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Add --strand option to orfs - #1

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Gulliby merged 1 commit into
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feature/orfs-strand
Oct 17, 2026
Merged

Gulliby merged 1 commit into
mainfrom
feature/orfs-strand

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@Gulliby Gulliby commented Oct 17, 2026

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Requested by gulliby

Before. seqmill orfs always scanned all six frames, so users who wanted one strand had to filter the table by the sign of the frame column.

After. seqmill orfs --strand both|forward|reverse (default both) limits the search to frames +1..+3 or -1..-3. Rows are identical to the full table minus the other strand. For example seqmill orfs --min 2 --strand reverse gene.fa prints the header and the -1 row; an empty selection exits 1; an invalid value exits 2 with seqmill: invalid --strand "up" (expected both, forward or reverse).

How. seqmill/tools/orfs.py (option and scan), the orfs line of the usage in seqmill/cli.py, the README usage line and orfs bullet, the usage constants in tests/test_cli.py and tests/test_main.py, and a new tests/test_orfs_strand.py (12 tests). 699 tests pass; ruff is clean.

@Gulliby Gulliby self-assigned this Oct 17, 2026
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Gulliby merged commit f03689f into main Oct 17, 2026
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