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New-organism gene ids become gene ids of the draft model, and grRules are split at whitespace and parentheses, and by COBRA also at "|" and "&". UniProt FASTA headers such as sp|P33284|HXK_KLULA passed through and broke the draft downstream. getModelFromHomology now raises an error naming the offending ids, as raven-toolbox does.
Function test results394 tests 355 ✅ 1m 41s ⏱️ Results for commit 48b3c52. |
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Development of this pull request continues in CompMetEng/RAVEN#3, which has the same commits on the copied history. |
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Main improvements in this PR:
getModelFromHomologynow raisesRAVEN:badInputwhen gene ids of the new organism contain whitespace, parentheses,|or&. These ids are written into the grRules of the draft model, which are split at whitespace and parentheses, and which COBRA also splits at|and&. A UniProt FASTA header such assp|P33284|HXK_KLULAwould otherwise become three genes in the draft model. Only ids that are mapped to a template gene are checked, and the error names the first three and suggests reducing UniProt headers to the accession.getModelFromHomologystates the requirement.tReconstructionhas a test,getModelFromHomologyRejectsGeneIdsThatSplit.The same check is in
get_model_from_homologyin raven-toolbox (SysBioChalmers/raven-toolbox#171).Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.