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fix: remove unconnected reactions
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reactions that agree with the following were removed:
- not connected to the main network (RAVEN function `subGraph`) 
- not annotated to any gene
- no other related reactions (involving those metabolites) are annotated with genes

These were primarily unconnected transport and exchange reactions.
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@edkerk
edkerk committed May 8, 2018
1 parent fef0b9e commit bbd9569
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Showing 3 changed files with 2 additions and 845 deletions.
18 changes: 0 additions & 18 deletions ModelFiles/txt/iYali.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -847,8 +847,6 @@ y001093 s_0794 + s_1212 + s_0578 -> s_1207 + s_1566 YALI0D07634g 0.00 1000.0
y001094 s_0434 + s_0580 -> s_0394 + s_0581 + s_0794 YALI0F10923g 0.00 1000.00 0.00
y001095 s_1408 + s_1550 <=> s_0803 + s_1388 YALI0C12749g or YALI0D25234g or YALI0F18216g -1000.00 1000.00 0.00
y001096 s_0029 <=> s_0028 -1000.00 1000.00 0.00
y001097 s_0035 <=> s_0036 -1000.00 1000.00 0.00
y001098 s_0172 -> s_0173 0.00 1000.00 0.00
y001099 s_0177 + s_0180 <=> s_0176 + s_0182 YALI0D02629g -1000.00 1000.00 0.00
y001100 s_0212 <=> s_0213 -1000.00 1000.00 0.00
y001101 s_0736 + s_0796 -> s_0734 + s_0794 YALI0A03135g or YALI0A07579g or YALI0A19558g or YALI0B09537g or YALI0D00495g or YALI0D15422g or YALI0D17688g or YALI0E07205g or YALI0F01078g 0.00 1000.00 0.00
Expand Down Expand Up @@ -959,7 +957,6 @@ y001238 s_0796 + s_1267 <=> s_0794 + s_1266 YALI0B16522g or YALI0B19338g or YA
y001239 s_0794 + s_1271 -> s_0799 + s_1273 YALI0E04048g 0.00 1000.00 0.00
y001241 s_0796 + s_0032 <=> s_0031 + s_0794 YALI0F06842g -1000.00 1000.00 0.00
y001242 s_1311 <=> s_1313 -1000.00 1000.00 0.00
y001243 s_1316 -> s_1317 0.00 1000.00 0.00
y001244 s_0796 + s_1324 <=> s_0794 + s_1322 YALI0A15125g or YALI0A21307g or YALI0E23859g or YALI0E31064g -1000.00 1000.00 0.00
y001245 s_0794 + s_1322 -> s_0799 + s_1326 YALI0C05753g or YALI0F14223g 0.00 1000.00 0.00
y001246 s_2856 + m1644 -> s_0793 + s_3324 + m1645 YALI0E28153g or YALI0A02453g 0.00 1000.00 0.00
Expand Down Expand Up @@ -997,17 +994,13 @@ y001545 s_0022 -> 0.00 1000.00 0.00
y001546 s_0026 -> 0.00 1000.00 0.00
y001547 s_0029 -> 0.00 1000.00 0.00
y001548 s_0032 -> 0.00 1000.00 0.00
y001549 s_0036 -> 0.00 1000.00 0.00
y001550 s_0058 -> 0.00 1000.00 0.00
y001551 s_0064 -> 0.00 1000.00 0.00
y001552 s_0067 -> 0.00 1000.00 0.00
y001553 s_0080 -> 0.00 1000.00 0.00
y001554 s_0084 -> 0.00 1000.00 0.00
y001560 s_1156 <=> s_1157 -1000.00 1000.00 0.00
y001562 s_0127 <=> s_0126 -1000.00 1000.00 0.00
y001563 s_0133 -> 0.00 1000.00 0.00
y001564 s_0135 -> 0.00 1000.00 0.00
y001565 s_0137 -> 0.00 1000.00 0.00
y001566 s_0139 -> 0.00 1000.00 0.00
y001567 s_0349 <=> s_0350 -1000.00 1000.00 0.00
y001568 s_0149 <=> s_0150 -1000.00 1000.00 0.00
Expand All @@ -1020,7 +1013,6 @@ y001577 s_0167 -> 0.00 1000.00 0.00
y001578 s_0166 <=> s_0167 -1000.00 1000.00 0.00
y001579 s_0166 <=> s_0168 -1000.00 1000.00 0.00
y001580 s_0170 -> 0.00 1000.00 0.00
y001581 s_0173 -> 0.00 1000.00 0.00
y001582 s_0937 <=> s_0938 -1000.00 1000.00 0.00
y001583 s_0937 <=> s_0939 -1000.00 1000.00 0.00
y001585 s_0178 <=> s_0179 -1000.00 1000.00 0.00
Expand Down Expand Up @@ -1062,7 +1054,6 @@ y001638 s_1237 -> s_1235 0.00 1000.00 0.00
y001639 s_0384 -> 0.00 1000.00 0.00
y001640 s_0383 <=> s_0385 -1000.00 1000.00 0.00
y001641 s_0391 -> 0.00 1000.00 0.00
y001642 s_0390 <=> s_0392 -1000.00 1000.00 0.00
y001643 s_0387 -> 0.00 1000.00 0.00
y001644 s_0394 <=> s_0398 -1000.00 1000.00 0.00
y001645 s_0394 <=> s_0395 -1000.00 1000.00 0.00
Expand Down Expand Up @@ -1108,7 +1099,6 @@ y001697 s_0456 <=> s_0458 -1000.00 1000.00 0.00
y001698 s_0529 <=> s_0530 -1000.00 1000.00 0.00
y001699 s_0529 <=> s_0533 -1000.00 1000.00 0.00
y001700 s_0534 <=> s_0529 -1000.00 1000.00 0.00
y001701 s_0536 <=> s_0535 -1000.00 1000.00 0.00
y001702 s_0544 -> 0.00 1000.00 0.00
y001703 s_0434 + s_0526 -> s_0394 + s_0467 YALI0F09339g 0.00 1000.00 0.00
y001704 s_0434 + s_0589 <=> s_0394 + s_0587 YALI0F09339g -1000.00 1000.00 0.00
Expand All @@ -1118,7 +1108,6 @@ y001707 s_0549 <=> s_0548 -1000.00 1000.00 0.00
y001708 s_0551 <=> s_0552 -1000.00 1000.00 0.00
y001709 s_0554 -> 0.00 1000.00 0.00
y001710 s_0559 -> 0.00 1000.00 0.00
y001711 s_0560 -> 0.00 1000.00 0.00
y001712 s_0562 -> 0.00 1000.00 0.00
y001714 s_0565 <=> -1.00 -1.00 0.00
y001715 s_0572 -> 0.00 1000.00 0.00
Expand All @@ -1130,12 +1119,9 @@ y001720 s_0582 <=> s_0583 -1000.00 1000.00 0.00
y001721 s_0587 <=> s_0588 -1000.00 1000.00 0.00
y001726 s_0591 <=> s_0593 -1000.00 1000.00 0.00
y001727 s_0597 -> 0.00 1000.00 0.00
y001728 s_0133 -> s_0132 0.00 1000.00 0.00
y001729 s_0434 + s_0584 <=> s_0394 + s_0582 YALI0F09339g -1000.00 1000.00 0.00
y001730 s_0611 -> 0.00 1000.00 0.00
y001731 s_0611 -> s_0610 0.00 1000.00 0.00
y001732 s_0135 -> s_0134 0.00 1000.00 0.00
y001733 s_0137 -> s_0136 0.00 1000.00 0.00
y001735 s_0139 -> s_0138 0.00 1000.00 0.00
y001737 s_0613 <=> s_0614 -1000.00 1000.00 0.00
y001738 s_0343 <=> s_0344 -1000.00 1000.00 0.00
Expand Down Expand Up @@ -1309,7 +1295,6 @@ y001944 s_1132 <=> s_1131 -1000.00 1000.00 0.00
y001945 s_1138 <=> s_1137 -1000.00 1000.00 0.00
y001946 s_1144 <=> s_1143 -1000.00 1000.00 0.00
y001947 s_1154 -> 0.00 1000.00 0.00
y001952 s_1186 -> 0.00 1000.00 0.00
y001963 s_1207 <=> s_1208 -1000.00 1000.00 0.00
y001964 s_1212 <=> s_1213 -1000.00 1000.00 0.00
y001965 s_0419 <=> s_0421 -1000.00 1000.00 0.00
Expand All @@ -1335,8 +1320,6 @@ y001993 s_1288 -> 0.00 1000.00 0.00
y001994 s_1295 -> 0.00 1000.00 0.00
y001995 s_1302 <=> s_1303 -1000.00 1000.00 0.00
y001996 s_1307 <=> s_1308 -1000.00 1000.00 0.00
y001999 s_1309 -> 0.00 1000.00 0.00
y002000 s_1317 -> 0.00 1000.00 0.00
y002001 s_1319 -> 0.00 1000.00 0.00
y002002 s_1318 <=> s_1319 -1000.00 1000.00 0.00
y002003 s_1318 <=> s_1320 -1000.00 1000.00 0.00
Expand Down Expand Up @@ -1726,7 +1709,6 @@ y003959 s_0528 <=> s_3219 -1000.00 1000.00 0.00
y003960 s_0541 <=> s_3093 -1000.00 1000.00 0.00
y003961 s_1326 <=> s_3228 -1000.00 1000.00 0.00
y003962 s_0636 <=> s_3095 -1000.00 1000.00 0.00
y003973 s_3709 <=> s_0672 -1000.00 1000.00 0.00
y003987 s_3710 <=> s_1337 -1000.00 1000.00 0.00
y003996 s_3711 <=> s_1346 -1000.00 1000.00 0.00
y004005 s_3712 <=> s_1351 -1000.00 1000.00 0.00
Expand Down
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