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elizabethmcd / metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs
GNU General Public License v3.0
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connect to kofamkoala #26

Closed elizabethmcd closed 4 years ago

elizabethmcd commented 4 years ago

option to point to exec_annotation file for threshold cutoffs

elizabethmcd commented 4 years ago

has to parse the exec_annotation file, get the argument for the score, and run that score with the hmmsearch for the specific HMM

elizabethmcd commented 4 years ago

only within the custom markers script and the single marker phylogeny, but have to think about how to pass the argument. Currently argument setup to point to the path of the exec_annotation file Can add additional argument for kofam=ON, to get the threshold score, and optional argument for the exec_annotation path in case the user already has it in the current working directory or somewhere in their path (kofam doesn't do that by default I don't think), so then set it manually

elizabethmcd commented 4 years ago

not the exec_annotation file, that's the kofam exectuable it's the ko_list