yeast 8.4.0 #229
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yeast 8.4.0 #229
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test if all model components are loaded when cobrapy is used
for compliance with cobrapy
feat: gene name compliance with cobrapy
…ctions" This reverts commit 3b83df2.
should be L-xylulose, not D-xylulose Co-Authored-By: Sebastián Mendoza Farías <snmendoz@uc.cl>
based on discussion from #187. Also features a function that prints duplicated stoichiometry Co-Authored-By: Sebastián Mendoza Farías <snmendoz@uc.cl>
same dicts as in commit 3b83df2 Co-Authored-By: Sebastián Mendoza Farías <snmendoz@uc.cl>
…X and KEGG) New reaction IDs are found during manual curation of reactions in the model. These IDs either replace the current model IDs or are added into the model (if no IDs were originally present). Inappropriately annotated or deprecated IDs have also been removed. Details of the changes, such as the rationale for the addition of IDs or changes of IDs are recorded in modifyID.tsv, under the various notes.
…aNetX, KEGG and ChEBI) New metabolite IDs are found during manual curation of metabolites in the model. These IDs either replace the current model IDs or are added into the model (if no IDs were originally present). Details of the changes, such as the rationale for the addition of IDs or changes of IDs are recorded in modifyID.tsv, under the various notes.
With the function mapIDsViaMNXref from RAVEN, model.rxnMetaNetXID is mapped as follows: 1) rxnMetaNetXID -> rxnKEGGID 2) rxnMetaNetXID -> rxnMetaCycID -> rxnKEGGID 3) rxnMetaNetXID -> rxnSEEDID -> rxnKEGGID Total unique rxnKEGGID added: 134
With the function mapIDsViaMNXref from RAVEN, model.metMetaNetXID is mapped as follows: 1) metMetaNetXID -> metKEGGID 2) metMetaNetXID -> metMetaCycID -> metKEGGID 3) metMetaNetXID -> metSEEDID -> metKEGGID Total unique metKEGGID added: 15
model.metChEBIID and model.metKEGGID is mapped to find new MNXMID(s). New MNXMID(s) will only be added if 1 of the following 3 criteria is met: a) Both metKEGGID and metChEBIID is mapped to the same MNXMID b) Only metKEGGID mapped to MNXMID, metFormula of new MNXMID matches model.metFormula c) Only metChEBIID mapped to MNXMID, metFormula of new MNXMID matches model.metFormula Total unique MNXMIDs added: 52
…yID.tsv Added lines 135 – 137, 168 – 170, 203 – 205 to remove metabolite ID annotation in model, based on modifyID.tsv. Minor correction made to modifyID.tsv: 1) Remove unnecessary metabolite and alternative metabolite ID entries which causes duplicated or lengthy notes 2) Correct errors generated when importing deprecated IDs into modifyID.tsv.
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
New mapKEGGID.m is able to check whether MetaCyc or modelSEED data is downloaded/imported successfully, and clear warning message will be displayed if download/import is unsuccessful.
- in repo, EOL should be kept as LF, to prevent issues with development on both Unix and Windows machines - applied this new setting to all files in repo - also few small tweaks on which files not to include when downloading repo as ZIP Co-authored-by: eiden309 <59604678+eiden309@users.noreply.github.com>
feat: specify EOL behaviour in gitattributes
Added functions for loading/saving the model in python in a more straightforward way. Also the id replacement is no longer necessary, as it was fixed in cobrapy. Updated the model as a test (will be reverted later)
minor changes, including shuffling of groups (as the latest cobrapy version still treats them as sets)
add a BiGG compliance flag that defaults to false when loading the model. If true, will read the annotation and use BiGG ids (if any)
model cannot be stored at this stage, as there are repeated ids in the BiGG dicts
introduce a copy suffix when id is repeated
taken from devel
feat: python I/O functions + BiGG compliance flag
Fix/unbalanced_rxns
BenjaSanchez
added
the
new release
feiranl
approved these changes
Jun 12, 2020
as RAVEN made a new release
hongzhonglu
approved these changes
Jun 13, 2020
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mapKEGGID.mandmapMNXMID.mfor adding ids in model. Used them to add missing KEGG and MetaNetX ids for both metabolites and reactions (PR Fix/update_IDs #220).read_yeast_modelandwrite_yeast_modelfor easier usage in python (PR feat: python I/O functions + BiGG compliance flag #224).checkSmatrixMNX.m, bringing the number down to 17 reactions (PR Fix/unbalanced_rxns #222).LFas EOL character (PR feat: specify EOL behaviour in gitattributes #221).NOTE: This release was made with the development version of COBRA toolbox, as the latest release is not able to keep BiGG ids.