added suffix collapse #173
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droush
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Dec 22, 2022
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Everything looks great.
I think this is a clever implementation that leverages the engineering of Web of Life. I've been doing OGU, ORF, or OGU/ORF and then collapsing as the workflow, instead of leveraging some of the features of classify. Might want to consider having a discussion about this sometime @qiyunzhu
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@droush Thanks! I have merged. Now I am going to test on WoL2. |
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This PR adds a new function to the
collapsecommand: it now can treat feature IDs like "G000123456_789" as genome-gene stratified features, and collapse on either the genomes or the genes. With this function, one no longer needs to do genome-gene (i.e., OGU-ORF) stratification fromclassify. Instead, one can just generate a gene (ORF) profile, and collapse it to both higher taxonomic and functional levels as a stratified profile.