Merge branch 'develop' into feat/gene-essentiality-workflow

code/addMetabolicNetwork.m

@@ -144,8 +144,11 @@
     newGenes = setdiff(newGenes, newModel.genes);
 end
 
-% append new genes to list of model genes
+% append new genes and their names to model
 newModel.genes = [newModel.genes; newGenes];
+emptyGeneNames = newGenes;
+emptyGeneNames(:) = {''};
+newModel.geneShortNames = [newModel.geneShortNames; emptyGeneNames];
 
 % add new columns to rxnGeneMat will be updated after the new reactions are added below.
 newModel.rxnGeneMat(:, end+1:end+numel(newGenes)) = 0;

code/test/sanityCheck.py

@@ -38,8 +38,12 @@ def checkRxnAnnotation(rxns):
     rxnList = get_column_from_tsv("model/reactions.tsv", "rxns")
     spontaneous = get_column_from_tsv("model/reactions.tsv", "spontaneous", False)
     rxnDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedReactions.tsv", "rxns")
-    assert set(rxnList).isdisjoint(set(rxnDeprecated)), "Deprecated reaction reused!"
-    assert rxnList == rxns, "Reaction annotation mismatch!"
+    rxnMisused = set(rxns).intersection(set(rxnDeprecated))
+    assert len(rxnMisused) == 0, "Deprecated reaction(s) used: {}".format(rxnMisused)
+    rxnMisused = set(rxns).difference(set(rxnList))
+    assert len(rxnMisused) == 0, "Reaction(s) not annotated in reactions.tsv: {}".format(rxnMisused)
+    rxnMisused = set(rxnList).difference(set(rxns))
+    assert len(rxnMisused) == 0, "Annotated reactions are missing from the model: {}".format(rxnMisused)  
     assert pd.api.types.is_numeric_dtype(spontaneous), "Spontaneous column should be in numeric!"
 
 
@@ -49,16 +53,22 @@ def checkMetAnnotation(mets):
     """
     metList = get_column_from_tsv("model/metabolites.tsv", "mets")
     metDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedMetabolites.tsv", "mets")
-    assert set(metList).isdisjoint(set(metDeprecated)), "Deprecated metabolite reused!"
-    assert metList == mets, "Metabolite annotation mismatch!"
-
+    metMisused = set(mets).intersection(set(metDeprecated))
+    assert len(metMisused) == 0, "Deprecated metabolite(s) used: {}".format(metMisused)
+    metMisused = set(mets).difference(set(metList))
+    assert len(metMisused) == 0, "Metabolite(s) not annotated in metabolites.tsv: {}".format(metMisused)
+    metMisused = set(metList).difference(set(mets))
+    assert len(metMisused) == 0, "Annotated metabolite(s) are missing from the model: {}".format(metMisused)  
 
 def checkGeneAnnotation(genes):
     """
     check consistency of gene lists between model and annotation file
     """
     geneList = get_column_from_tsv("model/genes.tsv", "genes")
-    assert geneList == genes, "Gene annotation mismatch!"
+    geneMisused = set(genes).difference(set(geneList))
+    assert len(geneMisused) == 0, "Gene(s) not annotated in genes.tsv: {}".format(geneMisused)
+    geneMisused = set(geneList).difference(set(genes))
+    assert len(geneMisused) == 0, "Annotated gene(s) are missing from the model: {}".format(geneMisused)  
 
 
 def find_unused_entities(model, entity_type):

code/updateAnimalGEM.m

@@ -1,4 +1,4 @@
-function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId)
+function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId,resetBiomass)
 % updateAnimalGEM
 %   Generate a model by using the Human-GEM as a template and taking into
 %   account species-specific pathways/reactions
@@ -11,7 +11,9 @@
 %   rxnsToAdd            the structure of species-specific reactions
 %   metsToAdd            the structure of species-specific metabolites
 %   modelId              model id
-%
+%   resetBiomass         reset biomass objective function to "biomass_components"
+%                        which is constituted by generic componenets that
+%                        suppose to occur in a eukaryotic cell (opt, default TRUE)
 %
 %   Output:
 %   animalGEM            an updated animal GEM
@@ -81,7 +83,8 @@
 
 
 %% Gap-filling
-[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman);
+[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman,resetBiomass);
+animalGEM.b = animalGEM.b(:,1);   % ensure b field in single column
 
 
 %% post-gapfilling procedures

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2228,4 +2228,22 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03368m"	"MAM03368"	""	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	""	"CE5169"	""	"CE5169"	""	""	"CE5169_m"
 "MAM03368x"	"MAM03368"	""	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	""	"CE5169"	""	"CE5169"	""	""	"CE5169_p"
 "MAM00902c"	"MAM00902"	""	""	""	""	""	""	"CE4820"	""	"CE4820"	"MNXM164259"	"m00902c"	"m00902c"
+"MAM00616m"	"MAM00616"	"cholcoar"	"C15613"	""	"CHEBI:37642"	"15942889"	"LMST01010218"	"CE5165"	"HC01348"	"cholcoar"	"MNXM549;MNXM90922;MNXM91096"	"m00616p"	"m00616p"
+"MAM00749m"	"MAM00749"	"cholcoads"	"C05460"	"HMDB0006889"	"CHEBI:27505"	"5280797"	"LMST01010217"	""	"HC01466"	"cholcoads"	"MNXM162945;MNXM2747"	"m00749m"	"m00749m"
+"MAM00036m"	"MAM00036"	""	"C05450"	""	"CHEBI:52050"	"46224537"	""	"CE5168"	""	"HC01459"	"MNXM732;MNXM827"	"m00036m"	"m00036m"
+"MAM00748m"	"MAM00748"	"cholcoaone"	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	"LMST01010216"	"CE5169"	"HC01473"	"cholcoaone"	"MNXM162946;MNXM873"	"m00748m"	"m00748m"
+"MAM03367m"	"MAM03367"	""	""	""	""	""	""	"CE5168"	""	"CE5168"	""	""	"CE5168_m"
+"MAM00618m"	"MAM00618"	"cholcoas"	"C17343"	""	"CHEBI:37643"	"15942888"	""	"CE5166"	""	"CE5166;cholcoas"	"MNXM1201;MNXM8131"	"m00618m"	"m00618m"
+"MAM01445m"	"MAM01445"	"cholate"	"C00695"	"HMDB0000619"	"CHEBI:16359"	"221493"	"LMST04010001"	""	"HC00502"	"cholate"	"MNXM450"	"m01445m"	"m01445m"
+"MAM01514m"	"MAM01514"	"cholcoa"	"C01794"	"HMDB0001374"	"CHEBI:15519"	"439573"	""	""	"HC00844"	"cholcoa"	"MNXM162468;MNXM431"	"m01514m"	"m01514m"
 "MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
+"MAM01268c"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268c"	"m01268c"
+"MAM01268m"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268m"	"m01268m"
+"MAM01268n"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268n"	"m01268n"
+"MAM01268x"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268p"	"m01268p"
+"MAM01268r"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268r"	"m01268r"
+"MAM01268e"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268s"	"m01268s"
+"MAM02757c"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757c"	"m02757c"
+"MAM02757l"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757l"	"m02757l"
+"MAM02757n"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757n"	"m02757n"
+"MAM01816n"	"MAM01816"	""	""	""	""	""	"PROTEIN"	""	""	"M01816"	""	"m01816n"	"m01816n"

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -194,4 +194,40 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03441"	""	"RE3150C"	""	""	""	"RE3150C"	"MNXR103806"	""	""	""	0	""	""	"RE3150C"
 "MAR10164"	""	""	""	""	""	"CE2516t"	""	""	""	""	0	""	""	"CE2516t"
 "MAR10433"	""	""	""	""	""	"EX_CE2516[e]"	""	""	""	""	0	""	""	"EX_CE2516[e]"
+"MAR01630"	""	""	""	""	"R-HSA-192325"	"HMR_1630"	"MNXR125295"	"HMR_1630"	"RCR20511"	""	0	""	""	"HMR_1630"
+"MAR01635"	"R08734"	""	"RE2624M"	""	"R-HSA-192056"	"HMR_1635;RE2624M"	"MNXR112240"	"HMR_1635"	"RCR13606"	""	0	"RHEA:40456"	"RHEA:40455"	"HMR_1635"
+"MAR01637"	""	""	"RE3247M"	"r0706"	"R-HSA-192335"	"HMR_1637;RE3247M"	"MNXR105369;MNXR124225"	"HMR_1637"	"RCR13607"	""	0	""	""	"HMR_1637"
+"MAR01644"	"R04813"	""	"RE3248M"	""	""	"HMR_1644"	""	"HMR_1644"	"RCR12830"	""	0	""	"RHEA:18933"	"HMR_1644"
+"MAR01653"	"R03719"	"SCPx"	"R03719X"	"r0628"	""	"HMR_1653"	"MNXR104297;MNXR108369"	"HMR_1653"	"RCR13610"	""	0	""	"RHEA:16865"	"HMR_1653"
+"MAR03754"	""	""	""	""	""	"RE3248M"	""	""	""	""	0	""	""	"RE3248M"
+"MAR03760"	""	""	""	""	""	"RE3250M"	""	""	""	""	0	""	""	"RE3250M"
+"MAR01656"	""	""	""	"r0990"	""	"r0990"	"MNXR105412"	"HMR_1656"	"RCR20134"	""	0	""	""	"HMR_1656"
+"MAR07758"	""	""	"RT0402"	""	""	"HMR_7758"	""	"HMR_7758"	"RCR20277"	""	0	""	""	"HMR_7758"
+"MAR01662"	"R07296"	""	"RE1834M"	""	""	"RE1834M"	"MNXR103558;MNXR110971"	"HMR_1662"	"RCR13611"	""	0	"RHEA:14542"	"RHEA:14541"	"HMR_1662"
+"MAR01666"	""	""	""	""	"R-HSA-193399"	"HMR_1666"	"MNXR125298"	"HMR_1666"	"RCR20514"	""	0	"RHEA:72683"	"RHEA:72683"	"HMR_1666"
+"MAR01458"	""	"HSD17B4x"	""	""	""	"HSD17B4x"	"MNXR100720"	""	""	""	0	""	""	"HSD17B4x"
+"MAR01651"	"R04812"	""	"RE3250M"	""	""	"HMR_1651"	""	"HMR_1651"	"RCR12831"	""	0	""	""	"HMR_1651"
+"MAR01639"	""	""	"RE3247X;RE3247M"	"r0706"	"R-HSA-192335"	"RE3247X;r0706;HMR_1637;RE3247M"	"MNXR105369;MNXR124225"	"HMR_1639;HMR_1637"	"RCR10917;RCR13607"	""	0	""	""	"HMR_1639;HMR_1637;MAR01637"
+"MAR03301"	""	""	"RE1516X"	""	""	""	""	"HMR_3301"	"RCR12606"	""	0	""	""	"HMR_3301"
+"MAR03306"	""	""	"RE1517X"	""	""	""	""	"HMR_3306"	"RCR12610"	""	0	""	""	"HMR_3306"
+"MAR03311"	""	""	"RE1518X"	""	""	""	""	"HMR_3311"	"RCR14519"	""	0	""	""	"HMR_3311"
+"MAR04966"	""	"FAOXC101C102x"	""	""	""	"FAOXC101C102x"	""	""	""	""	0	""	""	"FAOXC101C102x"
+"MAR03364"	""	""	"RE2913X"	""	""	""	""	"HMR_3364"	"RCR12576"	""	0	""	""	"HMR_3364"
+"MAR03369"	""	""	"RE2914X"	""	""	""	""	"HMR_3369"	"RCR12580"	""	0	""	""	"HMR_3369"
 "MAR09887"	""	"GLNB0AT3tc"	""	""	""	"GLNB0AT3tc"	""	""	""	""	0	""	""	"GLNB0AT3tc"
+"MAR00059"	""	"ACOX22x"	""	""	""	"ACOX22x"	"MNXR95389"	""	""	""	0	""	""	"ACOX22x"
+"MAR00024"	""	""	""	""	""	"HMR_0024"	""	"HMR_0024"	"RCR13367"	""	0	""	""	"HMR_0024"
+"MAR00025"	""	""	""	""	""	"HMR_0025;HMR_0030"	""	"HMR_0025;HMR_0030"	"RCR20226;RCR20227"	""	0	""	""	"HMR_0025;HMR_0030;MAR00030"
+"MAR00026"	""	""	""	""	""	"HMR_0026"	""	"HMR_0026"	"RCR21051"	""	0	""	""	"HMR_0026"
+"MAR00027"	""	""	""	""	""	"HMR_0027"	""	"HMR_0027"	"RCR21052"	""	0	""	""	"HMR_0027"
+"MAR00028"	""	""	""	""	""	"HMR_0028"	""	"HMR_0028"	"RCR21053"	""	0	""	""	"HMR_0028"
+"MAR00029"	""	""	""	""	""	"HMR_0029"	""	"HMR_0029"	"RCR40953"	""	0	""	""	"HMR_0029"
+"MAR05173"	""	""	""	""	""	"HMR_5173"	""	"HMR_5173"	"RCR14475"	""	0	""	""	"HMR_5173"
+"MAR05289"	""	""	""	""	""	"HMR_5289"	""	"HMR_5289"	"RCR14478"	""	0	""	""	"HMR_5289"
+"MAR13064"	""	""	""	""	""	"EX_M01268[e]"	""	""	""	""	0	""	""	"EX_M01268[e]"
+"MAR01515"	""	"MAOX"	""	""	""	"MAOX"	"MNXR101406"	""	""	""	0	"RHEA:59421"	"RHEA:59420"	"MAOX"
+"MAR00039"	""	"13DAMPPOX"	""	""	""	"13DAMPPOX"	"MNXR94687"	""	""	""	0	""	""	"13DAMPPOX"
+"MAR00096"	""	"BUP2"	""	""	""	"BUP2"	"MNXR96346"	""	""	""	0	""	""	"BUP2"
+"MAR02027"	""	"r0193"	""	""	""	"r0193"	"MNXR105313"	""	""	""	0	""	""	"r0193"
+"MAR02006"	""	"CPS_m"	""	""	""	"r0034"	""	""	""	""	0	""	""	"r0034"
+"MAR03940"	"R01795"	"PHETHPTOX"	"R01795C"	"r0399"	""	"r0399"	"MNXR102632;MNXR107174"	"HMR_3940"	"RCR11388"	""	0	""	"RHEA:30787"	"HMR_3940"

data/metabolicTasks/metabolicTasks_CellfieConsensus.txt

@@ -211,7 +211,7 @@
 				NAD+[m]	1	1	CO2[m]	1	1								
 							NADH[m]	1	1								
 	34	Synthesis of fructose-6-phosphate from erythrose-4-phosphate (HMP shunt)		fructose-6-phosphate[c]	1	1	erythrose-4-phosphate[c]	1	1								
-				GAP[c]	1	1	D-xylulose-5-phosphate[c]	1	1								
+				D-glyceraldehyde 3-phosphate[c]	1	1	D-xylulose-5-phosphate[c]	1	1								
 	35	Synthesis of ribose-5-phosphate		glucose[c]	1	1	ribose-5-phosphate[c]	1	1								
 				ATP[c]	1	1	ADP[c]	1	1								
 				NADP+[c]	2	2	H+[c]	3	3								
@@ -226,7 +226,7 @@
 	38	Glycogen degradation		glycogenin G4G7[c]	1	1	glucose[c]	8									
 				Pi[c]	3		NA[c]	1	1								
 				H2O[c]	8		glucose-1-phosphate[c]	3									
-	39	Fructose degradation (to glucose-3-phosphate)		fructose[c]	1	1	GAP[c]	2	2								
+	39	Fructose degradation (to glucose-3-phosphate)		fructose[c]	1	1	D-glyceraldehyde 3-phosphate[c]	2	2								
 				ATP[c]	2	2	ADP[c]	2	2								
 							H+[c]	2	2								
 	40	Fructose to glucose conversion (via fructose-6-phosphate)		fructose[c]	1	1	glucose[c]	1	1