aa position table - #18
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Summary of ChangesHello @Alex-Davydov, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request delivers a new capability to export Kabat CDR3 amino acid positions, providing more detailed data for specific analysis needs. This feature is seamlessly integrated into the existing workflow and user interface. Concurrently, the project's dependencies have undergone a significant update to ensure stability, performance, and compatibility with the latest ecosystem standards. Highlights
Changelog
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Code Review
This pull request introduces a new feature to export a table of amino acid positions for Kabat CDR3. The changes span across the model, UI, a Python script, and workflow templates to support this new functionality. The implementation is mostly correct, but I've found a critical bug in the main workflow that prevents the new export from being generated, as well as a leftover debug statement. I've also included a suggestion to improve code style in one of the workflow templates for better readability.
| if cdr3PositionsPf != undefined { | ||
| exports.kabatCdr3AaPositions = cdr3PositionsPf | ||
| } |
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The variable cdr3PositionsPf is used here but it's never assigned a value, so this block will never execute and the kabatCdr3AaPositions export will be missing.
To fix this, you should create a pframe from cdr3PositionsRaw and assign it to cdr3PositionsPf after cdr3PositionsRaw is created, for example on line 1073:
cdr3PositionsPf = pframes.fromSpecAndDataMap(cdr3PositionsRaw)
| numberingExec = numberingExec.arg("--out_tsv").arg("numbered.tsv").saveFile("numbered.tsv") | ||
| if exportCdr3Positions { | ||
| numberingExec = numberingExec. | ||
| arg("--out_cdr3_positions_tsv").arg("cdr3_positions.tsv"). | ||
| saveFile("cdr3_positions.tsv") | ||
| } | ||
| numberingExec = numberingExec. | ||
| arg("--out_tsv").arg("numbered.tsv"). | ||
| saveFile("numbered.tsv"). | ||
| printErrStreamToStdout(). | ||
| cache(24 * 60 * 60 * 1000). | ||
| run() |
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For better readability and to maintain a fluent interface style, you could restructure this part to keep the command-building chain more contiguous. This also makes it easier to add more conditional arguments in the future.
if exportCdr3Positions {
numberingExec = numberingExec.
arg("--out_cdr3_positions_tsv", "cdr3_positions.tsv").
saveFile("cdr3_positions.tsv")
}
numberingExec = numberingExec.
arg("--out_tsv", "numbered.tsv").
saveFile("numbered.tsv").
printErrStreamToStdout().
cache(24 * 60 * 60 * 1000).
run()
| }, | ||
| domain: json.decode(canonical.encode(clonotypeKeyDomain)) | ||
| } | ||
| ll.print("__THE_LOG__ newClonotypeKeySpec: " + json.encode(newClonotypeKeySpec)) |
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This appears to be a leftover debug statement. It should be removed before merging.
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