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Better placement count output table #49

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Robaina opened this issue Feb 25, 2022 · 0 comments · Fixed by #50
Closed

Better placement count output table #49

Robaina opened this issue Feb 25, 2022 · 0 comments · Fixed by #50
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Robaina commented Feb 25, 2022 •
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This issue proposes to change the format of the output table generated by:

https://github.com/Robaina/TRAITS/blob/b370d9336e2e33a8479928945c5e4dc38ab24ce9/code/phyloplacement/placement.py#L145-L148

  1. Merge counts from "Unspecified" and any empty taxonomic level, such as "f__" if counting at family level.
  2. Include header with info about sample name
  3. Possibly compute counts for all taxa at the same time?
  4. Also, selecting "good" clusters by id and by score threshold is redundant. Either one or the other would make more sense.
@Robaina Robaina self-assigned this Feb 25, 2022
@Robaina Robaina added the enhancement New feature or request label Feb 25, 2022
@Robaina Robaina changed the title Better placement cout output table Better placement count output table Feb 25, 2022
Robaina added a commit that referenced this issue Feb 25, 2022
@Robaina
Better placement count output table
f8ca75d 
Fixes #49
@Robaina Robaina mentioned this issue Feb 25, 2022
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Robaina added a commit that referenced this issue Feb 22, 2023
@Robaina
Better placement count output table
8d423e7 
Fixes #49
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Better placement count output table Robaina/MetaTag
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