Extracellular,0,1000
57+
Exchange,vitd3,Extracellular,-1,1000
58+
Exchange,ascb_L,Extracellular,0,1000
59+
Exchange,retinol,Extracellular,-10,1000
60+
Exchange,retinal,Extracellular,-10,1000
61+
Exchange,ala_B,Extracellular,-1,1000
62+
Exchange,ala_D,Extracellular,-1,1000
63+
Exchange,h2co3,Extracellular,-1000,1000
64+
Exchange,h2o2,Extracellular,-1000,1000
65+
Exchange,hco3,Extracellular,-1000,1000
66+
Exchange,orn,Extracellular,-1,1000
67+
Exchange,orn_D,Extracellular,-1,1000
68+
Exchange,so4,Extracellular,-1000,1000
69+
Exchange,ribflv,Extracellular,-1,1000
70+
Exchange,Lcystin,Extracellular,-1,1000

‎main/data/boundary_rxns/smB_boundary_rxns.csv‎

Lines changed: 70 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,70 +1,70 @@
1-
Boundary,Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2-
Demand,Exchange,glc_D,Extracellular,-100,1000
3-
Demand,Exchange,fe2,Extracellular,-1000,1000
4-
Demand,Exchange,gal,Extracellular,0,1000
5-
Demand,Exchange,zn2,Extracellular,-1000,1000
6-
Demand,Exchange,ca2,Extracellular,-1000,1000
7-
Demand,Exchange,na1,Extracellular,-1000,1000
8-
Demand,Exchange,cl,Extracellular,-1000,1000
9-
Demand,Exchange,k,Extracellular,-1000,1000
10-
Demand,Exchange,h,Extracellular,-1000,1000
11-
Demand,Exchange,h2o,Extracellular,-1000,1000
12-
Demand,Exchange,o2,Extracellular,-1000,1000
13-
Demand,Exchange,pi,Extracellular,-1000,1000
14-
Demand,Exchange,ppi,Extracellular,-1000,1000
15-
Demand,Exchange,co2,Extracellular,-1000,1000
16-
Demand,Exchange,nh4,Extracellular,-1000,1000
17-
Demand,Exchange,no2,Extracellular,-1000,1000
18-
Demand,Exchange,co,Extracellular,-1000,1000
19-
Demand,Exchange,asn_L,Extracellular,-1,1000
20-
Demand,Exchange,asp_L,Extracellular,-1,1000
21-
Demand,Exchange,glu_L,Extracellular,-1,1000
22-
Demand,Exchange,ile_L,Extracellular,-1,1000
23-
Demand,Exchange,leu_L,Extracellular,-1,1000
24-
Demand,Exchange,lys_L,Extracellular,-1,1000
25-
Demand,Exchange,met_L,Extracellular,-1,1000
26-
Demand,Exchange,pro_L,Extracellular,-1,1000
27-
Demand,Exchange,ser_L,Extracellular,-1,1000
28-
Demand,Exchange,val_L,Extracellular,-1,1000
29-
Demand,Exchange,gly,Extracellular,-1,1000
30-
Demand,Exchange,cys_L,Extracellular,-1,1000
31-
Demand,Exchange,ala_L,Extracellular,-1,1000
32-
Demand,Exchange,his_L,Extracellular,-1,1000
33-
Demand,Exchange,thr_L,Extracellular,-1,1000
34-
Demand,Exchange,gln_L,Extracellular,-1,1000
35-
Demand,Exchange,phe_L,Extracellular,-1,1000
36-
Demand,Exchange,tyr_L,Extracellular,-1,1000
37-
Demand,Exchange,arg_L,Extracellular,-1,1000
38-
Demand,Exchange,trp_L,Extracellular,-1,1000
39-
Demand,Exchange,eicostet,Extracellular,-1,1000
40-
Demand,Exchange,hdca,Extracellular,-1,1000
41-
Demand,Exchange,hdcea,Extracellular,-1,1000
42-
Demand,Exchange,lnlc,Extracellular,-1,1000
43-
Demand,Exchange,lnlnca,Extracellular,-1,1000
44-
Demand,Exchange,lnlncg,Extracellular,-1,1000
45-
Demand,Exchange,ocdca,Extracellular,-1,1000
46-
Demand,Exchange,ocdcea,Extracellular,-1,1000
47-
Demand,Exchange,thmmp,Extracellular,0,1000
48-
Demand,Exchange,thmtp,Extracellular,0,1000
49-
Demand,Exchange,ncam,Extracellular,0,1000
50-
Demand,Exchange,pnto_R,Extracellular,0,1000
51-
Demand,Exchange,pydxn,Extracellular,0,1000
52-
Demand,Exchange,pydx,Extracellular,0,1000
53-
Demand,Exchange,pydam,Extracellular,0,1000
54-
Demand,Exchange,btn,Extracellular,0,1000
55-
Demand,Exchange,fol,Extracellular,-10,1000
56-
Demand,Exchange,aqcobal,Extracellular,0,1000
57-
Demand,Exchange,vitd3,Extracellular,-1,1000
58-
Demand,Exchange,ascb_L,Extracellular,0,1000
59-
Demand,Exchange,retinol,Extracellular,-10,1000
60-
Demand,Exchange,retinal,Extracellular,-10,1000
61-
Demand,Exchange,ala_B,Extracellular,-1,1000
62-
Demand,Exchange,ala_D,Extracellular,-1,1000
63-
Demand,Exchange,h2co3,Extracellular,-1000,1000
64-
Demand,Exchange,h2o2,Extracellular,-1000,1000
65-
Demand,Exchange,hco3,Extracellular,-1000,1000
66-
Demand,Exchange,orn,Extracellular,-1,1000
67-
Demand,Exchange,orn_D,Extracellular,-1,1000
68-
Demand,Exchange,so4,Extracellular,-1000,1000
69-
Demand,Exchange,ribflv,Extracellular,-1,1000
70-
Demand,Exchange,Lcystin,Extracellular,-1,1000
1+
Boundary,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
2+
Exchange,glc_D,Extracellular,-100,1000
3+
Exchange,fe2,Extracellular,-1000,1000
4+
Exchange,gal,Extracellular,0,1000
5+
Exchange,zn2,Extracellular,-1000,1000
6+
Exchange,ca2,Extracellular,-1000,1000
7+
Exchange,na1,Extracellular,-1000,1000
8+
Exchange,cl,Extracellular,-1000,1000
9+
Exchange,k,Extracellular,-1000,1000
10+
Exchange,h,Extracellular,-1000,1000
11+
Exchange,h2o,Extracellular,-1000,1000
12+
Exchange,o2,Extracellular,-1000,1000
13+
Exchange,pi,Extracellular,-1000,1000
14+
Exchange,ppi,Extracellular,-1000,1000
15+
Exchange,co2,Extracellular,-1000,1000
16+
Exchange,nh4,Extracellular,-1000,1000
17+
Exchange,no2,Extracellular,-1000,1000
18+
Exchange,co,Extracellular,-1000,1000
19+
Exchange,asn_L,Extracellular,-1,1000
20+
Exchange,asp_L,Extracellular,-1,1000
21+
Exchange,glu_L,Extracellular,-1,1000
22+
Exchange,ile_L,Extracellular,-1,1000
23+
Exchange,leu_L,Extracellular,-1,1000
24+
Exchange,lys_L,Extracellular,-1,1000
25+
Exchange,met_L,Extracellular,-1,1000
26+
Exchange,pro_L,Extracellular,-1,1000
27+
Exchange,ser_L,Extracellular,-1,1000
28+
Exchange,val_L,Extracellular,-1,1000
29+
Exchange,gly,Extracellular,-1,1000
30+
Exchange,cys_L,Extracellular,-1,1000
31+
Exchange,ala_L,Extracellular,-1,1000
32+
Exchange,his_L,Extracellular,-1,1000
33+
Exchange,thr_L,Extracellular,-1,1000
34+
Exchange,gln_L,Extracellular,-1,1000
35+
Exchange,phe_L,Extracellular,-1,1000
36+
Exchange,tyr_L,Extracellular,-1,1000
37+
Exchange,arg_L,Extracellular,-1,1000
38+
Exchange,trp_L,Extracellular,-1,1000
39+
Exchange,eicostet,Extracellular,-1,1000
40+
Exchange,hdca,Extracellular,-1,1000
41+
Exchange,hdcea,Extracellular,-1,1000
42+
Exchange,lnlc,Extracellular,-1,1000
43+
Exchange,lnlnca,Extracellular,-1,1000
44+
Exchange,lnlncg,Extracellular,-1,1000
45+
Exchange,ocdca,Extracellular,-1,1000
46+
Exchange,ocdcea,Extracellular,-1,1000
47+
Exchange,thmmp,Extracellular,0,1000
48+
Exchange,thmtp,Extracellular,0,1000
49+
Exchange,ncam,Extracellular,0,1000
50+
Exchange,pnto_R,Extracellular,0,1000
51+
Exchange,pydxn,Extracellular,0,1000
52+
Exchange,pydx,Extracellular,0,1000
53+
Exchange,pydam,Extracellular,0,1000
54+
Exchange,btn,Extracellular,0,1000
55+
Exchange,fol,Extracellular,-10,1000
56+
Exchange,aqcobal,Extracellular,0,1000
57+
Exchange,vitd3,Extracellular,-1,1000
58+
Exchange,ascb_L,Extracellular,0,1000
59+
Exchange,retinol,Extracellular,-10,1000
60+
Exchange,retinal,Extracellular,-10,1000
61+
Exchange,ala_B,Extracellular,-1,1000
62+
Exchange,ala_D,Extracellular,-1,1000
63+
Exchange,h2co3,Extracellular,-1000,1000
64+
Exchange,h2o2,Extracellular,-1000,1000
65+
Exchange,hco3,Extracellular,-1000,1000
66+
Exchange,orn,Extracellular,-1,1000
67+
Exchange,orn_D,Extracellular,-1,1000
68+
Exchange,so4,Extracellular,-1000,1000
69+
Exchange,ribflv,Extracellular,-1,1000
70+
Exchange,Lcystin,Extracellular,-1,1000

0 commit comments

Comments
 (0)