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Fix the bug for MNX rxn ID in notes field #226

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merged 4 commits into from
Jun 23, 2020
+251 −71
Merged

Fix the bug for MNX rxn ID in notes field #226

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3941cde
fix-bug: mixed ID for MNXID and Notes
feiranl Jun 4, 2020
d3d7d71
fix: update with optimizeCbModel new output
feiranl Jun 4, 2020
c82e696
fix: update the missing BIGG IDs here in the notes part and also remo…
feiranl Jun 19, 2020
ce05769
Merge branch 'devel' into fix-MNXbug
BenjaSanchez Jun 22, 2020
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58 changes: 29 additions & 29 deletions ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv
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Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
rxnID rev GPR standard_name EC rxnID_kegg rxnID_MNX Source;reason
MNXR94845 1 3-(4-hydroxyphenyl)pyruvate transport MNXR94845 seed:rxn09802; unknown transporter
MNXR95431 1 acetate transport MNXR95431 rhea:27814; unknown transporter
MNXR95481 1 ADP-ribose transport MNXR95481 bigg:ADPRIBt; unknown transporter
MNXR99646 1 farnesyl diphosphate transport MNXR99646 seed:rxn13290; unknown transporter
MNXR101858 1 nicotinate transport MNXR101858 seed:rxn12806; unknown transporter
MNXR135002 1 O-phosphoethanolamine transport MNXR135002 seed:rxn05716; unknown transporter
MNXR102871 1 phosphate transport MNXR102871 rhea:32823; bigg:PItg; unknown transporter
MNXR106312 0 propionyl-CoA transport MNXR106312 bigg:r2499; unknown transporter
MNXR105076 1 UDP transport MNXR105076 bigg:UDPtg; unknown transporter
MNXR105076_2 1 UDP transport MNXR105076 bigg:UDPtg; unknown transporter
MNXR105127 1 UMP transport MNXR105127 rhea:27926; unknown transporter
MNXR104921 1 TRX1 disulphide transport MNXR104921 seed:rxn13406; unknown transporter
MNXR99110 1 oleate transport MNXR99110 rhea:33655; unknown transporter
MNXR95426 1 (R)-acetoin transport MNXR95426 bigg:ACTNt2r; unknown transporter
MNXR100259 1 L-glutamine transport MNXR100259 seed:rxn08625; bigg:GLNtm; unknown transporter
MNXR105127_2 1 UMP transport MNXR105127 rhea:27926; unknown transporter
MNXR95809 1 S-adenosyl-L-methionine transport MNXR95809 seed:rxn09784; bigg:AMETtn; unknown transporter
MNXR100449 1 glutathione transport MNXR100449 seed:rxn08677; unknown transporter
MNXR96123 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter
MNXR101385 1 D-mannose 6-phosphate transport MNXR101385 seed:rxn08880; unknown transporter
MNXR95416 1 O-acetyl-L-serine transport MNXR95416 rhea:29659; bigg:ACSERtmi; unknown transporter
MNXR100494 1 hydrogen sulfide transport MNXR100494 seed:rxn08689; unknown transporter
MNXR97002 1 L-cysteinylglycine transport MNXR97002 seed:rxn05529; unknown transporter
MNXR96123_2 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter
MNXR104966 1 thiosulfate transport MNXR104966 rhea:32807; unknown transporter
MNXR104460 1 sulphite transport MNXR104460 seed:rxn09260; unknown transporter
MNXR105071 1 UDP-D-glucose transport MNXR105071 seed:rxn09353; unknown transporter
MNXR105021 1 UDP-N-acetyl-alpha-D-glucosamine transport MNXR105021 seed:rxn09342; unknown transporter
rxnID rev GPR standard_name EC rxnID_kegg rxnID_MNX bigg Source;reason
MNXR94845 1 3-(4-hydroxyphenyl)pyruvate transport MNXR94845 seed:rxn09802; unknown transporter
MNXR95431 1 acetate transport MNXR95431 rhea:27814; unknown transporter
MNXR95481 1 ADP-ribose transport MNXR95481 ADPRIBt unknown transporter
MNXR99646 1 farnesyl diphosphate transport MNXR99646 seed:rxn13290; unknown transporter
MNXR101858 1 nicotinate transport MNXR101858 seed:rxn12806; unknown transporter
MNXR135002 1 O-phosphoethanolamine transport MNXR135002 seed:rxn05716; unknown transporter
MNXR102871 1 phosphate transport MNXR102871 PItg rhea:32823; unknown transporter
MNXR106312 0 propionyl-CoA transport MNXR106312 r2499 unknown transporter
MNXR105076 1 UDP transport MNXR105076 UDPtg unknown transporter
MNXR105076_2 1 UDP transport MNXR105076 UDPtg unknown transporter
MNXR105127 1 UMP transport MNXR105127 rhea:27926; unknown transporter
MNXR104921 1 TRX1 disulphide transport MNXR104921 seed:rxn13406; unknown transporter
MNXR99110 1 oleate transport MNXR99110 rhea:33655; unknown transporter
MNXR95426 1 (R)-acetoin transport MNXR95426 ACTNt2r unknown transporter
MNXR100259 1 L-glutamine transport MNXR100259 GLNtm seed:rxn08625; unknown transporter
MNXR105127_2 1 UMP transport MNXR105127 rhea:27926; unknown transporter
MNXR95809 1 S-adenosyl-L-methionine transport MNXR95809 AMETtn seed:rxn09784;unknown transporter
MNXR100449 1 glutathione transport MNXR100449 seed:rxn08677; unknown transporter
MNXR96123 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter
MNXR101385 1 D-mannose 6-phosphate transport MNXR101385 seed:rxn08880; unknown transporter
MNXR95416 1 O-acetyl-L-serine transport MNXR95416 ACSERtmi rhea:29659;unknown transporter
MNXR100494 1 hydrogen sulfide transport MNXR100494 seed:rxn08689; unknown transporter
MNXR97002 1 L-cysteinylglycine transport MNXR97002 seed:rxn05529; unknown transporter
MNXR96123_2 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter
MNXR104966 1 thiosulfate transport MNXR104966 rhea:32807; unknown transporter
MNXR104460 1 sulphite transport MNXR104460 seed:rxn09260; unknown transporter
MNXR105071 1 UDP-D-glucose transport MNXR105071 seed:rxn09353; unknown transporter
MNXR105021 1 UDP-N-acetyl-alpha-D-glucosamine transport MNXR105021 seed:rxn09342; unknown transporter
6 changes: 3 additions & 3 deletions ComplementaryScripts/modelCuration/CheckEnergyProduction.m
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,9 @@
mets,coefs,false,0,1000);
model_test = changeObjective(model_test,'GenerateATP', 1);
sol = optimizeCbModel(model_test);
if sol.obj <= 360 && sol.obj > 0 %later can be changed to the experimental value
if sol.f <= 360 && sol.f > 0 %later can be changed to the experimental value
energyResults = [energyResults; model.rxns(rxnID),'pass',num2str(sol.obj)];
elseif sol.obj > 360
elseif sol.f > 360
energyResults = [energyResults; model.rxns(rxnID),'Fail',num2str(sol.obj)];
else
energyResults = [energyResults; model.rxns(rxnID),'error','error'];
Expand All @@ -37,7 +37,7 @@
mets,coefs,false,0,1000);
model_test = changeObjective(model_test, model_test.rxns(end), 1);
sol = optimizeCbModel(model_test);
if sol.obj <= 120 && sol.obj > 0 %later can be changed to the experimental value
if sol.f <= 120 && sol.f > 0 %later can be changed to the experimental value
redoxResults = [redoxResults; model.rxns(rxnID),'pass',num2str(sol.obj)];
elseif sol.obj > 120
redoxResults = [redoxResults; model.rxns(rxnID),'Fail',num2str(sol.obj)];
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8 changes: 5 additions & 3 deletions ComplementaryScripts/modelCuration/addGapfillingRxnToGEM.m
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Original file line number Diff line number Diff line change
Expand Up @@ -21,15 +21,16 @@

% Load rxn properties data:
fid = fopen('../ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv','r');
rev = textscan(fid,'%s %s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
rev = textscan(fid,'%s %s %s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
newrxn.ID = rev{1};
newrxn.Rev = cellfun(@str2num, rev{2});
newrxn.GPR = rev{3};
newrxn.rxnNames = rev{4};
newrxn.rxnECNumbers = rev{5};
newrxn.rxnKEGGID = rev{6};
newrxn.rxnNotes = rev{7};
newrxn.rxnMetaNetXID = rev{8};
newrxn.rxnMetaNetXID = rev{7};
newrxn.rxnBiGGID = rev{8};
newrxn.rxnNotes = rev{9};
for i = 1:length(newrxn.rxnMetaNetXID)
if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR')
newrxn.rxnMetaNetXID{i} = '';
Expand Down Expand Up @@ -113,6 +114,7 @@
model.rxnECNumbers(rxnIndex) = newrxn.rxnECNumbers(i);
model.rxnKEGGID(rxnIndex) = newrxn.rxnKEGGID(i);
model.rxnMetaNetXID(rxnIndex) = newrxn.rxnMetaNetXID(i);
model.rxnBiGGID(rxnIndex) = newrxn.rxnBiGGID(i);
model.rxnConfidenceScores(rxnIndex) = 0;
model.rxnNotes{rxnIndex} = ['NOTES: added after Gapfilling (PR #185); ',newrxn.rxnNotes{i}];
end
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