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Fix-Phe, Tyr and Trp biosynthesis and Porphyrin metabolism #899

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merged 5 commits into from
Dec 17, 2024

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JHL-452b
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@JHL-452b JHL-452b commented Nov 5, 2024

Main improvements in this PR:

As proposed in #855

  • Remove ENSG00000184254 from MAR06749;
  • Remove ENSG00000184254 from MAR06754;
  • Remove ENSG00000184254 from MAR06761;
  • Remove ENSG00000184254 from MAR06767;
  • Remove ENSG00000184254 from MAR06791;
  • Remove ENSG00000130508, ENSG00000117592 from MAR06808;
  • Remove ENSG00000117592 from MAR06813;
  • Remove ENSG00000166507, ENSG00000140835, ENSG00000138653, ENSG00000136720, ENSG00000124302, ENSG00000183196, ENSG00000135702, ENSG00000171004, ENSG00000175040, ENSG00000175229 from MAR06829;
  • Remove ENSG00000167419, ENSG00000117592, ENSG00000130508 from MAR07628;
  • Remove ENSG00000184254 from MAR06748;
  • Remove ENSG00000196616 from MAR06756;
  • Remove ENSG00000184254 from MAR06760;
  • Remove ENSG00000151093 from MAR02781.

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected develop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

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JHL-452b commented Nov 5, 2024

Aha, it looks like the updated MACAW output is showing garbled text.🤔

@SysBioChalmers SysBioChalmers deleted a comment from github-actions bot Nov 5, 2024
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edkerk commented Nov 5, 2024

Should be resolved now, let's see what will be posted.

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github-actions bot commented Nov 5, 2024

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
- Found 1514 dead-end metabolites.
- Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 447 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

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

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github-actions bot commented Nov 5, 2024

This PR has been automatically tested with GH Actions. Here is the output of the gene essentiality test:

     cellLine     TP     TN     FP    FN     accuracy    sensitivity    specificity       F1         MCC   
__________ __ ____ __ ___ ________ ___________ ___________ ________ ________

{'DLD1' } 37 2175 62 277 0.86711 0.11783 0.97228 0.17918 0.1533
{'GBM' } 34 2156 65 295 0.85882 0.10334 0.97073 0.15888 0.12855
{'HCT116'} 46 2198 57 306 0.86076 0.13068 0.97472 0.2022 0.18491
{'HELA' } 31 2254 72 251 0.87615 0.10993 0.96905 0.16104 0.12592
{'RPE1' } 15 2194 84 257 0.86627 0.055147 0.96313 0.080863 0.029199
{'all' } 7 2396 96 109 0.9214 0.060345 0.96148 0.063927 0.023098

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

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JHL-452b commented Nov 5, 2024

Hooray, all the checks passed!

However, there is a small problem. If two or more PRs are submitted at the same time, will the server used for the checks crash? After all, each round check takes a long time, and the submission of multiple PRs may be unavoidable.

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edkerk commented Nov 5, 2024

The server doesn't crash, as the runs are queued. I think there might be something with submitting the results back, but if this appears I can manually restart the runs.

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LGTM! Please resolve the conflicts and merge this PR!

…osynthesis-Porphyrin_metabolism

# Conflicts:
#	data/testResults/README.md
@edkerk edkerk merged commit 8cc9173 into develop Dec 17, 2024
5 of 6 checks passed
@edkerk edkerk deleted the Fix_Phe_Tyr_Trp_biosynthesis-Porphyrin_metabolism branch December 17, 2024 00:49
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3 participants