Expose more options in workflow; clean up core Python scripts #10
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…cleanup summarize_AAV_alignment: - Use ruff to fix if-else block. - Remove unused imports and dead code. - Add a leading underscore to the names of unused loop variables. - Standardize docstrings, exceptions, string formatting, etc. No functional change.
The default AAV2 f/f info still comes from a global variable, not the new FASTA file, but the contents are identical and it can be used for local testing.
- Expose argument --target-gap-threshold to set what was (and still is) a global constant. - Reduce run time by 25% - Use more precise variable names - Remove some dead code
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test/Makefile: Fix a typo.
- Rename global MAX_DIFF_W_REF to MAX_MISSING_FLANK; settable by the same CLI arg --max-allowed-missing-flanking - Add global MAX_OUTSIDE_VECTOR and CLI arg --max-allowed-outside-vector, similar but referring to the margin just outside the vector region
Added input options: target_gap_threshold, max_allowed_outside_vector, max_allowed_missing_flanking, flipflop_fa
Also optionally take repcap_name (str) to count repcap mappings as before.
Add a hidden parameter "container_version" to streamline testing development builds.
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Add workflow input options to enable some investigations.
max_allowed_missing_flankingandflipflop_fatarget_gap_thresholdinto a script option and workflow inputmax_allowed_outside_vector, similar tomax_allowed_missing_flankingbut for the regions just outside the vector region (full reads overlapping the backbone a bit), while the latter now only refers to the portion of each ITR allowed to be missing.repcap_faandhelper_fainputs into a singlepackaging_fa, and optionally takerepcap_name(str) to count repcap mappings as such for that mapped reference inpackaging_fa. For dual constructs, the "repcap" region on the vector backbone can be explicitly annotated in the input BED file.Include type/subtype BAMs in Nextflow output.
Profiled both Python scripts and sped up
summarize_AAV_alignment.pyby about 25%. (The other spends almost all its time inside Parasail.)Cleaned up code with
ruff check.