MRG: modify annotate for flexibility
#2518
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MRG: LineageTree class to help with LINGroup ordering (#2496)
Note: based off of #2469 - Rewrites `build_tree`, `find_lca` functions as `LineageTree` class. Using same tests, we produce same results - Adds `ordered_paths` method to produce ~ordered lineages from tree for LINgroup ordered output. - Removes `num_bp_assigned` column because it was artificial anyway (our counts are all assigned at the genome level) and we're not trying to replicate a format exactly, as we are with `kreport` output, where we have this column. Note that LINgroups will not be ordered _absolutely_, as there will be some stochasticity as we descend the dictionary. Instead, related subpaths will be grouped. e.g. two potential outputs: ``` LINgroup_name LINgroup_prefix percent_containment num_bp_contained num_bp_assigned lg3 2;0;0 1.56 192000 0 lg1 0;0;0 5.82 714000 0 lg2 1;0;0 5.05 620000 0 lg3 1;0;1 0.65 80000 0 lg4 1;0;1;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 0.65 80000 80000 ``` ``` LINgroup_name LINgroup_prefix percent_containment num_bp_contained num_bp_assigned lg2 1;0;0 5.05 620000 0 lg3 1;0;1 0.65 80000 0 lg4 1;0;1;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 0.65 80000 80000 lg1 0;0;0 5.82 714000 0 lg3 2;0;0 1.56 192000 0 ``` In these examples, the `1;0`.. paths are always grouped together, but may come before or after the `0;0` and `2;0` groups
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Co-authored-by: C. Titus Brown <titus@idyll.org>
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Commits on Apr 5, 2023
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