General improvements - #11
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To follow convention and make things easier to read.
For improved readability.
Except assignment issues in hla allele data parsing, I ain't touching that just yet.
Now more granular but also more centralized.
Even more centralized.
No sense in keeping them in each script. Also they were out of date.
Better separation of script & code.
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Pull request overview
Centralizes command dispatch and configuration while refactoring scripts into callable functions.
Changes:
- Adds unified Python argument parsing and dispatch.
- Centralizes reference/data paths and extracts testable functions.
- Cleans obsolete metadata, commands, and packaging code.
Reviewed changes
Copilot reviewed 16 out of 16 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
arcasHLA |
Delegates dispatch to Python. |
scripts/arcasHLA.py |
Adds unified CLI dispatch. |
scripts/config.py |
Centralizes paths and parameters. |
scripts/arcas_utilities.py |
Adds executable validation. |
scripts/align.py |
Corrects Kallisto command construction. |
scripts/convert.py |
Extracts conversion API and parser. |
scripts/customize.py |
Extracts customization API and uses config. |
scripts/extract.py |
Extracts read-processing API and parser. |
scripts/genotype.py |
Extracts genotyping API and dependencies. |
scripts/merge.py |
Extracts merge API and parser. |
scripts/partial.py |
Extracts partial-genotyping API. |
scripts/quant.py |
Extracts quantification API and fixes commands. |
scripts/reference.py |
Centralizes reference management. |
setup.py |
Removes obsolete packaging definition. |
test/conftest.py |
Calls extraction directly in fixtures. |
test/test_arcasHLA.py |
Adds top-level help parsing coverage. |
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So we can use them as entrypoints later on.
As this has been only a collection of scripts packaged via conda, this was unsed.
Each part must be a list element.
Easier to debug.
scripts/arcasHLA.py already centralizes arg parsing and dependency checks, but the top-level `arcasHLA` wrapper still hand-rolled its own per-command dispatch and ad-hoc dependency warnings. Forward all invocations to the central dispatch script instead. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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