feat: gene essentiality workflow #675
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| - name: Run gene essentiality | ||
| id: essentiality | ||
| run: | | ||
| TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "ihuman = importYaml('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/') |
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@haowang-bioinfo the output of this line is very hard to capture/use. Do you have any suggestions to make this output more compact?
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As seen in this workflow run, the output is way too rich to fit in a PR comment. @haowang-bioinfo how would you suggest to change it to end up with a nice summary like here?
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no, I've never thought about this. Because they are non-binary indicators that are hard to be used for evaluating purpose in actions
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Also noting here this relevant research article Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells. |
yes, it mentioned another method gMCStool that can predict essential genes in context-specific models. Other checks than essentiality are also welcome |
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This PR has been automatically tested with GH Actions. Here is the output of the gene essentiality test:
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@mihai-sysbio Could you explain the reason for the failing task? |
The task isn't actually failing, really. As mentioned in the comment above, it's simply that the output of the gene essentiality is so long that it cannot be posted as a PR comment. I couldn't figure out how @haowang-bioinfo ran the calculations to obtain a much more compressed output. As visible in the workflow changes, the code here is just calling functions defined elsewhere. |
the concise output was an outcome of a series of manual operations of running functions, copy/paste results, and modifications with text editor |
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If these last manual steps could be ran as a function, then we would be ready to run the gene essentiality analysis on every PR 💪🏻 |
Main improvements in this PR:
This PR aims to automatise the gene essentiality checks as introduced in #563 with a GitHub workflow, also discussed in that PR thread.
I hereby confirm that I have:
developas a target branch