Merge branch 'develop' into pr/662

SysBioChalmers · Jun 26, 2023 · d562f56 · d562f56
2 parents 24ef6e6 + 97ba938
commit d562f56
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Showing 7 changed files with 179 additions and 831 deletions.
diff --git a/code/GPRs/simplifyGrRules.m b/code/GPRs/simplifyGrRules.m
@@ -176,7 +176,7 @@
 eqn = str2sym(eqn_str);
 
 % separate equation into terms/pieces ("children")
-eqn_pieces = arrayfun(@char,children(eqn),'UniformOutput',false);
+eqn_pieces = cellfun(@char,children(eqn),'UniformOutput',false);
 
 % find pieces that are further separable, and recursively separate until
 % all pieces are single genes
@@ -202,12 +202,14 @@
 %% Functions to test whether an equation is a collection of ORs or ANDs
 function res = is_or(eqn)
 % check if outermost operations contain ORs
-res = length(regexp(char(eqn),'\|')) > length(regexp(char(children(eqn)),'\|'));
+res = length(regexp(char(eqn),'\|')) > ...
+    sum(cell2mat(cellfun(@(x) length(regexp(char(x), '\|')), children(eqn), 'UniformOutput', false)));
 end
 
 function res = is_and(eqn)
 % check if outermost operations contain ANDs
-res = length(regexp(char(eqn),'&')) > length(regexp(char(children(eqn)),'&'));
+res = length(regexp(char(eqn),'&')) > ...
+    sum(cell2mat(cellfun(@(x) length(regexp(char(x), '\&')), children(eqn), 'UniformOutput', false)));
 end
 
 

diff --git a/code/test/sanityCheck.py b/code/test/sanityCheck.py
@@ -93,7 +93,7 @@ def checkUnusedEntities(model, entity_type):
 
     # collect unused entites
     unused_entities = find_unused_entities(model, entity_type)
-    assert len(unused_entities) == 0, f"Found unused {{entity_type}}!"
+    assert len(unused_entities) == 0, f"Found unused {entity_type}: {unused_entities}"
 
 
 if __name__ == "__main__":

diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2204,5 +2204,14 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
 "MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
+"MAM03318e"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_s"
+"MAM03318c"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_c"
+"MAM03318r"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_r"
+"MAM03318m"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_m"
+"MAM03325c"	"MAM03325"	"C08276"	"C08276"	"HMDB0001527"	"CHEBI:1438"	"563"	""	""	""	"C08276"	"MNXM2782"	""	"C08276_c"
+"MAM00591c"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591c"	"m00591c"
+"MAM00591e"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591s"	"m00591s"
+"MAM03162c"	"MAM03162"	""	"C05578"	""	"CHEBI:27404"	""	""	""	""	"M03162"	"MNXM2336"	"m03162c"	"m03162c"
+"MAM03231c"	"MAM03231"	""	""	""	"CHEBI:57277"	""	""	""	""	"3hppa"	""	""	"3hppa_c"
 "MAM03540c"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_c"
-"MAM03540e"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_s"
+"MAM03540e"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_s"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -103,11 +103,26 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
 "MAR08749"	""	"H2CO3D2"	""	""	""	"HMR_8749"	"MNXR100483"	"HMR_8749"	"RCR14128"	""	1	""	""	"HMR_8749"
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
+"MAR02035"	""	"r0310"	""	""	""	"r0310"	""	""	""	""	0	""	""	"r0310"
+"MAR03211"	"R00924"	""	""	"r0683"	""	"r0683"	"MNXR103101"	"HMR_3211"	"RCR14348"	""	0	""	""	"HMR_3211"
+"MAR03751"	"R02660"	""	"R02660M"	"r0560"	""	"r0560"	""	"HMR_3751"	"RCR14421"	""	0	""	""	"HMR_3751"
+"MAR03783"	"R03172"	""	"R03172M"	"r0603"	""	"r0603"	"MNXR108000"	"HMR_3783"	"RCR14424"	""	0	""	""	"HMR_3783"
+"MAR04242"	"R02487"	""	"R02487M"	"r0541"	""	"r0541"	"MNXR100293"	"HMR_4242"	"RCR14356"	""	0	""	"RHEA:30847"	"HMR_4242"
+"MAR03769"	"R04095"	""	"R04095M"	"r0655"	""	"r0655"	"MNXR95318"	"HMR_3769"	"RCR14423"	""	0	""	""	"HMR_3769"
+"MAR03838"	""	""	""	"r1453"	""	""	""	"HMR_3838"	"RCR14286"	""	0	""	""	"HMR_3838"
+"MAR02366"	""	"r1446"	""	""	""	"r1446"	""	""	""	""	0	""	""	"r1446"
+"MAR02367"	""	"r1447"	""	""	""	"r1447"	""	""	""	""	0	""	""	"r1447"
+"MAR02370"	""	"r1449"	""	""	""	"r1449"	""	""	""	""	0	""	""	"r1449"
+"MAR02372"	""	"r1450"	""	""	""	"r1450"	""	""	""	""	0	""	""	"r1450"
+"MAR02373"	""	"r1451"	""	""	""	"r1451"	""	""	""	""	0	""	""	"r1451"
+"MAR00483"	"R00849"	""	""	"r0205"	""	"r0205"	"MNXR106713"	"HMR_0483"	"RCR21050"	""	0	""	"RHEA:18977"	"HMR_0483"
+"MAR08743"	"R00408"	"SUCD1m"	""	""	""	"SUCD1m"	"MNXR99636"	"HMR_8743"	"RCR11674"	""	0	""	"RHEA:30343"	"HMR_8743"
 "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"
+"MAR02369"	""	"r1448"	""	""	""	"r1448"	""	""	""	""	0	""	""	"r1448"
 "MAR02185"	""	""	""	""	""	"r0701"	""	""	""	""	0	""	""	"r0701"
 "MAR11649"	""	""	""	""	""	"PAIL_hs_t1e"	""	""	""	""	0	""	""	"PAIL_hs_t1e"
 "MAR11729"	""	""	""	""	""	"2HXIC_Lt2e"	""	""	""	""	0	""	""	"2HXIC_Lt2e"
@@ -142,4 +157,21 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20015"	"R02549"	"ABUTD;ABUTDm;R_ABUTD;R_ABUTDm"	""	""	""	""	"MNXR95191"	""	""	""	0	"RHEA:19105"	""	""
 "MAR20014"	"R03283"	"R_TMABADH;TMABADH"	""	""	""	""	"MNXR104876"	""	""	""	0	"RHEA:17985"	""	""
 "MAR20052"	""	"ALDD21;RE3076X;R_ALDD21;R_RE3076X"	""	""	""	""	"MNXR95747"	""	""	""	0	"RHEA:44016"	""	""
-"MAR04506"	""	"C120CPT1"	""	""	""	"C120CPT1"	""	""	""	""	0	""	""	"C120CPT1"
+"MAR02276"	""	"r0993"	""	""	""	"r0993"	"MNXR105414"	""	""	""	0	""	""	"r0993"
+"MAR02277"	""	"r0994"	""	""	""	"r0994"	"MNXR105415"	""	""	""	0	""	""	"r0994"
+"MAR02384"	""	"r1495"	""	""	""	"r1495"	"MNXR105478"	""	""	""	0	""	""	"r1495"
+"MAR02390"	""	"r2157"	""	""	""	"r2157"	"MNXR106054"	""	""	""	0	""	""	"r2157"
+"MAR02392"	""	"r2158"	""	""	""	"r2158"	"MNXR106055"	""	""	""	0	""	""	"r2158"
+"MAR02394"	""	"r2159"	""	""	""	"r2159"	"MNXR106056"	""	""	""	0	""	""	"r2159"
+"MAR04144"	""	"EX_C02528_e"	""	""	""	"EX_C02528[e]"	"MNXR98101"	""	""	""	0	""	""	"EX_C02528[e]"
+"MAR10447"	""	"HC02220c"	""	""	""	"HC02220c"	""	""	""	""	0	""	""	"HC02220c"
+"MAR00941"	"R07041"	""	"R07041C"	""	""	""	"MNXR110751"	"HMR_0941"	"RCR12090"	""	0	""	""	"HMR_0941"
+"MAR06142"	""	""	""	"r2236"	""	""	"MNXR106133"	"HMR_6142"	"RCR40595"	"2.A.60.1.5"	0	""	""	"HMR_6142"
+"MAR06143"	""	""	""	"r2237"	""	""	"MNXR106134"	"HMR_6143"	"RCR40596"	"2.A.60.1.5"	0	""	""	"HMR_6143"
+"MAR06144"	""	""	""	"r2238"	""	""	"MNXR106135"	"HMR_6144"	"RCR40597"	"2.A.60.1.5"	0	""	""	"HMR_6144"
+"MAR06220"	""	""	""	"r2315"	""	""	"MNXR106212"	"HMR_6220"	"RCR40672"	"2.A.60.1.2"	0	""	""	"HMR_6220"
+"MAR06252"	""	""	""	"r2346"	""	""	"MNXR106235"	"HMR_6252"	"RCR40129"	""	0	""	""	"HMR_6252"
+"MAR09733"	"R03674"	""	""	""	""	"HMR_9733"	"MNXR108330"	"HMR_9733"	"RCR14346"	""	0	""	""	"HMR_9733"
+"MAR09734"	"R04884"	""	""	""	""	"HMR_9734"	"MNXR109190"	"HMR_9734"	"RCR14347"	""	0	"RHEA:33516"	"RHEA:33515"	"HMR_9734"
+"MAR10025"	""	""	""	""	""	""	""	""	""	""	0	""	""	"HMR_10025"
+"MAR04506"	""	"C120CPT1"	""	""	""	"C120CPT1"	""	""	""	""	0	""	""	"C120CPT1"