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fix: loadDatabases check for duplicate protIDs #349

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merged 1 commit into from
Aug 19, 2023

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@edkerk edkerk commented Aug 19, 2023

Main improvements in this PR:

  • Fixes:
    • loadDatabases throws error if duplicate protein IDs are found

Instructions on merging this PR:

  • This PR has develop as target branch, and will be resolved with a squash-merge.
  • This PR has main as target branch, and will be resolved with a merge commit.

@edkerk edkerk added this to the 3.1.2 milestone Aug 19, 2023
@edkerk edkerk requested a review from ae-tafur August 19, 2023 12:17
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This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

Note: In the case of multiple test runs, this post will be edited.

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It might be good print the list of duplicated entries ?

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edkerk commented Aug 19, 2023

It might be good print the list of duplicated entries ?

It prints the Uniprot IDs. If you duplicate the first entry in uniprot.tsv, the error message is:

Error using dispEM
Duplicate entries are found for the following proteins. Manually curate the 'uniprot.tsv' file, or adjust the
uniprot parameters in the model adapter:
	P39714

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It might be good print the list of duplicated entries ?

It prints the Uniprot IDs. If you duplicate the first entry in uniprot.tsv, the error message is:


Error using dispEM

Duplicate entries are found for the following proteins. Manually curate the 'uniprot.tsv' file, or adjust the

uniprot parameters in the model adapter:

	P39714

True! I misunderstood the final part of the code.

@edkerk edkerk merged commit 5af432a into develop Aug 19, 2023
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@edkerk edkerk deleted the fix/duplicateUniprotIDs branch August 19, 2023 13:53
edkerk added a commit that referenced this pull request Dec 2, 2023
* fix: loadDatabases check for duplicate protIDs (#349)

* fix: prevent NaN in light ecModels (#346)

* fix: calculateFfactor if paxDB has taxID !4 chars (#347)

* fix: runDLKcat if path has spaces (#352)

* refactor: FSEOF (#356)

* fix: FSEOF to 0.9 of teorethical max prod

* refactor: switch force objetive to target

* fix: remove unnecesary function

* fix: update input arguments

* fix: temporal solution k-score

* refactor: FSEOF

* feat: add gene essentiality to FSEOF

* fix: file writing

* feat: add cutoff based on quantile

* feat: report target transport reactions

* refactor: add cutoff for essentiality

* fix: bug identifying gene essentiality

* doc: move installations instructions to wiki (#357)

* move installation instructions to wiki

* GECKOInstaller checks for latest GECKO version

* fix: prevent duplications in protein pseudometabolites

* minor fixes

* doc: update documentation

* doc: swap gitter for GitHub Discussions

* fix: correct link to upgrade instructions

* fix: synchronize STEP numbers  protocol and paper

---------

Co-authored-by: Albert Tafur Rangel <[email protected]>
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2 participants