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read_alignment reads ZOMBI2's bundled alignments.fasta - #34
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A ZOMBI2 run written with --bundle keeps every family's alignment in one alignments.fasta, each header ending " fam<N>". read_alignment now reads that layout as well as one fam<N>.fasta per family. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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ZOMBI2 can now write a run's alignments as one file (
--bundle, AADavin/zombi2#464). That file isalignments.fasta, and each header is>n12_g1200 fam4.ph.zombi.read_alignment(run, family)now reads that layout as well as the per-familyalignments/fam<N>.fasta. It looks for the per-family file first, then for the bundled one, undersequences/or the run root as before. From the bundled file it takes the records whose header endsfam<N>, and strips that ending before mapping each name to its genome.tests/test_zombi.py: one family read from both layouts gives the same alignment.ruffandmypyare clean.🤖 Generated with Claude Code