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Update trait rules and rule parser checkout
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Lines changed: 61 additions & 12 deletions

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‎bin/assets/traits_rules.tsv‎

Lines changed: 60 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ Methanogen methanogen mcr & notOtherMethanogen energy
33
mcr K00399 | K00400 | K00401 | K00402 | K03421 | K03422 energy
44
notOtherMethanogen not(OtherAjMethanogen) energy
55
OtherAjMethanogen sulfatereducer | Denitrifier | AerobicAmmoniaOxidizer | comammox | annamox | Phototroph | ETC60 energy
6-
Aerobic Ammonia Oxidizer AerobicAmmoniaOxidizer AmmoniaMonooxygenase | AmmoniaMonooxygenase & HydroxylamineDehydrogenase energy
6+
Aerobic Ammonia Oxidizer AerobicAmmoniaOxidizer AmmoniaMonooxygenase | [AmmoniaMonooxygenase & HydroxylamineDehydrogenase] energy
77
AmmoniaMonooxygenase EC1.14.99.39 | K10944 | K10945 | K10946 energy
88
HydroxylamineDehydrogenase EC1.7.2.6 | K10535 energy
99
Comammox comammox AmmoniaMonooxygenase & NitriteOxidoreductase & HydrazineDeydrogenase energy
@@ -24,7 +24,7 @@ Phototroph Phototroph PhotosystemI | PhotosystemII energy
2424
percent60ComplexIA percent(60,ComplexIA) energy
2525
percent60ComplexIB percent(60,ComplexIB) energy
2626
percent60ComplexIC percent(60,ComplexIC) energy
27-
ComplexIA K00330,[K00331 & K00332 & [K00333 | K00331] & [K13378 | K13380]],K00334,K00335,K00336,K00337,K00338,K00339,K00340,[K00341 & K00342 | K15863],K00343 energy
27+
ComplexIA K00330,[K00331 & K00332 & [K00333 | K00331] & [K13378 | K13380]],K00334,K00335,K00336,K00337,K00338,K00339,K00340,[[K00341 & K00342] | K15863],K00343 energy
2828
ComplexIB K05574,K05582,K05581,K05579,K05572,K05580,K05578,K05576,K05577,K05575,K05573,K05583,K05584,K05585 energy
2929
ComplexIC K03945,K03946,K03947,K03948,K03949,K03950,K03951,K03952,K03953,K03954,K03955,K03956,K11352,K11353 energy
3030
Fermenter Fermenter not(NegativeForFermenter) energy
@@ -107,34 +107,83 @@ Simple Sugars Trehalose Trehalose K12437 | K02777 | K02819 | K01194 | K22934 | K
107107
Simple Sugars Lactose Lactose [K01190 | K12111 | K12112] | K12309 carbon
108108
Complex Polysaccharide Amorphous Cellulose Amorphous Cellulose [[GH94 | GH1 | GH2 | GH3 | GH5 | GH9 | GH16] | GH116] & [[GH5 | GH6 | GH7 | GH8 | GH9 | GH10 | GH124 | GH12 | GH44] | GH45] carbon
109109
Complex Polysaccharide Crystalline Cellulose Crystalline Cellulose [GH7 | GH48 | AA10 | AA15 | AA16 | AA9 | AA10 | AA11] | AA13 carbon
110-
Complex Polysaccharide Starch Starch [AA13 | GH13 | GH14 | GH57 | GH119] | GH126 & [GH133 | GH15] | GH97 carbon
110+
Complex Polysaccharide Starch Starch [[AA13 | GH13 | GH14 | GH57 | GH119] | GH126] & [[GH133 | GH15] | GH97] carbon
111111
Complex Polysaccharide Pectin Pectin [[GH28 | PL1 | PL2 | PL9 | PL10 | PL11 | PL22 | PL26 | PL3] | PL4] & [[GH78 | GH106 | GH138 | GH139 | GH143 | CE8 | GH105 | GH4 | CE12] | GH2] carbon
112112
Complex Polysaccharide Beta-mannan Beta-mannan [[GH113 | GH134 | GH26] | GH5] & [[GH26 | GH130 | GH113 | CE2 | CE17] | GH2] carbon
113-
Complex Polysaccharide Alpha-mannan Alpha-mannan [GH99 | GH76] & [GH76 | GH92 | GH38 | GH63 | GH47 | GH125] | GH130 carbon
113+
Complex Polysaccharide Alpha-mannan Alpha-mannan [[GH99 | GH76] & [GH76 | GH92 | GH38 | GH63 | GH47 | GH125]] | GH130 carbon
114114
Complex Polysaccharide Xyloglucan Xyloglucan [[GH5 | GH9 | GH12 | GH16 | GH44 | GH45 | GH48 | GH74] | AA9] & [[GH31 | GH43 | GH10] | GH2] carbon
115115
Complex Polysaccharide Xylan Xylan [[AA13 | GH13 | GH14 | GH57 | GH119] | GH126] & [[GH133 | GH15] | GH97] carbon
116116
Short-Chain Fatty Acids (SCFA) Acetate Acetate-Final Acetate-1 | Acetate-2 | Acetate-3 carbon
117-
Acetate-1 [Acetate-sub1 & [K00163 | K00161 | K00162] & K00627] | [K00174 | K00175] | [K00169 | K00170 | K00172 | K00189 | K00171 | K03737] & [K01905 | K22224 | K24012] carbon
117+
Acetate-1 [[Acetate-sub1 & [K00163 | K00161 | K00162] & K00627] | [K00174 | K00175] | [K00169 | K00170 | K00172 | K00189 | K00171 | K03737]] & [K01905 | K22224 | K24012] carbon
118118
Acetate-2 Acetate-sub1 & K01568 & [K00138 | K00128 | K14085 | K00149 | K00129] carbon
119119
Acetate-3 K001895 | K01913 carbon
120120
Acetate-sub1 [K00163 | K00161 | K00162 | K01568] carbon
121121
Short-Chain Fatty Acids (SCFA) Propionate Propionate-Final Propionate-1 | Propionate-2 | Propionate-3 carbon
122-
Propionate-1 [[K01899 | K01900 | K01902 | K01903 | K01899] & [K01847 | K01849 | K01848] & K00140 | K05606 & [K11264 | K03416] & Propionate-sub2] | Propionate-sub1 carbon
122+
Propionate-1 "[
123+
[K01899 | K01900 | K01902 | K01903 | K01899]
124+
& [K01847 | K01849 | K01848]
125+
& [K00140 | [K05606 & [K11264 | K03416 | K18426]]]
126+
& Propionate-sub2
127+
]
128+
| Propionate-sub1" carbon
123129
Propionate-2 [K01026 & [K20626 | K20627] & [K00248 | K00232] & Propionate-sub2] | Propionate-sub1 carbon
124130
Propionate-3 [[K01699 | K13919 | K13920] & K13922 & Propionate-sub2] | Propionate-sub1 carbon
125-
Propionate-sub1 [[K01206 | K01905 | K22224 | K24012] | [K13788 | K00625 | K15024 | K13923] | [K00169 | K00170 | K00172 | K00189 | K00171] | K00565 & [K00925 | K00932 | K19697]] carbon
131+
Propionate-sub1 "[
132+
[K01206 | K01905 | K22224 | K24012]
133+
| [
134+
[
135+
[K13788 | K00625 | K15024 | K13923]
136+
| [K00169 | K00170 | K00172 | K00189 | K00171]
137+
| K00656
138+
]
139+
& [K00925 | K00932 | K19697]
140+
]
141+
]" carbon
126142
Propionate-sub2 [K01895 | K01908] carbon
127143
Short-Chain Fatty Acids (SCFA) Butyrate Butyrate-Final Butyrate-1 | Butyrate-2 | Butyrate-3 | Butyrate-4 carbon
128144
Butyrate-1 K00626 & [K00074 | K00022 | K07516 | K01825 | K01782 | K07514] & [K01692 | K01825 | K01782 | K07515 | K07514 | K07511 | K01715] & Butyrate-sub1 carbon
129145
Butyrate-2 [K00135 | K08324 | K00135 | K00139 | K17761 | K08324] & Butyrate-sub2 & Butyrate-sub1 carbon
130146
Butyrate-3 K01580 & [K13524 | K07250 | K14268 | K00823 | K16871] & Butyrate-sub2 & Butyrate-sub1 carbon
131-
Butyrate-4 K01843 & [K01844 | K18011] & K18012 & K18013 & [K01034 | K01035] | [K18014 & [K01692 | K01825 | K01782 | K07515 | K07514 | K07511] & [K00022 | K01825 | K01782 | K07514]] & Butyrate-1 carbon
147+
Butyrate-4 "K01843
148+
& [K01844 | K18011]
149+
& K18012
150+
& K18013
151+
& [
152+
[K01034 | K01035]
153+
| [
154+
K18014
155+
& [K01692 | K01825 | K01782 | K07515 | K07514 | K07511]
156+
& [K00022 | K01825 | K01782 | K07514]
157+
]
158+
]
159+
& Butyrate-1" carbon
132160
Butyrate-sub1 [K00209 | K17829] & [K01034 | K01035 | K19709] carbon
133161
Butyrate-sub2 [K00043 | K08318 | K18120 | K18121] & K18122 & K14534 carbon
134-
Short-Chain Fatty Acids (SCFA) Lactate Lactate-Final Lactate-1 | Lactate-2 | Lactate-3 carbon
135-
Lactate-1 [K00844 | K00886 | K08074 | K00918 | K12407 | K00845 | K25026] & [K01810 | K06859 | K13810 | K15916] & [K24182 | K00850 | K16370 | K21071 | K00918 | K00895 | K21071] & [K01623 | K01624 | K01622 | K11645 | K16305 | K16306] & [K01803 & K00131 | K11389 | K18978] | [[K01803 & K00134 | K10705 | K00150] & K00927] | [[K01803 & K00134 | K10705 | K00150] & K01837] & [K01834 | K15634 | K01837 | K15633 | K15635] & [K01689 | K27394] | [K01006 | K01007] & K00016 carbon
162+
Short-Chain Fatty Acids (SCFA) Lactate Lactate-Final Lactate-1 | Lactate-2 | Lactate-3 carbon
163+
Lactate-1 "Lactate-sub1
164+
& [
165+
[
166+
[K00134 | K00150]
167+
& [K00927 | K01837]
168+
& [K01834 | K15633 | K15634 | K15635 | K01837]
169+
]
170+
| [
171+
[K11389 | K00131 | K18978]
172+
& [K01834 | K15633 | K15634 | K15635 | K01837]
173+
]
174+
| [
175+
[K00134 | K00150]
176+
& K01837 & K03103
177+
]
178+
]
179+
& [K01689 | K27394 | K00873 | K12406]
180+
& K00016" carbon
136181
Lactate-2 K00016 carbon
137182
Lactate-3 [K18124 | K18125 | K00115 | K19813 | K00117] & K01053 & K05308 & [K11395 | K18127] & K00016 carbon
183+
Lactate-sub1 "[K00844 | K00886 | K08074 | K00918 | K12407 | K00845 | K25026]
184+
& [K01810 | K06859 | K13810 | K15916]
185+
& [K24182 | K00850 | K16370 | K21071 | K00918 | K00895 | K21071]
186+
& [K01623 | K01624 | K01622 | K11645 | K16305 | K16306]" carbon
138187
Short-Chain Fatty Acids (SCFA) Formate Formate K00656 carbon
139188
Amino Acids Glutamate Glutamate K11067 | K00618 | K00619 | K14681 | K14682 | K00620 | K22476 | K22477 | K22478 | K19412 | K25032 | K00260 | K00261 | K00262 | K01915 | K00931 | K18538 | K18539 | K00603 | K01776 | K11204 | K11205 | K01909 | K06048 | K13559 | K01915 | K14272 | K05825 | K28204 | K19268 | K01846 | K01885 | K14163 | K09698 | K14223 | K01886 carbon
140189
Amino Acids Glycine Glycine K00659 | K00273 | K14272 | K00827 | K00830 | K14272 | K00281 | K00282 | K00283 | K00643 | K01620 | K20801 | K00639 | K18896 | K24071 | K00552 | K00613 | K00830 | K00600 | K10814 | K10815 | K10816 | K19967 | K21456 | K01920 | K00605 | K00382 | K02437 | K03153 | K01878 | K01879 | K01880 | K14164 carbon
@@ -145,4 +194,4 @@ Organic Acids Citrate Citrate K01681 | K27802 | K01682 | K05942 | K01648 | K0164
145194
Organic Acids Malate Malate K00025 | K00026 | K00024 | K00116 | K01676 | K01677 | K01678 | K01679 | K01675 | K01774 | K00051 | K22212 | K01638 | K08692 | K14067 | K00029 | K00028 | K14471 | K14472 carbon
146195
Aromatics/Phenolics Vanillin Vanillin K21802 | K24276 carbon
147196
Lipids Glycerol Glycerol K01189 | K07406 | K07407 | K00005 | K22251 | K18097 | K00864 | K06120 | K06121 | K06122 | K00011 | K00002 | K13979 carbon
148-
Microbial Compounds Chitin Chitin K01183 | K20547 | K13381 | K01452 carbon
197+
Microbial Compounds Chitin Chitin K01183 | K20547 | K13381 | K01452 carbon

‎bin/rule_parser‎

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