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Fix FAD/Ubiquinone Duplicates #613

Merged
merged 11 commits into from
Jun 21, 2023
Merged

Fix FAD/Ubiquinone Duplicates #613

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383970a
fix: remove ubiquinone-dependent versions of all duplicated reactions…
Devlin-Moyer Jun 7, 2023
924dd73
fix: update reactions data files
Devlin-Moyer Jun 7, 2023
676eaf2
fix: deleted extra omap line that I missed when removing reactions ea…
Devlin-Moyer Jun 7, 2023
ad198f7
fix: resolved merge conflict in deprecatedReactions.tsv
Devlin-Moyer Jun 8, 2023
6f266d4
fix: fixed typo in MAR20111 that was causing automated YAML validatio…
Devlin-Moyer Jun 8, 2023
76edfde
fix: add IVD to GPR of MAR03770
Devlin-Moyer Jun 8, 2023
f46d539
fix: remove MAR02369 for being redundant with MAR03149
Devlin-Moyer Jun 9, 2023
24a00d2
fix: merged references, EC codes, and GPRs of deleted reactions into …
Devlin-Moyer Jun 9, 2023
30a0613
fix: merged annotations of removed reactions with kept ones in reacti…
Devlin-Moyer Jun 9, 2023
f7f31f5
feat: improve test output for unused entities
mihai-sysbio Jun 9, 2023
3b2dc0b
fix: merge in latest develop branch
Devlin-Moyer Jun 20, 2023
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2 changes: 1 addition & 1 deletion code/test/sanityCheck.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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__":
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15 changes: 15 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -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"
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