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Add --strand option to orfs - #1
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Requested by gulliby
Before.
seqmill orfsalways scanned all six frames, so users who wanted one strand had to filter the table by the sign of theframecolumn.After.
seqmill orfs --strand both|forward|reverse(defaultboth) limits the search to frames +1..+3 or -1..-3. Rows are identical to the full table minus the other strand. For exampleseqmill orfs --min 2 --strand reverse gene.faprints the header and the-1row; an empty selection exits 1; an invalid value exits 2 withseqmill: invalid --strand "up" (expected both, forward or reverse).How.
seqmill/tools/orfs.py(option and scan), theorfsline of the usage inseqmill/cli.py, the README usage line andorfsbullet, the usage constants intests/test_cli.pyandtests/test_main.py, and a newtests/test_orfs_strand.py(12 tests). 699 tests pass; ruff is clean.