Migrate from BioExt/bealign to cawlign for sequence alignment#116
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stevenweaver merged 1 commit intomasterfrom Oct 14, 2025
Merged
Migrate from BioExt/bealign to cawlign for sequence alignment#116stevenweaver merged 1 commit intomasterfrom
stevenweaver merged 1 commit intomasterfrom
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Replace the two-step bealign+bam2msa alignment workflow with a single cawlign call. This migration simplifies the alignment process and removes the BioExt dependency. Key changes: - Replace bealign and bam2msa with cawlign for sequence alignment - Remove BAM intermediate file format, cawlign outputs FASTA directly - Add optional --cawlign CLI argument (defaults to 'cawlign' in PATH) - Add optional --score-matrix CLI argument (defaults to 'HIV_BETWEEN_F') - Add validate_cawlign() function to warn if cawlign is not found - Remove BioExt from install_requires in setup.py - Update phase numbering after removing BAM_FASTA_CONVERSION phase - Document cawlign v1.0.3+ as required non-PyPI dependency The cawlign command uses: - '-s SCORE_MATRIX' for alignment scoring - '-t codon' for codon-aware alignment (required for HIV_BETWEEN_F) - '-I' flag to include reference sequence in output - '-r reference' to specify reference sequence All existing tests pass with the new implementation.
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Summary
This PR migrates the HIV-TRACE alignment workflow from BioExt/bealign to cawlign, simplifying the alignment process and removing the BioExt dependency.
Changes Made
cawligncall instead of two-stepbealign+bam2msaprocess--cawlign: Path to cawlign executable (defaults to 'cawlign' in PATH)--score-matrix: Score matrix for alignment (defaults to 'HIV_BETWEEN_F')validate_cawlign()function warns if cawlign is not foundbioext >= 0.21.8from install_requiresBAM_FASTA_CONVERSIONphase, renumbered remaining phasesTechnical Details
The cawlign command uses:
-s SCORE_MATRIX: Alignment scoring matrix-t codon: Codon-aware alignment mode (required for HIV_BETWEEN_F)-I: Include reference sequence in output (equivalent to bealign's-K)-r reference: Specify reference sequence fileTesting
All 14 existing tests pass with the new implementation:
Dependencies
Breaking Changes
None. The changes are backward compatible - existing functionality is preserved with the new alignment tool.