Merge branch 'develop' into fix/CLYBL_rxns

SysBioChalmers · Jun 8, 2023 · 1f66cd7 · 1f66cd7
2 parents 728968c + 34dd975
commit 1f66cd7
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Showing 6 changed files with 11 additions and 61 deletions.
diff --git a/code/io/importYaml.m b/code/io/importYaml.m
@@ -28,14 +28,16 @@
 if verLessThan('matlab','9.9') %readlines introduced 2020b
     fid=fopen(yamlFilename);
     line_raw=cell(1000000,1);
+    i=1;
     while ~feof(fid)
         line_raw{i}=fgetl(fid);
         i=i+1;
     end
     line_raw(i:end)=[];
     line_raw=string(line_raw);
+    fclose(fid);
 else
-    line_raw=readlines(yamlFilename');
+    line_raw=readlines(yamlFilename);
 end
 
 line_key=regexprep(line_raw,'^ *-? ([^:]+)(:).*','$1');
@@ -274,7 +276,7 @@
     fprintf('\nimporting completed\nfollow-up processing...');
 end
 [~, model.metComps] = ismember(model.metComps, model.comps);
-model.metCharges = int64(str2double(model.metCharges));
+model.metCharges = str2double(model.metCharges);
 model.lb = str2double(model.lb);
 model.ub = str2double(model.ub);
 model.annotation.defaultLB = min(model.lb);

diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2200,5 +2200,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01421c"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421c"	"m01421c"
 "MAM01421m"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421m"	"m01421m"
 "MAM01421e"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421s"	"m01421s"
+"MAM03573m"	"MAM03573"	"etfox"	""	""	""	""	""	""	""	"etfox"	"MNXM11479"	""	"etfox_m"
+"MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
-"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
+"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -105,4 +105,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
 "MAR05294"	"R00362"	""	"R00362C"	"r1109"	""	"r1109"	"MNXR96731"	"HMR_5294"	"RCR11670"	""	0	"RHEA:10761"	"RHEA:10760"	"HMR_5294"
 "MAR11421"	""	"CITL"	""	""	""	"CITL"	"MNXR96731"	""	""	""	0	"RHEA:10761"	"RHEA:10760"	"CITL"
+"MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
+"MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -44993,22 +44993,6 @@
       - charge: 0
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03573m"
-      - name: "Electron Transfer Flavoprotein Oxidized"
-      - compartment: "m"
-      - formula: "R"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03574m"
-      - name: "Electron Transfer Flavoprotein Reduced"
-      - compartment: "m"
-      - formula: "RH2"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM01893e"
       - name: "1-Acyl Phosphoglycerol"
@@ -95242,11 +95226,11 @@
           - MAM03103m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000073578 and ENSG00000117118 and ENSG00000143252 and ENSG00000204370"
+      - gene_reaction_rule: "ENSG00000140374 or ENSG00000105379 or ENSG00000171503 or ENSG00000100033 or ENSG00000250799 or ENSG00000115159 or ENSG00000102967 or ENSG00000016391"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.5.5.1"
-      - references: ""
+      - references: "PMID:34428349"
       - subsystem:
           - "Oxidative phosphorylation"
       - confidence_score: 0
@@ -222109,42 +222093,6 @@
       - subsystem:
           - "N-glycan metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR00562"
-      - name: "Electron Transfer Flavoprotein"
-      - metabolites: !!omap
-          - MAM01802m: 1
-          - MAM01803m: -1
-          - MAM03573m: -1
-          - MAM03574m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105379 and ENSG00000140374"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:3170610;PMID:7601336"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR00563"
-      - name: "Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase"
-      - metabolites: !!omap
-          - MAM03102m: 1
-          - MAM03103m: -1
-          - MAM03573m: 1
-          - MAM03574m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000171503"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.5.5.1"
-      - references: "PMID:10444348;PMID:12049629"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR00564"
       - name: "Exchange of 1 Acyl Phosphoglycerol"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -5622,8 +5622,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03591g"	"MAM03591"	"glc1man"	""	""	""	"440240"	""	""	""	"glc1man"	"MNXM7382"	""	"glc1man_g"
 "MAM03592g"	"MAM03592"	"glc2man"	""	""	""	""	""	""	""	"glc2man"	"MNXM13501"	""	"glc2man_g"
 "MAM03593g"	"MAM03593"	"glc3man"	""	""	""	""	""	""	""	"glc3man"	"MNXM18136"	""	"glc3man_g"
-"MAM03573m"	"MAM03573"	"etfox"	""	""	""	""	""	""	""	"etfox"	"MNXM11479"	""	"etfox_m"
-"MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM01893e"	"MAM01893"	"1glyc_hs"	""	""	""	""	""	""	""	"1glyc_hs"	"MNXM13807"	""	"1glyc_hs_s"
 "MAM03315e"	"MAM03315"	"9_cis_retfa"	""	""	""	""	""	""	""	"9_cis_retfa"	"MNXM146565"	""	"9_cis_retfa_s"
 "MAM03577e"	"MAM03577"	"fucfuc12gal14acglcgalgluside_hs"	""	""	""	""	""	""	""	"fucfuc12gal14acglcgalgluside_hs"	"MNXM8840"	""	"fucfuc12gal14acglcgalgluside_hs_s"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -8254,8 +8254,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00480"	""	"ENMAN4g"	""	""	""	"ENMAN4g"	"MNXR97929"	""	""	""	0	""	""	"ENMAN4g"
 "MAR00485"	""	"ENMAN5g"	""	""	""	"ENMAN5g"	"MNXR97930"	""	""	""	0	""	""	"ENMAN5g"
 "MAR00554"	""	"ENMAN6g"	""	""	""	"ENMAN6g"	"MNXR97931"	""	""	""	0	""	""	"ENMAN6g"
-"MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
-"MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR00564"	""	"EX_1glyc_hs_e"	""	""	""	"EX_1glyc_hs[e]"	"MNXR97997"	""	""	""	0	""	""	"EX_1glyc_hs[e]"
 "MAR00565"	""	"EX_9_cis_retfa_e"	""	""	""	"EX_9_cis_retfa[e]"	"MNXR98098"	""	""	""	0	""	""	"EX_9_cis_retfa[e]"
 "MAR00566"	""	"EX_adrn_e"	""	""	""	"EX_adrn[e]"	"MNXR98235"	""	""	""	0	""	""	"EX_adrn[e]"