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feat: log duplicated ids to the column of rxnRetired #666

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merged 5 commits into from
Jun 25, 2023
Merged

feat: log duplicated ids to the column of rxnRetired #666

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29734c6
feat: log duplicated ids to the column of rxnRetired
haowang-bioinfo Jun 23, 2023
9ce2c5c
fix: correct misplaced retired reaction ID
haowang-bioinfo Jun 23, 2023
add54ab
fix: add MAR03783 as a duplicate for MAR03784
haowang-bioinfo Jun 23, 2023
63c5e7d
Merge branch 'develop' into feat/logDeprecatedIDsIn#613
haowang-bioinfo Jun 25, 2023
0c1d89e
Merge branch 'develop' into feat/logDeprecatedIDsIn#613
haowang-bioinfo Jun 25, 2023
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28 changes: 14 additions & 14 deletions model/reactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08517" "R01016" "MGSA2" "" "" "" "MGSA2" "MNXR101551;MNXR101552" "HMR_8517" "RCR11086" "" 0 "" "RHEA:17937" "HMR_8517"
"MAR04280" "R00703" "LDH_Lm" "R00703C" "r0172" "" "LDH_Lm" "MNXR101040" "HMR_4280" "RCR11087" "" 0 "" "RHEA:23444" "HMR_4280"
"MAR00153" "R00925" "ACS2" "" "r0218" "" "ACS2" "MNXR106753;MNXR95222" "HMR_0153" "RCR10460" "" 0 "RHEA:20374" "RHEA:20373" "HMR_0153"
"MAR03212" "R00924" "PPCOAOm" "" "r0683" "" "PPCOAOm;r0683" "MNXR103101" "HMR_3212;HMR_3211" "RCR11088;RCR14348" "" 0 "" "" "HMR_3212"
"MAR03212" "R00924" "PPCOAOm" "" "r0683" "" "PPCOAOm;r0683" "MNXR103101" "HMR_3212;HMR_3211" "RCR11088;RCR14348" "" 0 "" "" "HMR_3212;MAR03211"
"MAR03797" "R00925" "ACCOALm" "" "r0219" "" "ACCOALm" "MNXR106753;MNXR95222" "HMR_3797" "RCR14211" "" 0 "RHEA:20376" "RHEA:20373" "HMR_3797"
"MAR03800" "" "OBDHm" "" "r1154" "" "r1154" "MNXR102133" "HMR_3800" "RCR10461" "" 0 "" "" "HMR_3800"
"MAR04105" "R00233" "MCD" "" "r0063" "" "MCD" "MNXR101412" "HMR_4105" "RCR10285" "" 0 "RHEA:18782" "RHEA:18781" "HMR_4105"
Expand Down Expand Up @@ -634,17 +634,17 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08608" "R02894" "DRIBt" "" "" "" "HMR_8608" "MNXR97783" "HMR_8608" "RCR14308" "" 0 "" "" "HMR_8608"
"MAR08609" "R01251" "P5CRm" "" "" "" "P5CRm" "MNXR102302" "HMR_8609" "RCR10244" "" 0 "" "RHEA:14109" "HMR_8609"
"MAR08610" "R10507" "PROD2" "" "" "" "PROD2" "MNXR103187" "HMR_8610" "RCR10316" "" 0 "" "" "HMR_8610"
"MAR08611" "R10507" "PROD2m" "" "r1453" "" "PROD2m" "MNXR103187" "HMR_8611;HMR_3838" "RCR11294;RCR14286" "" 0 "" "" "HMR_8611;HMR_3838"
"MAR08611" "R10507" "PROD2m" "" "r1453" "" "PROD2m" "MNXR103187" "HMR_8611;HMR_3838" "RCR11294;RCR14286" "" 0 "" "" "HMR_8611;HMR_3838;MAR03838"
"MAR04285" "R00713" "" "R00713C" "r0178" "" "r0178" "MNXR104540" "HMR_4285" "RCR11295" "" 0 "RHEA:13218" "RHEA:13217" "HMR_4285"
"MAR00457" "R01514" "" "R01514C" "r0339" "" "r0339" "MNXR100328" "HMR_0457" "RCR11296" "" 0 "RHEA:23517" "RHEA:23516" "HMR_0457"
"MAR00460" "R01514" "" "R01514C" "r0340" "" "r0340" "MNXR100328" "HMR_0460" "RCR11297" "" 0 "RHEA:23517" "RHEA:23516" "HMR_0460"
"MAR03750" "" "" "RE2429M" "" "" "RE2429M" "MNXR103672" "HMR_3750" "RCR14309" "" 0 "" "" "HMR_3750"
"MAR03752" "R02660" "ACOAD9m" "R02660M" "r0560" "" "ACOAD9m;r0560" "" "HMR_3752;HMR_3751" "RCR14310;RCR14421" "" 0 "" "" "HMR_3752;HMR_3751"
"MAR03770" "R04095" "ACOAD8m" "R04095M" "r0655" "" "ACOAD8m;r0655" "MNXR95318" "HMR_3770;HMR_3769" "RCR14311;RCR14423" "" 0 "" "" "HMR_3770;HMR_3769"
"MAR03752" "R02660" "ACOAD9m" "R02660M" "r0560" "" "ACOAD9m;r0560" "" "HMR_3752;HMR_3751" "RCR14310;RCR14421" "" 0 "" "" "HMR_3752;HMR_3751;MAR03751"
"MAR03770" "R04095" "ACOAD8m" "R04095M" "r0655" "" "ACOAD8m;r0655" "MNXR95318" "HMR_3770;HMR_3769" "RCR14311;RCR14423" "" 0 "" "" "HMR_3770;HMR_3769;MAR03769"
"MAR03771" "" "" "RE2427M" "" "" "RE2427M" "MNXR103670" "HMR_3771" "RCR14312" "" 0 "" "" "HMR_3771"
"MAR03772" "" "" "RE2111M" "" "" "RE2111M" "MNXR103609" "HMR_3772" "RCR14313" "" 0 "" "" "HMR_3772"
"MAR03782" "" "" "RE2428M" "" "" "RE2428M" "MNXR103671" "HMR_3782" "RCR14314" "" 0 "" "" "HMR_3782"
"MAR03784" "R03172" "ACOAD10m" "R03172M" "r0603" "" "ACOAD10m;r0603" "MNXR108000" "HMR_3784;HMR_3783" "RCR11298;RCR14424" "" 0 "" "" "HMR_3784;HMR_3783"
"MAR03784" "R03172" "ACOAD10m" "R03172M" "r0603" "" "ACOAD10m;r0603" "MNXR108000" "HMR_3784;HMR_3783" "RCR11298;RCR14424" "" 0 "" "" "HMR_3784;HMR_3783;MAR03783"
"MAR03794" "" "" "RE2031M" "" "" "RE2031M" "MNXR103592" "HMR_3794" "RCR14315" "" 0 "" "" "HMR_3794"
"MAR03839" "R01513" "PGCD" "R01513C" "r0338" "" "PGCD" "MNXR102527" "HMR_3839" "RCR11299" "" 0 "" "RHEA:12641" "HMR_3839"
"MAR03841" "R04173" "PSERT" "R04173C" "r0663" "" "PSERT" "MNXR103225" "HMR_3841" "RCR11300" "" 0 "" "RHEA:14329" "HMR_3841"
Expand Down Expand Up @@ -817,7 +817,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04232" "" "" "RE0549C" "" "" "RE0549C" "MNXR103449" "HMR_4232" "RCR10536" "" 0 "" "" "HMR_4232"
"MAR04233" "R03889" "" "" "r0645" "" "r0645" "MNXR95796" "HMR_4233" "RCR11396" "" 0 "" "RHEA:14469" "HMR_4233"
"MAR04235" "R01938" "AMCOXO" "" "r0449" "" "AMCOXO" "MNXR95807" "HMR_4235" "RCR11397" "" 0 "" "" "HMR_4235"
"MAR04243" "R02487" "GLUTCOADHm" "R02487M" "r0541" "" "GLUTCOADHm;r0541" "MNXR100293" "HMR_4243;HMR_4242" "RCR11398;RCR14356" "" 0 "" "RHEA:30847" "HMR_4243;HMR_4242"
"MAR04243" "R02487" "GLUTCOADHm" "R02487M" "r0541" "" "GLUTCOADHm;r0541" "MNXR100293" "HMR_4243;HMR_4242" "RCR11398;RCR14356" "" 0 "" "RHEA:30847" "HMR_4243;HMR_4242;MAR04242"
"MAR04244" "R04171" "3HKYNAKGAT" "R04171C" "r0662" "" "3HKYNAKGAT" "MNXR108708;MNXR94895" "HMR_4244" "RCR11399" "" 0 "" "RHEA:65888" "HMR_4244"
"MAR04245" "R03954" "" "" "r0647" "" "r0647" "MNXR105360;MNXR108552" "HMR_4245" "RCR11400" "" 0 "RHEA:65893" "RHEA:65892" "HMR_4245"
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I am not sure about the reason this one appears not in the last column

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@haowang-bioinfo haowang-bioinfo Jun 23, 2023 •
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good spot! this is actually my mistake, now is corrected in 9ce2c5c

"MAR04246" "" "" "RE2349C" "" "" "RE2349C" "" "HMR_4246" "RCR11401" "" 0 "" "" "HMR_4246"
Expand Down Expand Up @@ -1335,7 +1335,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04458" "R01325" "" "R01325C" "r0317" "" "r0317" "MNXR105321;MNXR95386" "HMR_4458" "RCR10106" "" 0 "RHEA:10231" "RHEA:10228" "HMR_4458"
"MAR04465" "R01392" "HPYRRy" "R01392C" "r0327" "" "HPYRRy" "MNXR100336" "HMR_4465" "RCR11666" "" 0 "" "RHEA:18657" "HMR_4465"
"MAR04589" "R01900" "" "R01900C" "r0426" "" "r0426" "MNXR105342;MNXR95387" "HMR_4589" "RCR10352" "" 0 "" "RHEA:22144" "HMR_4589"
"MAR04652" "R00408;R02164" "r0509;SUCD1m" "R02164C" "r0509" "" "r0509;SUCD1m" "MNXR107340;MNXR99636" "HMR_4652;HMR_8743" "RCR14481;RCR11674" "" 0 "" "RHEA:13713;RHEA:30343" "HMR_4652;HMR_8743"
"MAR04652" "R00408;R02164" "r0509;SUCD1m" "R02164C" "r0509" "" "r0509;SUCD1m" "MNXR107340;MNXR99636" "HMR_4652;HMR_8743" "RCR14481;RCR11674" "" 0 "" "RHEA:13713;RHEA:30343" "HMR_4652;HMR_8743;MAR08743"
"MAR06413" "R03316" "" "R03316M" "r0620" "" "r0620" "MNXR105357;MNXR108089" "HMR_6413" "RCR11672" "" 0 "" "" "HMR_6413"
"MAR06414" "R02570" "" "R02570C" "r0556" "" "r0556" "MNXR107585;MNXR95656" "HMR_6414" "RCR14482" "" 0 "" "RHEA:15213" "HMR_6414"
"MAR07704" "R00466" "GLXO2p" "" "" "" "GLXO2p" "MNXR100305" "HMR_7704" "RCR10605" "" 0 "" "RHEA:14837" "HMR_7704"
Expand Down Expand Up @@ -2651,27 +2651,27 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03116" "R07760" "" "" "" "" "HMR_3116" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116"
"MAR03117" "" "" "" "" "" "HMR_3117" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117"
"MAR03118" "" "" "" "" "" "HMR_3118" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118"
"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310"
"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035"
"MAR03122" "R04738" "" "R04738X" "r0716" "" "r0716" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122"
"MAR03123" "R04737" "" "R04737X" "r0714" "" "r0714" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123"
"MAR03125" "R03991" "" "R03991X" "r0653" "" "r0653" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125"
"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449"
"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370"
"MAR03129" "R04740" "" "R04740X" "r0720" "" "r0720" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129"
"MAR03130" "R04739" "" "R04739X" "r0718" "" "r0718" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130"
"MAR03132" "R03858" "" "R03858X" "r0639" "" "r0639" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132"
"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447"
"MAR03136" "R04170" "r1446" "R04170X" "r0660" "" "r0660;r1446" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446"
"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367"
"MAR03136" "R04170" "r1446" "R04170X" "r0660" "" "r0660;r1446" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366"
"MAR03137" "R04741" "" "R04741X" "r0722" "" "r0722" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137"
"MAR03139" "R04742" "" "R04742X" "r0724" "" "r0724" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139"
"MAR03142" "R04754" "r1451" "" "" "R-HSA-77345" "HMR_3142;r1451" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451"
"MAR03142" "R04754" "r1451" "" "" "R-HSA-77345" "HMR_3142;r1451" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373"
"MAR03143" "R04744" "" "R04744X" "r0728" "" "r0728" "MNXR97889" "HMR_3143" "RCR12646" "" 0 "" "RHEA:31191" "HMR_3143"
"MAR03144" "R04743" "" "R04743X" "r0726" "" "r0726" "MNXR100545" "HMR_3144" "RCR12647" "" 0 "" "RHEA:31187" "HMR_3144"
"MAR03146" "R03778" "" "R03778X" "r0634" "" "r0634" "MNXR95198" "HMR_3146" "RCR12648" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146"
"MAR03149" "R03777" "r1448" "" "" "R-HSA-77338" "HMR_3149;r1448" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448"
"MAR03149" "R03777" "r1448" "" "" "R-HSA-77338" "HMR_3149;r1448" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369"
"MAR03150" "R04746" "" "R04746M" "r0731" "" "r0731" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150"
"MAR03151" "R04745" "" "R04745M" "r0730" "" "r0730" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151"
"MAR03153" "R04747" "" "R04747M" "r0732" "" "r0732" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153"
"MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450"
"MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372"
"MAR03157" "R04749" "" "R04749M" "r0734" "" "r0734" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157"
"MAR03158" "R04748" "" "R04748M" "r0733" "R-HSA-77323" "r0733" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158"
"MAR03160" "R01177" "" "R01177M" "r0287" "R-HSA-77321" "r0287" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160"
Expand Down